From 6dff9bbd4768096477ddaede3469cf3ce432f745 Mon Sep 17 00:00:00 2001 From: jdzm Date: Tue, 16 Dec 2025 14:03:08 +0100 Subject: [PATCH 01/14] added .gitignore with common folders --- .gitignore | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) create mode 100644 .gitignore diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..6098fa9 --- /dev/null +++ b/.gitignore @@ -0,0 +1,16 @@ +# Output files +results/ +final/ +tmp/ +input/ + +# Snakemake folder +.snakemake/ + +# IDE +.vscode/ +.idea/ + +# OS +.DS_Store +Thumbs.db From 65efaf58aef9272b371367c71c5b460b622dcddd Mon Sep 17 00:00:00 2001 From: jdzm Date: Tue, 16 Dec 2025 14:03:39 +0100 Subject: [PATCH 02/14] removed old log files --- .../2020-08-16T155314.250876.snakemake.log | 28 --- .../2020-08-16T155340.718245.snakemake.log | 19 -- .../2020-08-16T160645.278170.snakemake.log | 24 --- .../2020-08-16T162317.217954.snakemake.log | 24 --- .../2020-08-16T162458.954662.snakemake.log | 26 --- 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shell: - cat read_len_distrbution.txt | soort -rn > read_len_distrbution1.txt - (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!) - -Removing output files of failed job select_longread since they might be corrupted: -read_len_distrbution1.txt -Shutting down, this might take some time. -Exiting because a job execution failed. Look above for error message -Complete log: /data/user/huangf/Arginini/script-test/Only-long-read/snakemake/.snakemake/log/2020-08-16T155314.250876.snakemake.log diff --git a/.snakemake/log/2020-08-16T155340.718245.snakemake.log b/.snakemake/log/2020-08-16T155340.718245.snakemake.log deleted file mode 100644 index a538ce6..0000000 --- a/.snakemake/log/2020-08-16T155340.718245.snakemake.log +++ /dev/null @@ -1,19 +0,0 @@ -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Job counts: - count jobs - 1 select_longread - 1 - -[Sun Aug 16 15:53:40 2020] -rule select_longread: - input: read_len_distrbution.txt - output: read_len_distrbution1.txt - jobid: 0 - -[Sun Aug 16 15:53:40 2020] -Finished job 0. -1 of 1 steps (100%) done -Complete log: /data/user/huangf/Arginini/script-test/Only-long-read/snakemake/.snakemake/log/2020-08-16T155340.718245.snakemake.log diff --git a/.snakemake/log/2020-08-16T160645.278170.snakemake.log b/.snakemake/log/2020-08-16T160645.278170.snakemake.log deleted file mode 100644 index e6de54b..0000000 --- a/.snakemake/log/2020-08-16T160645.278170.snakemake.log +++ /dev/null @@ -1,24 +0,0 @@ -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Job counts: - count jobs - 1 longread_len - 1 - -[Sun Aug 16 16:06:45 2020] -rule longread_len: - input: /data/user/huangf/Arginini/script-test/Only-long-read/snakemake/data/m150118_055507_00127_c100673182550000001823137502061570_s1_p0.bas.h5.fastq - jobid: 0 - -[Sun Aug 16 16:06:45 2020] -Error in rule longread_len: - jobid: 0 - shell: - read_length_distribution.py /data/user/huangf/Arginini/script-test/Only-long-read/snakemake/data/m150118_055507_00127_c100673182550000001823137502061570_s1_p0.bas.h5.fastq - (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!) - -Shutting down, this might take some time. -Exiting because a job execution failed. Look above for error message -Complete log: /data/user/huangf/Arginini/script-test/Only-long-read/snakemake/.snakemake/log/2020-08-16T160645.278170.snakemake.log diff --git a/.snakemake/log/2020-08-16T162317.217954.snakemake.log b/.snakemake/log/2020-08-16T162317.217954.snakemake.log deleted file mode 100644 index b7b87d3..0000000 --- a/.snakemake/log/2020-08-16T162317.217954.snakemake.log +++ /dev/null @@ -1,24 +0,0 @@ -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Job counts: - count jobs - 1 longread_len - 1 - -[Sun Aug 16 16:23:17 2020] -rule longread_len: - input: /data/user/huangf/Arginini/script-test/Only-long-read/snakemake/data/m150118_055507_00127_c100673182550000001823137502061570_s1_p0.bas.h5.fastq - jobid: 0 - -[Sun Aug 16 16:23:17 2020] -Error in rule longread_len: - jobid: 0 - shell: - read_length_distribution.py /data/user/huangf/Arginini/script-test/Only-long-read/snakemake/data/m150118_055507_00127_c100673182550000001823137502061570_s1_p0.bas.h5.fastq - (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!) - -Shutting down, this might take some time. -Exiting because a job execution failed. Look above for error message -Complete log: /data/user/huangf/Arginini/script-test/Only-long-read/snakemake/.snakemake/log/2020-08-16T162317.217954.snakemake.log diff --git a/.snakemake/log/2020-08-16T162458.954662.snakemake.log b/.snakemake/log/2020-08-16T162458.954662.snakemake.log deleted file mode 100644 index 2923ba4..0000000 --- a/.snakemake/log/2020-08-16T162458.954662.snakemake.log +++ /dev/null @@ -1,26 +0,0 @@ -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Job counts: - count jobs - 1 longread_len - 1 - -[Sun Aug 16 16:24:58 2020] -rule longread_len: - input: /data/user/huangf/Arginini/script-test/Only-long-read/snakemake/data/m150118_055507_00127_c100673182550000001823137502061570_s1_p0.bas.h5.fastq - jobid: 0 - -[Sun Aug 16 16:24:59 2020] -Error in rule longread_len: - jobid: 0 - -RuleException: -NameError in line 6 of /data/user/huangf/Arginini/script-test/Only-long-read/snakemake/snakefile: -The name 'input' is unknown in this context. Please make sure that you defined that variable. Also note that braces not used for variable access have to be escaped by repeating them, i.e. {{print $1}} - File "/data/user/huangf/Arginini/script-test/Only-long-read/snakemake/snakefile", line 6, in __rule_longread_len - File "/home/huangf/.conda/envs/snakemake/lib/python3.8/concurrent/futures/thread.py", line 57, in run -Shutting down, this might take some time. -Exiting because a job execution failed. Look above for error message -Complete log: /data/user/huangf/Arginini/script-test/Only-long-read/snakemake/.snakemake/log/2020-08-16T162458.954662.snakemake.log diff --git a/.snakemake/log/2020-08-16T162556.231025.snakemake.log b/.snakemake/log/2020-08-16T162556.231025.snakemake.log deleted file mode 100644 index 721627a..0000000 --- a/.snakemake/log/2020-08-16T162556.231025.snakemake.log +++ /dev/null @@ -1,18 +0,0 @@ -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Job counts: - count jobs - 1 longread_len - 1 - -[Sun Aug 16 16:25:56 2020] -rule longread_len: - input: /data/user/huangf/Arginini/script-test/Only-long-read/snakemake/data/m150118_055507_00127_c100673182550000001823137502061570_s1_p0.bas.h5.fastq - jobid: 0 - -[Sun Aug 16 16:25:58 2020] -Finished job 0. -1 of 1 steps (100%) done -Complete log: /data/user/huangf/Arginini/script-test/Only-long-read/snakemake/.snakemake/log/2020-08-16T162556.231025.snakemake.log diff --git a/.snakemake/log/2020-08-16T230537.593217.snakemake.log b/.snakemake/log/2020-08-16T230537.593217.snakemake.log deleted file mode 100644 index ff9e87e..0000000 --- a/.snakemake/log/2020-08-16T230537.593217.snakemake.log +++ /dev/null @@ -1,3 +0,0 @@ -IndentationError in line 23 of : -unindent does not match any outer indentation level (, line 23) - File "/home/huangf/.conda/envs/snakemake/lib/python3.8/tokenize.py", line 512, in _tokenize diff --git a/.snakemake/log/2020-09-02T162535.227586.snakemake.log b/.snakemake/log/2020-09-02T162535.227586.snakemake.log deleted file mode 100644 index 9f5bbd7..0000000 --- a/.snakemake/log/2020-09-02T162535.227586.snakemake.log +++ /dev/null @@ -1,3 +0,0 @@ -WorkflowError in line 5 of /data/user/huangf/Arginini/original/snakemake/snakefile: -Config file is not valid JSON or YAML. In case of YAML, make sure to not mix whitespace and tab indentation. - File "/data/user/huangf/Arginini/original/snakemake/snakefile", line 5, in diff --git a/.snakemake/log/2020-09-02T162705.348567.snakemake.log b/.snakemake/log/2020-09-02T162705.348567.snakemake.log deleted file mode 100644 index 9f5bbd7..0000000 --- a/.snakemake/log/2020-09-02T162705.348567.snakemake.log +++ /dev/null @@ -1,3 +0,0 @@ -WorkflowError in line 5 of /data/user/huangf/Arginini/original/snakemake/snakefile: -Config file is not valid JSON or YAML. In case of YAML, make sure to not mix whitespace and tab indentation. - File "/data/user/huangf/Arginini/original/snakemake/snakefile", line 5, in diff --git a/.snakemake/log/2020-09-02T214639.772048.snakemake.log b/.snakemake/log/2020-09-02T214639.772048.snakemake.log deleted file mode 100644 index 9f5bbd7..0000000 --- a/.snakemake/log/2020-09-02T214639.772048.snakemake.log +++ /dev/null @@ -1,3 +0,0 @@ -WorkflowError in line 5 of /data/user/huangf/Arginini/original/snakemake/snakefile: -Config file is not valid JSON or YAML. In case of YAML, make sure to not mix whitespace and tab indentation. - File "/data/user/huangf/Arginini/original/snakemake/snakefile", line 5, in diff --git a/.snakemake/log/2020-09-02T214911.951092.snakemake.log b/.snakemake/log/2020-09-02T214911.951092.snakemake.log deleted file mode 100644 index 9f76481..0000000 --- a/.snakemake/log/2020-09-02T214911.951092.snakemake.log +++ /dev/null @@ -1,3 +0,0 @@ -WorkflowError in line 8 of /data/user/huangf/Arginini/original/snakemake/snakefile: -Failed to open /data/user/huangf/Arginini/original/snakemake/selectLongRead.smk. - File "/data/user/huangf/Arginini/original/snakemake/snakefile", line 8, in diff --git a/.snakemake/log/2020-09-02T215205.356166.snakemake.log b/.snakemake/log/2020-09-02T215205.356166.snakemake.log deleted file mode 100644 index ea19b70..0000000 --- a/.snakemake/log/2020-09-02T215205.356166.snakemake.log +++ /dev/null @@ -1,4 +0,0 @@ -SyntaxError: -Input and output files have to be specified as strings or lists of strings. - File "/data/user/huangf/Arginini/original/snakemake/snakefile", line 8, in - File "/data/user/huangf/Arginini/original/snakemake/rules/selectLongRead.smk", line 18, in diff --git a/.snakemake/log/2020-09-03T104017.791861.snakemake.log b/.snakemake/log/2020-09-03T104017.791861.snakemake.log deleted file mode 100644 index ea19b70..0000000 --- a/.snakemake/log/2020-09-03T104017.791861.snakemake.log +++ /dev/null @@ -1,4 +0,0 @@ -SyntaxError: -Input and output files have to be specified as strings or lists of strings. - File "/data/user/huangf/Arginini/original/snakemake/snakefile", line 8, in - File "/data/user/huangf/Arginini/original/snakemake/rules/selectLongRead.smk", line 18, in diff --git a/.snakemake/log/2020-09-03T110509.834936.snakemake.log b/.snakemake/log/2020-09-03T110509.834936.snakemake.log deleted file mode 100644 index ea19b70..0000000 --- a/.snakemake/log/2020-09-03T110509.834936.snakemake.log +++ /dev/null @@ -1,4 +0,0 @@ -SyntaxError: -Input and output files have to be specified as strings or lists of strings. - File "/data/user/huangf/Arginini/original/snakemake/snakefile", line 8, in - File "/data/user/huangf/Arginini/original/snakemake/rules/selectLongRead.smk", line 18, in diff --git a/.snakemake/log/2020-09-04T000613.998343.snakemake.log b/.snakemake/log/2020-09-04T000613.998343.snakemake.log deleted file mode 100644 index ea19b70..0000000 --- a/.snakemake/log/2020-09-04T000613.998343.snakemake.log +++ /dev/null @@ -1,4 +0,0 @@ -SyntaxError: -Input and output files have to be specified as strings or lists of strings. - File "/data/user/huangf/Arginini/original/snakemake/snakefile", line 8, in - File "/data/user/huangf/Arginini/original/snakemake/rules/selectLongRead.smk", line 18, in diff --git a/.snakemake/log/2020-09-04T001439.290323.snakemake.log b/.snakemake/log/2020-09-04T001439.290323.snakemake.log deleted file mode 100644 index ea19b70..0000000 --- a/.snakemake/log/2020-09-04T001439.290323.snakemake.log +++ /dev/null @@ -1,4 +0,0 @@ -SyntaxError: -Input and output files have to be specified as strings or lists of strings. - File "/data/user/huangf/Arginini/original/snakemake/snakefile", line 8, in - File "/data/user/huangf/Arginini/original/snakemake/rules/selectLongRead.smk", line 18, in diff --git a/.snakemake/log/2020-09-04T001642.218036.snakemake.log b/.snakemake/log/2020-09-04T001642.218036.snakemake.log deleted file mode 100644 index ea19b70..0000000 --- a/.snakemake/log/2020-09-04T001642.218036.snakemake.log +++ /dev/null @@ -1,4 +0,0 @@ -SyntaxError: -Input and output files have to be specified as strings or lists of strings. - File "/data/user/huangf/Arginini/original/snakemake/snakefile", line 8, in - File "/data/user/huangf/Arginini/original/snakemake/rules/selectLongRead.smk", line 18, in diff --git a/.snakemake/log/2020-09-04T001715.774042.snakemake.log b/.snakemake/log/2020-09-04T001715.774042.snakemake.log deleted file mode 100644 index 322acab..0000000 --- a/.snakemake/log/2020-09-04T001715.774042.snakemake.log +++ /dev/null @@ -1,3 +0,0 @@ -SyntaxError in line 8 of /data/user/huangf/Arginini/original/snakemake/rules/selectLongRead.smk: -invalid syntax - File "/data/user/huangf/Arginini/original/snakemake/snakefile", line 8, in diff --git a/.snakemake/log/2020-09-04T001750.640996.snakemake.log b/.snakemake/log/2020-09-04T001750.640996.snakemake.log deleted file mode 100644 index 322acab..0000000 --- a/.snakemake/log/2020-09-04T001750.640996.snakemake.log +++ /dev/null @@ -1,3 +0,0 @@ -SyntaxError in line 8 of /data/user/huangf/Arginini/original/snakemake/rules/selectLongRead.smk: -invalid syntax - File "/data/user/huangf/Arginini/original/snakemake/snakefile", line 8, in diff --git a/.snakemake/log/2020-09-04T001915.749542.snakemake.log b/.snakemake/log/2020-09-04T001915.749542.snakemake.log deleted file mode 100644 index c0b106f..0000000 --- a/.snakemake/log/2020-09-04T001915.749542.snakemake.log +++ /dev/null @@ -1,4 +0,0 @@ -SyntaxError: -Input and output files have to be specified as strings or lists of strings. - File "/data/user/huangf/Arginini/original/snakemake/snakefile", line 8, in - File "/data/user/huangf/Arginini/original/snakemake/rules/selectLongRead.smk", line 19, in diff --git a/.snakemake/log/2020-09-04T002039.667061.snakemake.log b/.snakemake/log/2020-09-04T002039.667061.snakemake.log deleted file mode 100644 index dd0aef2..0000000 --- a/.snakemake/log/2020-09-04T002039.667061.snakemake.log +++ /dev/null @@ -1,3 +0,0 @@ -SyntaxError in line 12 of /data/user/huangf/Arginini/original/snakemake/rules/selectLongRead.smk: -invalid syntax - File "/data/user/huangf/Arginini/original/snakemake/snakefile", line 8, in diff --git a/.snakemake/log/2020-09-04T002119.797699.snakemake.log b/.snakemake/log/2020-09-04T002119.797699.snakemake.log deleted file mode 100644 index 24308c1..0000000 --- a/.snakemake/log/2020-09-04T002119.797699.snakemake.log +++ /dev/null @@ -1,4 +0,0 @@ -CreateRuleException in line 14 of /data/user/huangf/Arginini/original/snakemake/rules/secondround.smk: -The name select_longestContig is already used by another rule - File "/data/user/huangf/Arginini/original/snakemake/snakefile", line 11, in - File "/data/user/huangf/Arginini/original/snakemake/rules/secondround.smk", line 14, in diff --git a/.snakemake/log/2020-09-04T002229.926403.snakemake.log b/.snakemake/log/2020-09-04T002229.926403.snakemake.log deleted file mode 100644 index 24308c1..0000000 --- a/.snakemake/log/2020-09-04T002229.926403.snakemake.log +++ /dev/null @@ -1,4 +0,0 @@ -CreateRuleException in line 14 of /data/user/huangf/Arginini/original/snakemake/rules/secondround.smk: -The name select_longestContig is already used by another rule - File "/data/user/huangf/Arginini/original/snakemake/snakefile", line 11, in - File "/data/user/huangf/Arginini/original/snakemake/rules/secondround.smk", line 14, in diff --git a/.snakemake/log/2020-09-04T002353.999053.snakemake.log b/.snakemake/log/2020-09-04T002353.999053.snakemake.log deleted file mode 100644 index 24308c1..0000000 --- a/.snakemake/log/2020-09-04T002353.999053.snakemake.log +++ /dev/null @@ -1,4 +0,0 @@ -CreateRuleException in line 14 of /data/user/huangf/Arginini/original/snakemake/rules/secondround.smk: -The name select_longestContig is already used by another rule - File "/data/user/huangf/Arginini/original/snakemake/snakefile", line 11, in - File "/data/user/huangf/Arginini/original/snakemake/rules/secondround.smk", line 14, in diff --git a/.snakemake/log/2020-09-04T002535.258818.snakemake.log b/.snakemake/log/2020-09-04T002535.258818.snakemake.log deleted file mode 100644 index 24308c1..0000000 --- a/.snakemake/log/2020-09-04T002535.258818.snakemake.log +++ /dev/null @@ -1,4 +0,0 @@ -CreateRuleException in line 14 of /data/user/huangf/Arginini/original/snakemake/rules/secondround.smk: -The name select_longestContig is already used by another rule - File "/data/user/huangf/Arginini/original/snakemake/snakefile", line 11, in - File "/data/user/huangf/Arginini/original/snakemake/rules/secondround.smk", line 14, in diff --git a/.snakemake/log/2020-09-04T100922.980997.snakemake.log b/.snakemake/log/2020-09-04T100922.980997.snakemake.log deleted file mode 100644 index 3e9da83..0000000 --- a/.snakemake/log/2020-09-04T100922.980997.snakemake.log +++ /dev/null @@ -1,4 +0,0 @@ -CreateRuleException in line 10 of /data/user/huangf/Arginini/original/snakemake/rules/polish.smk: -The name polish_round1 is already used by another rule - File "/data/user/huangf/Arginini/original/snakemake/snakefile", line 13, in - File "/data/user/huangf/Arginini/original/snakemake/rules/polish.smk", line 10, in diff --git a/.snakemake/log/2020-09-04T102647.061646.snakemake.log b/.snakemake/log/2020-09-04T102647.061646.snakemake.log deleted file mode 100644 index ea984e2..0000000 --- a/.snakemake/log/2020-09-04T102647.061646.snakemake.log +++ /dev/null @@ -1,5 +0,0 @@ -Building DAG of jobs... -MissingInputException in line 16 of /data/user/huangf/Arginini/original/snakemake/rules/tworoundMerge.smk: -Missing input files for rule mergeFa: -output/EndSeq -output/BeginSeq diff --git a/.snakemake/log/2020-09-04T132100.091789.snakemake.log b/.snakemake/log/2020-09-04T132100.091789.snakemake.log deleted file mode 100644 index d8f32d8..0000000 --- a/.snakemake/log/2020-09-04T132100.091789.snakemake.log +++ /dev/null @@ -1,5 +0,0 @@ -Building DAG of jobs... -MissingInputException in line 10 of /data/user/huangf/Arginini/original/snakemake/rules/selectLongRead.smk: -Missing input files for rule select_longread: -{config['nanopore']} -1000000 diff --git a/.snakemake/log/2020-09-04T133610.858201.snakemake.log b/.snakemake/log/2020-09-04T133610.858201.snakemake.log deleted file mode 100644 index c0b106f..0000000 --- a/.snakemake/log/2020-09-04T133610.858201.snakemake.log +++ /dev/null @@ -1,4 +0,0 @@ -SyntaxError: -Input and output files have to be specified as strings or lists of strings. - File "/data/user/huangf/Arginini/original/snakemake/snakefile", line 8, in - File "/data/user/huangf/Arginini/original/snakemake/rules/selectLongRead.smk", line 19, in diff --git a/.snakemake/log/2020-09-04T133940.002742.snakemake.log b/.snakemake/log/2020-09-04T133940.002742.snakemake.log deleted file mode 100644 index 8030265..0000000 --- a/.snakemake/log/2020-09-04T133940.002742.snakemake.log +++ /dev/null @@ -1,156 +0,0 @@ -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 2 -Rules claiming more threads will be scaled down. -Job counts: - count jobs - 1 Oneline_fa - 1 Oneline_fa_2 - 1 all - 1 first_assemble - 1 fq_to_fa - 1 longread_len - 1 longread_polish - 1 merge - 1 mergeFa - 1 polish_round1 - 1 polish_round2 - 1 polish_round3 - 1 polish_round5 - 1 rearrange - 1 select_longContig - 1 select_longestContig - 1 select_longread - 1 short_to_long - 1 tworun_align - 19 - -[Fri Sep 4 13:39:40 2020] -rule longread_len: - input: data/rawdata.fastq - output: output/read_len_distrbution_2.txt - jobid: 18 - -[Fri Sep 4 13:39:43 2020] -Finished job 18. -1 of 19 steps (5%) done - -[Fri Sep 4 13:39:43 2020] -rule select_longread: - input: data/rawdata.fastq, output/read_len_distrbution_2.txt - output: output/filter_length.fq, output/left_filter_length.fq - jobid: 16 - -[Fri Sep 4 13:39:44 2020] -Finished job 16. -2 of 19 steps (11%) done - -[Fri Sep 4 13:39:44 2020] -rule fq_to_fa: - input: output/filter_length.fq - output: output/filter_length.fa - jobid: 15 - -[Fri Sep 4 13:39:44 2020] -Finished job 15. -3 of 19 steps (16%) done - -[Fri Sep 4 13:39:44 2020] -rule short_to_long: - input: output/filter_length.fa, output/left_filter_length.fq - output: output/short_to_long.sam - jobid: 17 - -[Fri Sep 4 13:41:37 2020] -Finished job 17. -4 of 19 steps (21%) done - -[Fri Sep 4 13:41:37 2020] -rule longread_polish: - input: output/filter_length.fa, output/left_filter_length.fq, output/short_to_long.sam - output: output/long_racon_corrected.fa - jobid: 14 - -[Fri Sep 4 13:43:44 2020] -Finished job 14. -5 of 19 steps (26%) done - -[Fri Sep 4 13:43:44 2020] -rule first_assemble: - input: output/long_racon_corrected.fa - output: output/assembly.fasta - jobid: 13 - -[Fri Sep 4 13:56:11 2020] -Finished job 13. -6 of 19 steps (32%) done - -[Fri Sep 4 13:56:11 2020] -rule select_longContig: - input: output/assembly.fasta - output: output/secondrun.fa - jobid: 11 - - -[Fri Sep 4 13:56:11 2020] -rule select_longestContig: - input: output/assembly.fasta - output: output/firstrun.fa - jobid: 12 - -[Fri Sep 4 13:56:14 2020] -Finished job 11. -7 of 19 steps (37%) done - -[Fri Sep 4 13:56:14 2020] -rule Oneline_fa_2: - input: output/secondrun.fa - output: output/secondrunSeq - jobid: 9 - -[Fri Sep 4 13:56:14 2020] -Finished job 12. -8 of 19 steps (42%) done - -[Fri Sep 4 13:56:14 2020] -rule tworun_align: - input: output/secondrun.fa, output/firstrun.fa - output: output/first_second.paf - jobid: 8 - -[Fri Sep 4 13:56:14 2020] -Finished job 9. -9 of 19 steps (47%) done - -[Fri Sep 4 13:56:14 2020] -rule Oneline_fa: - input: output/firstrun.fa - output: output/firstrunSeq - jobid: 10 - -[Fri Sep 4 13:56:14 2020] -Finished job 10. -10 of 19 steps (53%) done -[Fri Sep 4 13:56:14 2020] -Finished job 8. -11 of 19 steps (58%) done - -[Fri Sep 4 13:56:14 2020] -rule merge: - input: output/first_second.paf, output/secondrunSeq, output/firstrunSeq - output: output/BeginSeq, output/EndSeq - jobid: 7 - -[Fri Sep 4 13:56:14 2020] -Error in rule merge: - jobid: 7 - output: output/BeginSeq, output/EndSeq - shell: - python script/merge-new.py output/first_second.paf output/secondrunSeq output/firstrunSeq output/BeginSeq output/EndSeq - (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!) - -Removing output files of failed job merge since they might be corrupted: -output/BeginSeq, output/EndSeq -Shutting down, this might take some time. -Exiting because a job execution failed. Look above for error message -Complete log: /data/user/huangf/Arginini/original/snakemake/.snakemake/log/2020-09-04T133940.002742.snakemake.log diff --git a/.snakemake/log/2020-09-04T213007.505639.snakemake.log b/.snakemake/log/2020-09-04T213007.505639.snakemake.log deleted file mode 100644 index faaf3fe..0000000 --- a/.snakemake/log/2020-09-04T213007.505639.snakemake.log +++ /dev/null @@ -1,3 +0,0 @@ -SyntaxError in line 13 of /data/user/huangf/Arginini/original/snakemake/rules/tworoundMerge.smk: -invalid syntax - File "/data/user/huangf/Arginini/original/snakemake/snakefile", line 12, in diff --git a/.snakemake/log/2020-09-04T213144.726670.snakemake.log b/.snakemake/log/2020-09-04T213144.726670.snakemake.log deleted file mode 100644 index bb6d9bd..0000000 --- a/.snakemake/log/2020-09-04T213144.726670.snakemake.log +++ /dev/null @@ -1,176 +0,0 @@ -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 2 -Rules claiming more threads will be scaled down. -Job counts: - count jobs - 1 Oneline_fa - 1 Oneline_fa_2 - 1 all - 1 first_assemble - 1 fq_to_fa - 1 longread_len - 1 longread_polish - 1 merge - 1 mergeFa - 1 polish_round1 - 1 polish_round2 - 1 polish_round3 - 1 polish_round5 - 1 rearrange - 1 select_longContig - 1 select_longestContig - 1 select_longread - 1 short_to_long - 1 tworun_align - 19 - -[Fri Sep 4 21:31:45 2020] -rule longread_len: - input: data/rawdata.fastq - output: output/read_len_distrbution_2.txt - jobid: 18 - -[Fri Sep 4 21:31:45 2020] -Finished job 18. -1 of 19 steps (5%) done - -[Fri Sep 4 21:31:45 2020] -rule select_longread: - input: data/rawdata.fastq, output/read_len_distrbution_2.txt - output: output/filter_length.fq, output/left_filter_length.fq - jobid: 16 - -[Fri Sep 4 21:31:46 2020] -Finished job 16. -2 of 19 steps (11%) done - -[Fri Sep 4 21:31:46 2020] -rule fq_to_fa: - input: output/filter_length.fq - output: output/filter_length.fa - jobid: 15 - -[Fri Sep 4 21:31:47 2020] -Finished job 15. -3 of 19 steps (16%) done - -[Fri Sep 4 21:31:47 2020] -rule short_to_long: - input: output/filter_length.fa, output/left_filter_length.fq - output: output/short_to_long.sam - jobid: 17 - -[Fri Sep 4 21:33:34 2020] -Finished job 17. -4 of 19 steps (21%) done - -[Fri Sep 4 21:33:34 2020] -rule longread_polish: - input: output/filter_length.fa, output/left_filter_length.fq, output/short_to_long.sam - output: output/long_racon_corrected.fa - jobid: 14 - -[Fri Sep 4 21:35:39 2020] -Finished job 14. -5 of 19 steps (26%) done - -[Fri Sep 4 21:35:39 2020] -rule first_assemble: - input: output/long_racon_corrected.fa - output: output/assembly.fasta - jobid: 13 - -[Fri Sep 4 21:47:46 2020] -Finished job 13. -6 of 19 steps (32%) done - -[Fri Sep 4 21:47:46 2020] -rule select_longestContig: - input: output/assembly.fasta - output: output/firstrun.fa - jobid: 12 - - -[Fri Sep 4 21:47:46 2020] -rule select_longContig: - input: output/assembly.fasta - output: output/secondrun.fa - jobid: 11 - -[Fri Sep 4 21:47:48 2020] -Finished job 11. -7 of 19 steps (37%) done - -[Fri Sep 4 21:47:48 2020] -rule Oneline_fa_2: - input: output/secondrun.fa - output: output/secondrunSeq - jobid: 10 - -[Fri Sep 4 21:47:48 2020] -Finished job 12. -8 of 19 steps (42%) done - -[Fri Sep 4 21:47:48 2020] -rule tworun_align: - input: output/secondrun.fa, output/firstrun.fa - output: output/first_second.paf - jobid: 8 - -[Fri Sep 4 21:47:48 2020] -Finished job 10. -9 of 19 steps (47%) done - -[Fri Sep 4 21:47:48 2020] -rule Oneline_fa: - input: output/firstrun.fa - output: output/firstrunSeq - jobid: 9 - -[Fri Sep 4 21:47:48 2020] -Finished job 9. -10 of 19 steps (53%) done -[Fri Sep 4 21:47:49 2020] -Finished job 8. -11 of 19 steps (58%) done - -[Fri Sep 4 21:47:49 2020] -rule merge: - input: output/first_second.paf, output/firstrunSeq, output/secondrunSeq - output: output/BeginSeq, output/EndSeq - jobid: 7 - -[Fri Sep 4 21:47:49 2020] -Finished job 7. -12 of 19 steps (63%) done - -[Fri Sep 4 21:47:49 2020] -rule mergeFa: - input: output/BeginSeq, output/EndSeq - output: output/First_second_merge.fa - jobid: 6 - -[Fri Sep 4 21:47:49 2020] -Finished job 6. -13 of 19 steps (68%) done - -[Fri Sep 4 21:47:49 2020] -rule polish_round1: - input: output/First_second_merge.fa, data/rawdata.fastq - output: output/racon_polish_1.fa - jobid: 5 - -[Fri Sep 4 21:47:51 2020] -Error in rule polish_round1: - jobid: 5 - output: output/racon_polish_1.fa - shell: - minimap2 -ax map-ont output/First_second_merge.fa data/rawdata.fastq > output/rawfq-merged.sam && racon data/rawdata.fastq output/rawfq-merged.sam output/First_second_merge.fa > output/racon_polish_1.fa - (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!) - -Removing output files of failed job polish_round1 since they might be corrupted: -output/racon_polish_1.fa -Shutting down, this might take some time. -Exiting because a job execution failed. Look above for error message -Complete log: /data/user/huangf/Arginini/original/snakemake/.snakemake/log/2020-09-04T213144.726670.snakemake.log diff --git a/.snakemake/log/2020-09-05T121001.600122.snakemake.log b/.snakemake/log/2020-09-05T121001.600122.snakemake.log deleted file mode 100644 index 5a1e506..0000000 --- a/.snakemake/log/2020-09-05T121001.600122.snakemake.log +++ /dev/null @@ -1,3 +0,0 @@ -KeyError in line 12 of /data/user/huangf/Arginini/original/snakemake/snakefile: -'nanopore' - File "/data/user/huangf/Arginini/original/snakemake/snakefile", line 12, in diff --git a/.snakemake/log/2020-09-05T121104.796446.snakemake.log b/.snakemake/log/2020-09-05T121104.796446.snakemake.log deleted file mode 100644 index 5a1e506..0000000 --- a/.snakemake/log/2020-09-05T121104.796446.snakemake.log +++ /dev/null @@ -1,3 +0,0 @@ -KeyError in line 12 of /data/user/huangf/Arginini/original/snakemake/snakefile: -'nanopore' - File "/data/user/huangf/Arginini/original/snakemake/snakefile", line 12, in diff --git a/.snakemake/log/2020-09-05T122130.531365.snakemake.log b/.snakemake/log/2020-09-05T122130.531365.snakemake.log deleted file mode 100644 index 5a1e506..0000000 --- a/.snakemake/log/2020-09-05T122130.531365.snakemake.log +++ /dev/null @@ -1,3 +0,0 @@ -KeyError in line 12 of /data/user/huangf/Arginini/original/snakemake/snakefile: -'nanopore' - File "/data/user/huangf/Arginini/original/snakemake/snakefile", line 12, in diff --git a/.snakemake/log/2020-09-05T122345.948264.snakemake.log b/.snakemake/log/2020-09-05T122345.948264.snakemake.log deleted file mode 100644 index 5a1e506..0000000 --- a/.snakemake/log/2020-09-05T122345.948264.snakemake.log +++ /dev/null @@ -1,3 +0,0 @@ -KeyError in line 12 of /data/user/huangf/Arginini/original/snakemake/snakefile: -'nanopore' - File "/data/user/huangf/Arginini/original/snakemake/snakefile", line 12, in diff --git a/.snakemake/log/2020-09-05T122408.689869.snakemake.log b/.snakemake/log/2020-09-05T122408.689869.snakemake.log deleted file mode 100644 index 5a1e506..0000000 --- a/.snakemake/log/2020-09-05T122408.689869.snakemake.log +++ /dev/null @@ -1,3 +0,0 @@ -KeyError in line 12 of /data/user/huangf/Arginini/original/snakemake/snakefile: -'nanopore' - File "/data/user/huangf/Arginini/original/snakemake/snakefile", line 12, in diff --git a/.snakemake/log/2020-09-05T213429.886593.snakemake.log b/.snakemake/log/2020-09-05T213429.886593.snakemake.log deleted file mode 100644 index 43b3328..0000000 --- a/.snakemake/log/2020-09-05T213429.886593.snakemake.log +++ /dev/null @@ -1,3 +0,0 @@ -KeyError in line 15 of /data/user/huangf/Arginini/original/snakemake/snakefile: -'nanopore' - File "/data/user/huangf/Arginini/original/snakemake/snakefile", line 15, in diff --git a/.snakemake/log/2020-09-05T213525.080623.snakemake.log b/.snakemake/log/2020-09-05T213525.080623.snakemake.log deleted file mode 100644 index 13b5711..0000000 --- a/.snakemake/log/2020-09-05T213525.080623.snakemake.log +++ /dev/null @@ -1,40 +0,0 @@ -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 2 -Rules claiming more threads will be scaled down. -Job counts: - count jobs - 1 all - 1 rawfq_firstrun - 1 select_longestContig - 3 - -[Sat Sep 5 21:35:25 2020] -rule select_longestContig: - input: output/assembly.fasta - output: output/firstrun.fa - jobid: 2 - -[Sat Sep 5 21:35:27 2020] -Finished job 2. -1 of 3 steps (33%) done - -[Sat Sep 5 21:35:27 2020] -rule rawfq_firstrun: - input: output/firstrun.fa, data/rawdata.fastq - output: output/rawfq-firstrun-srt.bam - jobid: 1 - -[Sat Sep 5 21:36:19 2020] -Finished job 1. -2 of 3 steps (67%) done - -[Sat Sep 5 21:36:19 2020] -localrule all: - input: output/rawfq-firstrun-srt.bam - jobid: 0 - -[Sat Sep 5 21:36:19 2020] -Finished job 0. -3 of 3 steps (100%) done -Complete log: /data/user/huangf/Arginini/original/snakemake/.snakemake/log/2020-09-05T213525.080623.snakemake.log diff --git a/.snakemake/log/2020-09-06T105411.720019.snakemake.log b/.snakemake/log/2020-09-06T105411.720019.snakemake.log deleted file mode 100644 index 222d27e..0000000 --- a/.snakemake/log/2020-09-06T105411.720019.snakemake.log +++ /dev/null @@ -1,4 +0,0 @@ -Building DAG of jobs... -MissingInputException in line 20 of /data/user/huangf/Arginini/original/snakemake/snakefile: -Missing input files for rule all: -EndReads_dupl_remove.fa diff --git a/.snakemake/log/2020-09-06T105447.133356.snakemake.log b/.snakemake/log/2020-09-06T105447.133356.snakemake.log deleted file mode 100644 index 9400167..0000000 --- a/.snakemake/log/2020-09-06T105447.133356.snakemake.log +++ /dev/null @@ -1,139 +0,0 @@ -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 2 -Rules claiming more threads will be scaled down. -Job counts: - count jobs - 1 all - 1 endReads_select - 1 first_assemble - 1 fq_to_fa - 1 longread_len - 1 longread_polish - 1 merge_end_reads - 1 rawfq_firstrun - 1 remove_dupl - 1 select_longestContig - 1 select_longread - 1 short_to_long - 12 - -[Sun Sep 6 10:54:47 2020] -rule longread_len: - input: data/rawdata.fastq - output: output/read_len_distrbution_2.txt - jobid: 11 - -[Sun Sep 6 10:54:47 2020] -Finished job 11. -1 of 12 steps (8%) done - -[Sun Sep 6 10:54:47 2020] -rule select_longread: - input: data/rawdata.fastq, output/read_len_distrbution_2.txt - output: output/filter_length.fq, output/left_filter_length.fq - jobid: 9 - -[Sun Sep 6 10:54:48 2020] -Finished job 9. -2 of 12 steps (17%) done - -[Sun Sep 6 10:54:48 2020] -rule fq_to_fa: - input: output/filter_length.fq - output: output/filter_length.fa - jobid: 8 - -[Sun Sep 6 10:54:48 2020] -Finished job 8. -3 of 12 steps (25%) done - -[Sun Sep 6 10:54:48 2020] -rule short_to_long: - input: output/filter_length.fa, output/left_filter_length.fq - output: output/short_to_long.sam - jobid: 10 - -[Sun Sep 6 10:56:34 2020] -Finished job 10. -4 of 12 steps (33%) done - -[Sun Sep 6 10:56:34 2020] -rule longread_polish: - input: output/filter_length.fa, output/left_filter_length.fq, output/short_to_long.sam - output: output/long_racon_corrected.fa - jobid: 7 - -[Sun Sep 6 10:58:36 2020] -Finished job 7. -5 of 12 steps (42%) done - -[Sun Sep 6 10:58:36 2020] -rule first_assemble: - input: output/long_racon_corrected.fa - output: output/assembly.fasta - jobid: 6 - -[Sun Sep 6 11:10:38 2020] -Finished job 6. -6 of 12 steps (50%) done - -[Sun Sep 6 11:10:38 2020] -rule select_longestContig: - input: output/assembly.fasta - output: output/firstrun.fa - jobid: 4 - -[Sun Sep 6 11:10:38 2020] -Finished job 4. -7 of 12 steps (58%) done - -[Sun Sep 6 11:10:38 2020] -rule rawfq_firstrun: - input: output/firstrun.fa, data/rawdata.fastq - output: output/rawfq-firstrun-srt.bam - jobid: 5 - -[Sun Sep 6 11:11:30 2020] -Finished job 5. -8 of 12 steps (67%) done - -[Sun Sep 6 11:11:30 2020] -rule endReads_select: - input: output/firstrun.fa, output/rawfq-firstrun-srt.bam - output: output/EndAlign.fq, output/beginAlign.fq - jobid: 3 - -[Sun Sep 6 11:11:30 2020] -Finished job 3. -9 of 12 steps (75%) done - -[Sun Sep 6 11:11:30 2020] -rule merge_end_reads: - input: output/EndAlign.fq, output/beginAlign.fq - output: output/EndReads.fq, output/EndReads.fa - jobid: 2 - -[Sun Sep 6 11:11:30 2020] -Finished job 2. -10 of 12 steps (83%) done - -[Sun Sep 6 11:11:30 2020] -rule remove_dupl: - input: output/EndReads.fa - output: output/EndReads_dupl_remove.fa - jobid: 1 - -[Sun Sep 6 11:11:30 2020] -Finished job 1. -11 of 12 steps (92%) done - -[Sun Sep 6 11:11:30 2020] -localrule all: - input: output/EndReads_dupl_remove.fa - jobid: 0 - -[Sun Sep 6 11:11:30 2020] -Finished job 0. -12 of 12 steps (100%) done -Complete log: /data/user/huangf/Arginini/original/snakemake/.snakemake/log/2020-09-06T105447.133356.snakemake.log diff --git a/.snakemake/log/2020-09-06T141132.053473.snakemake.log b/.snakemake/log/2020-09-06T141132.053473.snakemake.log deleted file mode 100644 index e45f16b..0000000 --- a/.snakemake/log/2020-09-06T141132.053473.snakemake.log +++ /dev/null @@ -1,97 +0,0 @@ -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 2 -Rules claiming more threads will be scaled down. -Job counts: - count jobs - 1 all - 1 endReads_select - 1 first_assemble - 1 fq_to_fa - 1 longread_len - 1 longread_polish - 1 merge_end_reads - 1 rawfq_firstrun - 1 remove_dupl - 1 select_longestContig - 1 select_longread - 1 short_to_long - 12 - -[Sun Sep 6 14:11:32 2020] -rule longread_len: - input: data/rawdata.fastq - output: output/read_len_distrbution_2.txt - jobid: 11 - -[Sun Sep 6 14:11:32 2020] -Finished job 11. -1 of 12 steps (8%) done - -[Sun Sep 6 14:11:32 2020] -rule select_longread: - input: data/rawdata.fastq, output/read_len_distrbution_2.txt - output: output/filter_length.fq, output/left_filter_length.fq - jobid: 9 - -[Sun Sep 6 14:11:33 2020] -Finished job 9. -2 of 12 steps (17%) done - -[Sun Sep 6 14:11:33 2020] -rule fq_to_fa: - input: output/filter_length.fq - output: output/filter_length.fa - jobid: 8 - -[Sun Sep 6 14:11:33 2020] -Finished job 8. -3 of 12 steps (25%) done - -[Sun Sep 6 14:11:33 2020] -rule short_to_long: - input: output/filter_length.fa, output/left_filter_length.fq - output: output/short_to_long.sam - jobid: 10 - -[Sun Sep 6 14:13:23 2020] -Finished job 10. -4 of 12 steps (33%) done - -[Sun Sep 6 14:13:23 2020] -rule longread_polish: - input: output/filter_length.fa, output/left_filter_length.fq, output/short_to_long.sam - output: output/long_racon_corrected.fa - jobid: 7 - -[Sun Sep 6 14:15:27 2020] -Finished job 7. -5 of 12 steps (42%) done - -[Sun Sep 6 14:15:27 2020] -rule first_assemble: - input: output/long_racon_corrected.fa - output: output/assembly.fasta - jobid: 6 - -[Sun Sep 6 14:27:31 2020] -Finished job 6. -6 of 12 steps (50%) done - -[Sun Sep 6 14:27:31 2020] -rule select_longestContig: - input: output/assembly.fasta - output: output/firstrun.fa - jobid: 4 - -[Sun Sep 6 14:27:31 2020] -Error in rule select_longestContig: - jobid: 4 - output: output/firstrun.fa - shell: - python script/select_plasmidID_longest_contig.py output/assembly.fasta output/firstrun.fa - (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!) - -Shutting down, this might take some time. -Exiting because a job execution failed. Look above for error message -Complete log: /data/user/huangf/Arginini/original/snakemake/.snakemake/log/2020-09-06T141132.053473.snakemake.log diff --git a/.snakemake/log/2020-09-06T144047.956811.snakemake.log b/.snakemake/log/2020-09-06T144047.956811.snakemake.log deleted file mode 100644 index cfc976c..0000000 --- a/.snakemake/log/2020-09-06T144047.956811.snakemake.log +++ /dev/null @@ -1,139 +0,0 @@ -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 2 -Rules claiming more threads will be scaled down. -Job counts: - count jobs - 1 all - 1 endReads_select - 1 first_assemble - 1 fq_to_fa - 1 longread_len - 1 longread_polish - 1 merge_end_reads - 1 rawfq_firstrun - 1 remove_dupl - 1 select_longestContig - 1 select_longread - 1 short_to_long - 12 - -[Sun Sep 6 14:40:48 2020] -rule longread_len: - input: data/rawdata.fastq - output: output/read_len_distrbution_2.txt - jobid: 11 - -[Sun Sep 6 14:40:48 2020] -Finished job 11. -1 of 12 steps (8%) done - -[Sun Sep 6 14:40:48 2020] -rule select_longread: - input: data/rawdata.fastq, output/read_len_distrbution_2.txt - output: output/filter_length.fq, output/left_filter_length.fq - jobid: 9 - -[Sun Sep 6 14:40:49 2020] -Finished job 9. -2 of 12 steps (17%) done - -[Sun Sep 6 14:40:49 2020] -rule fq_to_fa: - input: output/filter_length.fq - output: output/filter_length.fa - jobid: 8 - -[Sun Sep 6 14:40:49 2020] -Finished job 8. -3 of 12 steps (25%) done - -[Sun Sep 6 14:40:49 2020] -rule short_to_long: - input: output/filter_length.fa, output/left_filter_length.fq - output: output/short_to_long.sam - jobid: 10 - -[Sun Sep 6 14:42:39 2020] -Finished job 10. -4 of 12 steps (33%) done - -[Sun Sep 6 14:42:39 2020] -rule longread_polish: - input: output/filter_length.fa, output/left_filter_length.fq, output/short_to_long.sam - output: output/long_racon_corrected.fa - jobid: 7 - -[Sun Sep 6 14:44:42 2020] -Finished job 7. -5 of 12 steps (42%) done - -[Sun Sep 6 14:44:42 2020] -rule first_assemble: - input: output/long_racon_corrected.fa - output: output/assembly.fasta - jobid: 6 - -[Sun Sep 6 14:56:54 2020] -Finished job 6. -6 of 12 steps (50%) done - -[Sun Sep 6 14:56:54 2020] -rule select_longestContig: - input: output/assembly.fasta - output: output/firstrun.fa - jobid: 4 - -[Sun Sep 6 14:56:55 2020] -Finished job 4. -7 of 12 steps (58%) done - -[Sun Sep 6 14:56:55 2020] -rule rawfq_firstrun: - input: output/firstrun.fa, data/rawdata.fastq - output: output/rawfq-firstrun-srt.bam - jobid: 5 - -[Sun Sep 6 14:57:46 2020] -Finished job 5. -8 of 12 steps (67%) done - -[Sun Sep 6 14:57:46 2020] -rule endReads_select: - input: output/firstrun.fa, output/rawfq-firstrun-srt.bam - output: output/EndAlign.fq, output/beginAlign.fq - jobid: 3 - -[Sun Sep 6 14:57:46 2020] -Finished job 3. -9 of 12 steps (75%) done - -[Sun Sep 6 14:57:46 2020] -rule merge_end_reads: - input: output/EndAlign.fq, output/beginAlign.fq - output: output/EndReads.fq, output/EndReads.fa - jobid: 2 - -[Sun Sep 6 14:57:47 2020] -Finished job 2. -10 of 12 steps (83%) done - -[Sun Sep 6 14:57:47 2020] -rule remove_dupl: - input: output/EndReads.fa - output: output/EndReads_dupl_remove.fa - jobid: 1 - -[Sun Sep 6 14:57:47 2020] -Finished job 1. -11 of 12 steps (92%) done - -[Sun Sep 6 14:57:47 2020] -localrule all: - input: output/EndReads_dupl_remove.fa - jobid: 0 - -[Sun Sep 6 14:57:47 2020] -Finished job 0. -12 of 12 steps (100%) done -Complete log: /data/user/huangf/Arginini/original/snakemake/.snakemake/log/2020-09-06T144047.956811.snakemake.log diff --git a/.snakemake/log/2020-09-06T161306.158840.snakemake.log b/.snakemake/log/2020-09-06T161306.158840.snakemake.log deleted file mode 100644 index 48a1ef8..0000000 --- a/.snakemake/log/2020-09-06T161306.158840.snakemake.log +++ /dev/null @@ -1,40 +0,0 @@ -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 2 -Rules claiming more threads will be scaled down. -Job counts: - count jobs - 1 all - 1 merge_end_reads - 1 remove_dupl - 3 - -[Sun Sep 6 16:13:06 2020] -rule merge_end_reads: - input: output/EndAlign.fq, output/beginAlign.fq - output: output/EndReads.fq, output/EndReads.fa - jobid: 2 - -[Sun Sep 6 16:13:06 2020] -Finished job 2. -1 of 3 steps (33%) done - -[Sun Sep 6 16:13:06 2020] -rule remove_dupl: - input: output/EndReads.fa - output: output/EndReads_dupl_remove.fa - jobid: 1 - -[Sun Sep 6 16:13:06 2020] -Finished job 1. -2 of 3 steps (67%) done - -[Sun Sep 6 16:13:06 2020] -localrule all: - input: output/EndReads_dupl_remove.fa - jobid: 0 - -[Sun Sep 6 16:13:06 2020] -Finished job 0. -3 of 3 steps (100%) done -Complete log: /data/user/huangf/Arginini/original/snakemake/.snakemake/log/2020-09-06T161306.158840.snakemake.log diff --git a/.snakemake/log/2020-09-06T162318.902955.snakemake.log b/.snakemake/log/2020-09-06T162318.902955.snakemake.log deleted file mode 100644 index 754f2c4..0000000 --- a/.snakemake/log/2020-09-06T162318.902955.snakemake.log +++ /dev/null @@ -1,3 +0,0 @@ -KeyError in line 8 of /data/user/huangf/Arginini/original/snakemake/snakefile: -'nanopore' - File "/data/user/huangf/Arginini/original/snakemake/snakefile", line 8, in diff --git a/.snakemake/log/2020-09-06T162401.539727.snakemake.log b/.snakemake/log/2020-09-06T162401.539727.snakemake.log deleted file mode 100644 index a5ff723..0000000 --- a/.snakemake/log/2020-09-06T162401.539727.snakemake.log +++ /dev/null @@ -1,51 +0,0 @@ -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 2 -Rules claiming more threads will be scaled down. -Job counts: - count jobs - 1 all - 1 endReads_select - 1 merge_end_reads - 1 remove_dupl - 4 - -[Sun Sep 6 16:24:01 2020] -rule endReads_select: - input: output/firstrun.fa - output: output/EndAlign.fq, output/beginAlign.fq - jobid: 3 - -[Sun Sep 6 16:24:01 2020] -Finished job 3. -1 of 4 steps (25%) done - -[Sun Sep 6 16:24:01 2020] -rule merge_end_reads: - input: output/EndAlign.fq, output/beginAlign.fq - output: output/EndReads.fq, output/EndReads.fa - jobid: 2 - -[Sun Sep 6 16:24:01 2020] -Finished job 2. -2 of 4 steps (50%) done - -[Sun Sep 6 16:24:01 2020] -rule remove_dupl: - input: output/EndReads.fa - output: output/EndReads_dupl_remove.fa - jobid: 1 - -[Sun Sep 6 16:24:01 2020] -Finished job 1. -3 of 4 steps (75%) done - -[Sun Sep 6 16:24:01 2020] -localrule all: - input: output/EndReads_dupl_remove.fa - jobid: 0 - -[Sun Sep 6 16:24:01 2020] -Finished job 0. -4 of 4 steps (100%) done -Complete log: /data/user/huangf/Arginini/original/snakemake/.snakemake/log/2020-09-06T162401.539727.snakemake.log diff --git a/.snakemake/log/2020-09-06T162729.438481.snakemake.log b/.snakemake/log/2020-09-06T162729.438481.snakemake.log deleted file mode 100644 index 759ec3f..0000000 --- a/.snakemake/log/2020-09-06T162729.438481.snakemake.log +++ /dev/null @@ -1,3 +0,0 @@ -Building DAG of jobs... -Nothing to be done. -Complete log: /data/user/huangf/Arginini/original/snakemake/.snakemake/log/2020-09-06T162729.438481.snakemake.log diff --git a/.snakemake/log/2020-09-06T162820.823552.snakemake.log b/.snakemake/log/2020-09-06T162820.823552.snakemake.log deleted file mode 100644 index 7c4bd34..0000000 --- a/.snakemake/log/2020-09-06T162820.823552.snakemake.log +++ /dev/null @@ -1,51 +0,0 @@ -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 2 -Rules claiming more threads will be scaled down. -Job counts: - count jobs - 1 all - 1 endReads_select - 1 merge_end_reads - 1 remove_dupl - 4 - -[Sun Sep 6 16:28:20 2020] -rule endReads_select: - input: output/firstrun.fa - output: output/EndAlign.fq, output/beginAlign.fq - jobid: 3 - -[Sun Sep 6 16:28:20 2020] -Finished job 3. -1 of 4 steps (25%) done - -[Sun Sep 6 16:28:20 2020] -rule merge_end_reads: - input: output/EndAlign.fq, output/beginAlign.fq - output: output/EndReads.fq, output/EndReads.fa - jobid: 2 - -[Sun Sep 6 16:28:21 2020] -Finished job 2. -2 of 4 steps (50%) done - -[Sun Sep 6 16:28:21 2020] -rule remove_dupl: - input: output/EndReads.fa - output: output/EndReads_dupl_remove.fa - jobid: 1 - -[Sun Sep 6 16:28:21 2020] -Finished job 1. -3 of 4 steps (75%) done - -[Sun Sep 6 16:28:21 2020] -localrule all: - input: output/EndReads_dupl_remove.fa - jobid: 0 - -[Sun Sep 6 16:28:21 2020] -Finished job 0. -4 of 4 steps (100%) done -Complete log: /data/user/huangf/Arginini/original/snakemake/.snakemake/log/2020-09-06T162820.823552.snakemake.log diff --git a/.snakemake/log/2020-09-06T163233.880795.snakemake.log b/.snakemake/log/2020-09-06T163233.880795.snakemake.log deleted file mode 100644 index e987326..0000000 --- a/.snakemake/log/2020-09-06T163233.880795.snakemake.log +++ /dev/null @@ -1,62 +0,0 @@ -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 2 -Rules claiming more threads will be scaled down. -Job counts: - count jobs - 1 all - 1 endReads_select - 1 merge_end_reads - 1 rawfq_firstrun - 1 remove_dupl - 5 - -[Sun Sep 6 16:32:33 2020] -rule rawfq_firstrun: - input: output/firstrun.fa, data/rawdata.fastq - output: output/rawfq-firstrun-srt.bam - jobid: 4 - -[Sun Sep 6 16:33:25 2020] -Finished job 4. -1 of 5 steps (20%) done - -[Sun Sep 6 16:33:25 2020] -rule endReads_select: - input: output/firstrun.fa, output/rawfq-firstrun-srt.bam - output: output/EndAlign.fq, output/beginAlign.fq - jobid: 3 - -[Sun Sep 6 16:33:25 2020] -Finished job 3. -2 of 5 steps (40%) done - -[Sun Sep 6 16:33:25 2020] -rule merge_end_reads: - input: output/EndAlign.fq, output/beginAlign.fq - output: output/EndReads.fq, output/EndReads.fa - jobid: 2 - -[Sun Sep 6 16:33:25 2020] -Finished job 2. -3 of 5 steps (60%) done - -[Sun Sep 6 16:33:25 2020] -rule remove_dupl: - input: output/EndReads.fa - output: output/EndReads_dupl_remove.fa - jobid: 1 - -[Sun Sep 6 16:33:25 2020] -Finished job 1. -4 of 5 steps (80%) done - -[Sun Sep 6 16:33:25 2020] -localrule all: - input: output/EndReads_dupl_remove.fa - jobid: 0 - -[Sun Sep 6 16:33:25 2020] -Finished job 0. -5 of 5 steps (100%) done -Complete log: /data/user/huangf/Arginini/original/snakemake/.snakemake/log/2020-09-06T163233.880795.snakemake.log diff --git a/.snakemake/log/2020-09-06T164255.851644.snakemake.log b/.snakemake/log/2020-09-06T164255.851644.snakemake.log deleted file mode 100644 index efc6d2b..0000000 --- a/.snakemake/log/2020-09-06T164255.851644.snakemake.log +++ /dev/null @@ -1,73 +0,0 @@ -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 2 -Rules claiming more threads will be scaled down. -Job counts: - count jobs - 1 all - 1 endReads_select - 1 merge_end_reads - 1 rawfq_firstrun - 1 remove_dupl - 1 samtools_sort - 6 - -[Sun Sep 6 16:42:55 2020] -rule rawfq_firstrun: - input: output/firstrun.fa, data/rawdata.fastq - output: output/rawfq_firstrun.bam - jobid: 5 - -[Sun Sep 6 16:43:31 2020] -Finished job 5. -1 of 6 steps (17%) done - -[Sun Sep 6 16:43:31 2020] -rule samtools_sort: - input: output/rawfq_firstrun.bam - output: output/rawfq_firstrun_srt.bam - jobid: 4 - -[Sun Sep 6 16:43:48 2020] -Finished job 4. -2 of 6 steps (33%) done - -[Sun Sep 6 16:43:48 2020] -rule endReads_select: - input: output/firstrun.fa, output/rawfq_firstrun_srt.bam - output: output/EndAlign.fq, output/beginAlign.fq - jobid: 3 - -[Sun Sep 6 16:43:48 2020] -Finished job 3. -3 of 6 steps (50%) done - -[Sun Sep 6 16:43:48 2020] -rule merge_end_reads: - input: output/EndAlign.fq, output/beginAlign.fq - output: output/EndReads.fq, output/EndReads.fa - jobid: 2 - -[Sun Sep 6 16:43:49 2020] -Finished job 2. -4 of 6 steps (67%) done - -[Sun Sep 6 16:43:49 2020] -rule remove_dupl: - input: output/EndReads.fa - output: output/EndReads_dupl_remove.fa - jobid: 1 - -[Sun Sep 6 16:43:49 2020] -Finished job 1. -5 of 6 steps (83%) done - -[Sun Sep 6 16:43:49 2020] -localrule all: - input: output/EndReads_dupl_remove.fa - jobid: 0 - -[Sun Sep 6 16:43:49 2020] -Finished job 0. -6 of 6 steps (100%) done -Complete log: /data/user/huangf/Arginini/original/snakemake/.snakemake/log/2020-09-06T164255.851644.snakemake.log diff --git a/.snakemake/log/2020-09-06T164641.900505.snakemake.log b/.snakemake/log/2020-09-06T164641.900505.snakemake.log deleted file mode 100644 index ca31380..0000000 --- a/.snakemake/log/2020-09-06T164641.900505.snakemake.log +++ /dev/null @@ -1,51 +0,0 @@ -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 2 -Rules claiming more threads will be scaled down. -Job counts: - count jobs - 1 all - 1 endReads_select - 1 merge_end_reads - 1 remove_dupl - 4 - -[Sun Sep 6 16:46:41 2020] -rule endReads_select: - input: output/firstrun.fa, output/rawfq_firstrun_srt.bam - output: output/EndAlign.fq, output/beginAlign.fq - jobid: 3 - -[Sun Sep 6 16:46:42 2020] -Finished job 3. -1 of 4 steps (25%) done - -[Sun Sep 6 16:46:42 2020] -rule merge_end_reads: - input: output/EndAlign.fq, output/beginAlign.fq - output: output/EndReads.fq, output/EndReads.fa - jobid: 2 - -[Sun Sep 6 16:46:42 2020] -Finished job 2. -2 of 4 steps (50%) done - -[Sun Sep 6 16:46:42 2020] -rule remove_dupl: - input: output/EndReads.fa - output: output/EndReads_dupl_remove.fa - jobid: 1 - -[Sun Sep 6 16:46:42 2020] -Finished job 1. -3 of 4 steps (75%) done - -[Sun Sep 6 16:46:42 2020] -localrule all: - input: output/EndReads_dupl_remove.fa - jobid: 0 - -[Sun Sep 6 16:46:42 2020] -Finished job 0. -4 of 4 steps (100%) done -Complete log: /data/user/huangf/Arginini/original/snakemake/.snakemake/log/2020-09-06T164641.900505.snakemake.log diff --git a/.snakemake/log/2020-09-06T164941.074371.snakemake.log b/.snakemake/log/2020-09-06T164941.074371.snakemake.log deleted file mode 100644 index 52f2ffe..0000000 --- a/.snakemake/log/2020-09-06T164941.074371.snakemake.log +++ /dev/null @@ -1,3 +0,0 @@ -Building DAG of jobs... -Nothing to be done. -Complete log: /data/user/huangf/Arginini/original/snakemake/.snakemake/log/2020-09-06T164941.074371.snakemake.log diff --git a/.snakemake/log/2020-09-06T165012.233320.snakemake.log b/.snakemake/log/2020-09-06T165012.233320.snakemake.log deleted file mode 100644 index 1085ab3..0000000 --- a/.snakemake/log/2020-09-06T165012.233320.snakemake.log +++ /dev/null @@ -1,73 +0,0 @@ -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 2 -Rules claiming more threads will be scaled down. -Job counts: - count jobs - 1 all - 1 endReads_select - 1 merge_end_reads - 1 rawfq_firstrun - 1 remove_dupl - 1 samtools_sort - 6 - -[Sun Sep 6 16:50:12 2020] -rule rawfq_firstrun: - input: output/firstrun.fa, data/rawdata.fastq - output: output/rawfq_firstrun.bam - jobid: 5 - -[Sun Sep 6 16:50:48 2020] -Finished job 5. -1 of 6 steps (17%) done - -[Sun Sep 6 16:50:48 2020] -rule samtools_sort: - input: output/rawfq_firstrun.bam - output: output/rawfq_firstrun_srt.bam - jobid: 4 - -[Sun Sep 6 16:51:06 2020] -Finished job 4. -2 of 6 steps (33%) done - -[Sun Sep 6 16:51:06 2020] -rule endReads_select: - input: output/firstrun.fa, output/rawfq_firstrun_srt.bam - output: output/EndAlign.fq, output/beginAlign.fq - jobid: 3 - -[Sun Sep 6 16:51:06 2020] -Finished job 3. -3 of 6 steps (50%) done - -[Sun Sep 6 16:51:06 2020] -rule merge_end_reads: - input: output/EndAlign.fq, output/beginAlign.fq - output: output/EndReads.fq, output/EndReads.fa - jobid: 2 - -[Sun Sep 6 16:51:06 2020] -Finished job 2. -4 of 6 steps (67%) done - -[Sun Sep 6 16:51:06 2020] -rule remove_dupl: - input: output/EndReads.fa - output: output/EndReads_dupl_remove.fa - jobid: 1 - -[Sun Sep 6 16:51:06 2020] -Finished job 1. -5 of 6 steps (83%) done - -[Sun Sep 6 16:51:06 2020] -localrule all: - input: output/EndReads_dupl_remove.fa - jobid: 0 - -[Sun Sep 6 16:51:06 2020] -Finished job 0. -6 of 6 steps (100%) done -Complete log: /data/user/huangf/Arginini/original/snakemake/.snakemake/log/2020-09-06T165012.233320.snakemake.log diff --git a/.snakemake/log/2020-09-06T213110.941525.snakemake.log b/.snakemake/log/2020-09-06T213110.941525.snakemake.log deleted file mode 100644 index 9e418e9..0000000 --- a/.snakemake/log/2020-09-06T213110.941525.snakemake.log +++ /dev/null @@ -1,51 +0,0 @@ -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 2 -Rules claiming more threads will be scaled down. -Job counts: - count jobs - 1 all - 1 endReads_select - 1 merge_end_reads - 1 remove_dupl - 4 - -[Sun Sep 6 21:31:11 2020] -rule endReads_select: - input: output/firstrun.fa, output/rawfq_firstrun_srt.bam - output: output/EndAlign.fq, output/beginAlign.fq - jobid: 3 - -[Sun Sep 6 21:31:11 2020] -Finished job 3. -1 of 4 steps (25%) done - -[Sun Sep 6 21:31:11 2020] -rule merge_end_reads: - input: output/EndAlign.fq, output/beginAlign.fq - output: output/EndReads.fq, output/EndReads.fa - jobid: 2 - -[Sun Sep 6 21:31:11 2020] -Finished job 2. -2 of 4 steps (50%) done - -[Sun Sep 6 21:31:11 2020] -rule remove_dupl: - input: output/EndReads.fa - output: output/EndReads_dupl_remove.fa - jobid: 1 - -[Sun Sep 6 21:31:11 2020] -Finished job 1. -3 of 4 steps (75%) done - -[Sun Sep 6 21:31:11 2020] -localrule all: - input: output/EndReads_dupl_remove.fa - jobid: 0 - -[Sun Sep 6 21:31:11 2020] -Finished job 0. -4 of 4 steps (100%) done -Complete log: /data/user/huangf/Arginini/original/snakemake/.snakemake/log/2020-09-06T213110.941525.snakemake.log diff --git a/.snakemake/log/2020-09-06T214102.530285.snakemake.log b/.snakemake/log/2020-09-06T214102.530285.snakemake.log deleted file mode 100644 index 3be3acf..0000000 --- a/.snakemake/log/2020-09-06T214102.530285.snakemake.log +++ /dev/null @@ -1,139 +0,0 @@ -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 2 -Rules claiming more threads will be scaled down. -Job counts: - count jobs - 1 all - 1 endReads_select - 1 first_assemble - 1 fq_to_fa - 1 longread_len - 1 longread_polish - 1 merge_end_reads - 1 rawfq_firstrun - 1 remove_dupl - 1 select_longestContig - 1 select_longread - 1 short_to_long - 12 - -[Sun Sep 6 21:41:02 2020] -rule longread_len: - input: data/rawdata.fastq - output: output/read_len_distrbution_2.txt - jobid: 11 - -[Sun Sep 6 21:41:03 2020] -Finished job 11. -1 of 12 steps (8%) done - -[Sun Sep 6 21:41:03 2020] -rule select_longread: - input: data/rawdata.fastq, output/read_len_distrbution_2.txt - output: output/filter_length.fq, output/left_filter_length.fq - jobid: 9 - -[Sun Sep 6 21:41:04 2020] -Finished job 9. -2 of 12 steps (17%) done - -[Sun Sep 6 21:41:04 2020] -rule fq_to_fa: - input: output/filter_length.fq - output: output/filter_length.fa - jobid: 8 - -[Sun Sep 6 21:41:04 2020] -Finished job 8. -3 of 12 steps (25%) done - -[Sun Sep 6 21:41:04 2020] -rule short_to_long: - input: output/filter_length.fa, output/left_filter_length.fq - output: output/short_to_long.sam - jobid: 10 - -[Sun Sep 6 21:42:54 2020] -Finished job 10. -4 of 12 steps (33%) done - -[Sun Sep 6 21:42:54 2020] -rule longread_polish: - input: output/filter_length.fa, output/left_filter_length.fq, output/short_to_long.sam - output: output/long_racon_corrected.fa - jobid: 7 - -[Sun Sep 6 21:45:00 2020] -Finished job 7. -5 of 12 steps (42%) done - -[Sun Sep 6 21:45:00 2020] -rule first_assemble: - input: output/long_racon_corrected.fa - output: output/assembly.fasta - jobid: 6 - -[Sun Sep 6 21:57:28 2020] -Finished job 6. -6 of 12 steps (50%) done - -[Sun Sep 6 21:57:28 2020] -rule select_longestContig: - input: output/assembly.fasta - output: output/firstrun.fa - jobid: 4 - -[Sun Sep 6 21:57:30 2020] -Finished job 4. -7 of 12 steps (58%) done - -[Sun Sep 6 21:57:30 2020] -rule rawfq_firstrun: - input: output/firstrun.fa, data/rawdata.fastq - output: output/rawfq-firstrun-srt.bam - jobid: 5 - -[Sun Sep 6 21:58:22 2020] -Finished job 5. -8 of 12 steps (67%) done - -[Sun Sep 6 21:58:22 2020] -rule endReads_select: - input: output/firstrun.fa, output/rawfq-firstrun-srt.bam - output: output/EndAlign.fq, output/beginAlign.fq - jobid: 3 - -[Sun Sep 6 21:58:22 2020] -Finished job 3. -9 of 12 steps (75%) done - -[Sun Sep 6 21:58:22 2020] -rule merge_end_reads: - input: output/EndAlign.fq, output/beginAlign.fq - output: output/EndReads.fq, output/EndReads.fa - jobid: 2 - -[Sun Sep 6 21:58:22 2020] -Finished job 2. -10 of 12 steps (83%) done - -[Sun Sep 6 21:58:22 2020] -rule remove_dupl: - input: output/EndReads.fa - output: output/EndReads_dupl_remove.fa - jobid: 1 - -[Sun Sep 6 21:58:22 2020] -Finished job 1. -11 of 12 steps (92%) done - -[Sun Sep 6 21:58:22 2020] -localrule all: - input: output/EndReads_dupl_remove.fa - jobid: 0 - -[Sun Sep 6 21:58:22 2020] -Finished job 0. -12 of 12 steps (100%) done -Complete log: /data/user/huangf/Arginini/original/snakemake/.snakemake/log/2020-09-06T214102.530285.snakemake.log diff --git a/.snakemake/log/2020-09-06T230912.036253.snakemake.log b/.snakemake/log/2020-09-06T230912.036253.snakemake.log deleted file mode 100644 index 36f5365..0000000 --- a/.snakemake/log/2020-09-06T230912.036253.snakemake.log +++ /dev/null @@ -1,139 +0,0 @@ -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 2 -Rules claiming more threads will be scaled down. -Job counts: - count jobs - 1 all - 1 endReads_select - 1 first_assemble - 1 fq_to_fa - 1 longread_len - 1 longread_polish - 1 merge_end_reads - 1 rawfq_firstrun - 1 remove_dupl - 1 select_longestContig - 1 select_longread - 1 short_to_long - 12 - -[Sun Sep 6 23:09:12 2020] -rule longread_len: - input: data/rawdata.fastq - output: output/read_len_distrbution_2.txt - jobid: 11 - -[Sun Sep 6 23:09:12 2020] -Finished job 11. -1 of 12 steps (8%) done - -[Sun Sep 6 23:09:12 2020] -rule select_longread: - input: data/rawdata.fastq, output/read_len_distrbution_2.txt - output: output/filter_length.fq, output/left_filter_length.fq - jobid: 9 - -[Sun Sep 6 23:09:13 2020] -Finished job 9. -2 of 12 steps (17%) done - -[Sun Sep 6 23:09:13 2020] -rule fq_to_fa: - input: output/filter_length.fq - output: output/filter_length.fa - jobid: 8 - -[Sun Sep 6 23:09:13 2020] -Finished job 8. -3 of 12 steps (25%) done - -[Sun Sep 6 23:09:13 2020] -rule short_to_long: - input: output/filter_length.fa, output/left_filter_length.fq - output: output/short_to_long.sam - jobid: 10 - -[Sun Sep 6 23:11:05 2020] -Finished job 10. -4 of 12 steps (33%) done - -[Sun Sep 6 23:11:05 2020] -rule longread_polish: - input: output/filter_length.fa, output/left_filter_length.fq, output/short_to_long.sam - output: output/long_racon_corrected.fa - jobid: 7 - -[Sun Sep 6 23:13:13 2020] -Finished job 7. -5 of 12 steps (42%) done - -[Sun Sep 6 23:13:13 2020] -rule first_assemble: - input: output/long_racon_corrected.fa - output: output/assembly.fasta - jobid: 6 - -[Sun Sep 6 23:25:47 2020] -Finished job 6. -6 of 12 steps (50%) done - -[Sun Sep 6 23:25:47 2020] -rule select_longestContig: - input: output/assembly.fasta - output: output/firstrun.fa - jobid: 4 - -[Sun Sep 6 23:25:47 2020] -Finished job 4. -7 of 12 steps (58%) done - -[Sun Sep 6 23:25:47 2020] -rule rawfq_firstrun: - input: output/firstrun.fa, data/rawdata.fastq - output: output/rawfq-firstrun-srt.bam - jobid: 5 - -[Sun Sep 6 23:26:39 2020] -Finished job 5. -8 of 12 steps (67%) done - -[Sun Sep 6 23:26:39 2020] -rule endReads_select: - input: output/firstrun.fa, output/rawfq-firstrun-srt.bam - output: output/EndAlign.fq, output/beginAlign.fq - jobid: 3 - -[Sun Sep 6 23:26:39 2020] -Finished job 3. -9 of 12 steps (75%) done - -[Sun Sep 6 23:26:39 2020] -rule merge_end_reads: - input: output/EndAlign.fq, output/beginAlign.fq - output: output/EndReads.fq, output/EndReads.fa - jobid: 2 - -[Sun Sep 6 23:26:39 2020] -Finished job 2. -10 of 12 steps (83%) done - -[Sun Sep 6 23:26:39 2020] -rule remove_dupl: - input: output/EndReads.fa - output: output/EndReads_dupl_remove.fa - jobid: 1 - -[Sun Sep 6 23:26:39 2020] -Finished job 1. -11 of 12 steps (92%) done - -[Sun Sep 6 23:26:39 2020] -localrule all: - input: output/EndReads_dupl_remove.fa - jobid: 0 - -[Sun Sep 6 23:26:39 2020] -Finished job 0. -12 of 12 steps (100%) done -Complete log: /data/user/huangf/Arginini/original/snakemake/.snakemake/log/2020-09-06T230912.036253.snakemake.log diff --git a/.snakemake/log/2020-09-07T002118.483595.snakemake.log b/.snakemake/log/2020-09-07T002118.483595.snakemake.log deleted file mode 100644 index 025e0aa..0000000 --- a/.snakemake/log/2020-09-07T002118.483595.snakemake.log +++ /dev/null @@ -1,3 +0,0 @@ -SyntaxError in line 5 of /data/user/huangf/Arginini/original/snakemake/rules/selectEndRead.smk: -invalid syntax - File "/data/user/huangf/Arginini/original/snakemake/snakefile", line 10, in diff --git a/.snakemake/log/2020-09-07T002233.537556.snakemake.log b/.snakemake/log/2020-09-07T002233.537556.snakemake.log deleted file mode 100644 index 144d31b..0000000 --- a/.snakemake/log/2020-09-07T002233.537556.snakemake.log +++ /dev/null @@ -1,139 +0,0 @@ -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 2 -Rules claiming more threads will be scaled down. -Job counts: - count jobs - 1 all - 1 endReads_select - 1 first_assemble - 1 fq_to_fa - 1 longread_len - 1 longread_polish - 1 merge_end_reads - 1 rawfq_firstrun - 1 remove_dupl - 1 select_longestContig - 1 select_longread - 1 short_to_long - 12 - -[Mon Sep 7 00:22:33 2020] -rule longread_len: - input: data/rawdata.fastq - output: output/read_len_distrbution_2.txt - jobid: 11 - -[Mon Sep 7 00:22:34 2020] -Finished job 11. -1 of 12 steps (8%) done - -[Mon Sep 7 00:22:34 2020] -rule select_longread: - input: data/rawdata.fastq, output/read_len_distrbution_2.txt - output: output/filter_length.fq, output/left_filter_length.fq - jobid: 9 - -[Mon Sep 7 00:22:35 2020] -Finished job 9. -2 of 12 steps (17%) done - -[Mon Sep 7 00:22:35 2020] -rule fq_to_fa: - input: output/filter_length.fq - output: output/filter_length.fa - jobid: 8 - -[Mon Sep 7 00:22:35 2020] -Finished job 8. -3 of 12 steps (25%) done - -[Mon Sep 7 00:22:35 2020] -rule short_to_long: - input: output/filter_length.fa, output/left_filter_length.fq - output: output/short_to_long.sam - jobid: 10 - -[Mon Sep 7 00:24:22 2020] -Finished job 10. -4 of 12 steps (33%) done - -[Mon Sep 7 00:24:22 2020] -rule longread_polish: - input: output/filter_length.fa, output/left_filter_length.fq, output/short_to_long.sam - output: output/long_racon_corrected.fa - jobid: 7 - -[Mon Sep 7 00:26:25 2020] -Finished job 7. -5 of 12 steps (42%) done - -[Mon Sep 7 00:26:25 2020] -rule first_assemble: - input: output/long_racon_corrected.fa - output: output/assembly.fasta - jobid: 6 - -[Mon Sep 7 00:38:35 2020] -Finished job 6. -6 of 12 steps (50%) done - -[Mon Sep 7 00:38:35 2020] -rule select_longestContig: - input: output/assembly.fasta - output: output/firstrun.fa - jobid: 4 - -[Mon Sep 7 00:38:35 2020] -Finished job 4. -7 of 12 steps (58%) done - -[Mon Sep 7 00:38:35 2020] -rule rawfq_firstrun: - input: output/firstrun.fa, data/rawdata.fastq - output: output/rawfq-firstrun-srt.bam, output/rawfq-firstrun-srt.bam.bai - jobid: 5 - -[Mon Sep 7 00:39:29 2020] -Finished job 5. -8 of 12 steps (67%) done - -[Mon Sep 7 00:39:29 2020] -rule endReads_select: - input: output/firstrun.fa, output/rawfq-firstrun-srt.bam, output/rawfq-firstrun-srt.bam.bai - output: output/EndAlign.fq, output/beginAlign.fq - jobid: 3 - -[Mon Sep 7 00:39:30 2020] -Finished job 3. -9 of 12 steps (75%) done - -[Mon Sep 7 00:39:30 2020] -rule merge_end_reads: - input: output/EndAlign.fq, output/beginAlign.fq - output: output/EndReads.fq, output/EndReads.fa - jobid: 2 - -[Mon Sep 7 00:39:30 2020] -Finished job 2. -10 of 12 steps (83%) done - -[Mon Sep 7 00:39:30 2020] -rule remove_dupl: - input: output/EndReads.fa - output: output/EndReads_dupl_remove.fa - jobid: 1 - -[Mon Sep 7 00:39:30 2020] -Finished job 1. -11 of 12 steps (92%) done - -[Mon Sep 7 00:39:30 2020] -localrule all: - input: output/EndReads_dupl_remove.fa - jobid: 0 - -[Mon Sep 7 00:39:30 2020] -Finished job 0. -12 of 12 steps (100%) done -Complete log: /data/user/huangf/Arginini/original/snakemake/.snakemake/log/2020-09-07T002233.537556.snakemake.log diff --git a/.snakemake/log/2020-09-07T111010.118229.snakemake.log b/.snakemake/log/2020-09-07T111010.118229.snakemake.log deleted file mode 100644 index 769e4eb..0000000 --- a/.snakemake/log/2020-09-07T111010.118229.snakemake.log +++ /dev/null @@ -1,40 +0,0 @@ -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 2 -Rules claiming more threads will be scaled down. -Job counts: - count jobs - 1 Oneline_fa_2 - 1 all - 1 select_longContig - 3 - -[Mon Sep 7 11:10:10 2020] -rule select_longContig: - input: output/assembly.fasta - output: output/secondrun.fa - jobid: 2 - -[Mon Sep 7 11:10:10 2020] -Finished job 2. -1 of 3 steps (33%) done - -[Mon Sep 7 11:10:10 2020] -rule Oneline_fa_2: - input: output/secondrun.fa - output: output/secondrunSeq - jobid: 1 - -[Mon Sep 7 11:10:10 2020] -Finished job 1. -2 of 3 steps (67%) done - -[Mon Sep 7 11:10:10 2020] -localrule all: - input: output/secondrunSeq - jobid: 0 - -[Mon Sep 7 11:10:10 2020] -Finished job 0. -3 of 3 steps (100%) done -Complete log: /data/user/huangf/Arginini/original/snakemake/.snakemake/log/2020-09-07T111010.118229.snakemake.log diff --git a/.snakemake/log/2020-09-07T111209.448744.snakemake.log b/.snakemake/log/2020-09-07T111209.448744.snakemake.log deleted file mode 100644 index da6d1cb..0000000 --- a/.snakemake/log/2020-09-07T111209.448744.snakemake.log +++ /dev/null @@ -1,40 +0,0 @@ -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 2 -Rules claiming more threads will be scaled down. -Job counts: - count jobs - 1 Oneline_fa_2 - 1 all - 1 select_longContig - 3 - -[Mon Sep 7 11:12:09 2020] -rule select_longContig: - input: output/assembly.fasta - output: output/secondrun.fa - jobid: 2 - -[Mon Sep 7 11:12:09 2020] -Finished job 2. -1 of 3 steps (33%) done - -[Mon Sep 7 11:12:09 2020] -rule Oneline_fa_2: - input: output/secondrun.fa - output: output/secondrunSeq - jobid: 1 - -[Mon Sep 7 11:12:09 2020] -Finished job 1. -2 of 3 steps (67%) done - -[Mon Sep 7 11:12:09 2020] -localrule all: - input: output/secondrunSeq - jobid: 0 - -[Mon Sep 7 11:12:09 2020] -Finished job 0. -3 of 3 steps (100%) done -Complete log: /data/user/huangf/Arginini/original/snakemake/.snakemake/log/2020-09-07T111209.448744.snakemake.log diff --git a/.snakemake/log/2020-09-07T111314.562329.snakemake.log b/.snakemake/log/2020-09-07T111314.562329.snakemake.log deleted file mode 100644 index ae8c762..0000000 --- a/.snakemake/log/2020-09-07T111314.562329.snakemake.log +++ /dev/null @@ -1,40 +0,0 @@ -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 2 -Rules claiming more threads will be scaled down. -Job counts: - count jobs - 1 Oneline_fa_2 - 1 all - 1 select_longContig - 3 - -[Mon Sep 7 11:13:14 2020] -rule select_longContig: - input: output/assembly.fasta - output: output/secondrun.fa - jobid: 2 - -[Mon Sep 7 11:13:14 2020] -Finished job 2. -1 of 3 steps (33%) done - -[Mon Sep 7 11:13:14 2020] -rule Oneline_fa_2: - input: output/secondrun.fa - output: output/secondrunSeq - jobid: 1 - -[Mon Sep 7 11:13:14 2020] -Finished job 1. -2 of 3 steps (67%) done - -[Mon Sep 7 11:13:14 2020] -localrule all: - input: output/secondrunSeq - jobid: 0 - -[Mon Sep 7 11:13:14 2020] -Finished job 0. -3 of 3 steps (100%) done -Complete log: /data/user/huangf/Arginini/original/snakemake/.snakemake/log/2020-09-07T111314.562329.snakemake.log diff --git a/.snakemake/log/2020-09-07T120319.826983.snakemake.log b/.snakemake/log/2020-09-07T120319.826983.snakemake.log deleted file mode 100644 index 8713ff3..0000000 --- a/.snakemake/log/2020-09-07T120319.826983.snakemake.log +++ /dev/null @@ -1,3 +0,0 @@ -NameError in line 19 of /data/user/huangf/Arginini/original/snakemake/snakefile: -name 'reassembleSize' is not defined - File "/data/user/huangf/Arginini/original/snakemake/snakefile", line 19, in diff --git a/.snakemake/log/2020-09-07T120337.300039.snakemake.log b/.snakemake/log/2020-09-07T120337.300039.snakemake.log deleted file mode 100644 index 5ad9e17..0000000 --- a/.snakemake/log/2020-09-07T120337.300039.snakemake.log +++ /dev/null @@ -1,3 +0,0 @@ -Building DAG of jobs... -Nothing to be done. -Complete log: /data/user/huangf/Arginini/original/snakemake/.snakemake/log/2020-09-07T120337.300039.snakemake.log diff --git a/.snakemake/log/2020-09-07T134815.752298.snakemake.log b/.snakemake/log/2020-09-07T134815.752298.snakemake.log deleted file mode 100644 index 8fdfd3c..0000000 --- a/.snakemake/log/2020-09-07T134815.752298.snakemake.log +++ /dev/null @@ -1,24 +0,0 @@ -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 2 -Rules claiming more threads will be scaled down. -Job counts: - count jobs - 1 second_assembly - 1 - -[Mon Sep 7 13:48:15 2020] -rule second_assembly: - input: output/EndReads_dupl_remove.fa - jobid: 0 - -[Mon Sep 7 13:48:16 2020] -Error in rule second_assembly: - jobid: 0 - shell: - flye --nano-raw output/EndReads_dupl_remove.fa --min-overlap 1000 --asm-coverage 50 --genome-size 281317.0 --out-dir output/secondrun - (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!) - -Shutting down, this might take some time. -Exiting because a job execution failed. Look above for error message -Complete log: /data/user/huangf/Arginini/original/snakemake/.snakemake/log/2020-09-07T134815.752298.snakemake.log diff --git a/.snakemake/log/2020-09-07T134947.995125.snakemake.log b/.snakemake/log/2020-09-07T134947.995125.snakemake.log deleted file mode 100644 index f01c9b5..0000000 --- a/.snakemake/log/2020-09-07T134947.995125.snakemake.log +++ /dev/null @@ -1,23 +0,0 @@ -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 2 -Rules claiming more threads will be scaled down. -Job counts: - count jobs - 1 second_assembly - 1 - -[Mon Sep 7 13:49:48 2020] -rule second_assembly: - input: output/EndReads_dupl_remove.fa - jobid: 0 - -Terminating processes on user request, this might take some time. -[Mon Sep 7 13:59:41 2020] -Error in rule second_assembly: - jobid: 0 - shell: - flye --nano-raw output/EndReads_dupl_remove.fa --min-overlap 1000 --asm-coverage 50 --genome-size 281317 --out-dir output/secondrun - (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!) - -Complete log: /data/user/huangf/Arginini/original/snakemake/.snakemake/log/2020-09-07T134947.995125.snakemake.log diff --git a/.snakemake/log/2020-09-07T142412.116984.snakemake.log b/.snakemake/log/2020-09-07T142412.116984.snakemake.log deleted file mode 100644 index b168fc0..0000000 --- a/.snakemake/log/2020-09-07T142412.116984.snakemake.log +++ /dev/null @@ -1,3 +0,0 @@ -WorkflowError in line 11 of /data/user/huangf/Arginini/original/snakemake/snakefile: -Failed to open /data/user/huangf/Arginini/original/snakemake/rearrangeStart.smk. - File "/data/user/huangf/Arginini/original/snakemake/snakefile", line 11, in diff --git a/.snakemake/log/2020-09-07T142439.901298.snakemake.log b/.snakemake/log/2020-09-07T142439.901298.snakemake.log deleted file mode 100644 index 9f4be15..0000000 --- a/.snakemake/log/2020-09-07T142439.901298.snakemake.log +++ /dev/null @@ -1,66 +0,0 @@ -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 2 -Rules claiming more threads will be scaled down. -Job counts: - count jobs - 1 all - 1 merge - 1 mergeFa - 1 polish_round1 - 1 polish_round2 - 1 polish_round3 - 1 polish_round5 - 1 rearrange - 1 tworun_align - 9 - -[Mon Sep 7 14:24:39 2020] -rule tworun_align: - input: output/secondrun.fa, output/firstrun.fa - output: output/first_second.paf - jobid: 8 - -[Mon Sep 7 14:24:40 2020] -Finished job 8. -1 of 9 steps (11%) done - -[Mon Sep 7 14:24:40 2020] -rule merge: - input: output/first_second.paf, output/firstrun.fa, output/secondrun.fa - output: output/BeginSeq, output/EndSeq - jobid: 7 - -[Mon Sep 7 14:24:40 2020] -Finished job 7. -2 of 9 steps (22%) done - -[Mon Sep 7 14:24:40 2020] -rule mergeFa: - input: output/BeginSeq, output/EndSeq - output: output/First_second_merge.fa - jobid: 6 - -[Mon Sep 7 14:24:40 2020] -Finished job 6. -3 of 9 steps (33%) done - -[Mon Sep 7 14:24:40 2020] -rule polish_round1: - input: output/First_second_merge.fa, data/rawdata.fastq - output: output/racon_polish_1.fa - jobid: 5 - -[Mon Sep 7 14:24:42 2020] -Error in rule polish_round1: - jobid: 5 - output: output/racon_polish_1.fa - shell: - minimap2 -ax map-ont output/First_second_merge.fa data/rawdata.fastq > output/rawfq_merged.sam && racon data/rawdata.fastq output/rawfq_merged.sam output/First_second_merge.fa > output/racon_polish_1.fa - (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!) - -Removing output files of failed job polish_round1 since they might be corrupted: -output/racon_polish_1.fa -Shutting down, this might take some time. -Exiting because a job execution failed. Look above for error message -Complete log: /data/user/huangf/Arginini/original/snakemake/.snakemake/log/2020-09-07T142439.901298.snakemake.log diff --git a/.snakemake/log/2020-09-07T143647.634070.snakemake.log b/.snakemake/log/2020-09-07T143647.634070.snakemake.log deleted file mode 100644 index 761eb96..0000000 --- a/.snakemake/log/2020-09-07T143647.634070.snakemake.log +++ /dev/null @@ -1,4 +0,0 @@ -Building DAG of jobs... -MissingInputException in line 19 of /data/user/huangf/Arginini/original/snakemake/rules/secondround.smk: -Missing input files for rule select_longContig: -output/secondrun/assembly.fasta diff --git a/.snakemake/log/2020-09-07T143755.862095.snakemake.log b/.snakemake/log/2020-09-07T143755.862095.snakemake.log deleted file mode 100644 index 761eb96..0000000 --- a/.snakemake/log/2020-09-07T143755.862095.snakemake.log +++ /dev/null @@ -1,4 +0,0 @@ -Building DAG of jobs... -MissingInputException in line 19 of /data/user/huangf/Arginini/original/snakemake/rules/secondround.smk: -Missing input files for rule select_longContig: -output/secondrun/assembly.fasta diff --git a/.snakemake/log/2020-09-07T143931.770944.snakemake.log b/.snakemake/log/2020-09-07T143931.770944.snakemake.log deleted file mode 100644 index 456577c..0000000 --- a/.snakemake/log/2020-09-07T143931.770944.snakemake.log +++ /dev/null @@ -1,122 +0,0 @@ -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 2 -Rules claiming more threads will be scaled down. -Job counts: - count jobs - 1 all - 1 merge - 1 mergeFa - 1 polish_round1 - 1 polish_round2 - 1 polish_round3 - 1 polish_round5 - 1 rearrange - 1 second_assembly - 1 select_longContig - 1 tworun_align - 11 - -[Mon Sep 7 14:39:31 2020] -rule second_assembly: - input: output/EndReads_dupl_remove.fa - output: output/secondrun/assembly.fasta - jobid: 10 - -[Mon Sep 7 14:50:10 2020] -Finished job 10. -1 of 11 steps (9%) done - -[Mon Sep 7 14:50:10 2020] -rule select_longContig: - input: output/secondrun/assembly.fasta - output: output/secondrun.fa - jobid: 9 - -[Mon Sep 7 14:50:10 2020] -Finished job 9. -2 of 11 steps (18%) done - -[Mon Sep 7 14:50:10 2020] -rule tworun_align: - input: output/secondrun.fa, output/firstrun.fa - output: output/first_second.paf - jobid: 8 - -[Mon Sep 7 14:50:11 2020] -Finished job 8. -3 of 11 steps (27%) done - -[Mon Sep 7 14:50:11 2020] -rule merge: - input: output/first_second.paf, output/firstrun.fa, output/secondrun.fa - output: output/BeginSeq, output/EndSeq - jobid: 7 - -[Mon Sep 7 14:50:11 2020] -Finished job 7. -4 of 11 steps (36%) done - -[Mon Sep 7 14:50:11 2020] -rule mergeFa: - input: output/BeginSeq, output/EndSeq - output: output/First_second_merge.fa - jobid: 6 - -[Mon Sep 7 14:50:11 2020] -Finished job 6. -5 of 11 steps (45%) done - -[Mon Sep 7 14:50:11 2020] -rule polish_round1: - input: output/First_second_merge.fa, data/rawdata.fastq - output: output/racon_polish_1.fa - jobid: 5 - -[Mon Sep 7 14:55:56 2020] -Finished job 5. -6 of 11 steps (55%) done - -[Mon Sep 7 14:55:56 2020] -rule polish_round2: - input: output/racon_polish_1.fa, data/rawdata.fastq - output: output/racon_polish_2.fa - jobid: 4 - -[Mon Sep 7 15:01:45 2020] -Finished job 4. -7 of 11 steps (64%) done - -[Mon Sep 7 15:01:45 2020] -rule polish_round3: - input: output/racon_polish_2.fa, data/rawdata.fastq - output: output/racon_polish_3.fa - jobid: 3 - -[Mon Sep 7 15:07:36 2020] -Finished job 3. -8 of 11 steps (73%) done - -[Mon Sep 7 15:07:36 2020] -rule polish_round5: - input: output/racon_polish_3.fa, data/rawdata.fastq - output: output/racon_polish_4.fa - jobid: 2 - -[Mon Sep 7 15:13:16 2020] -Finished job 2. -9 of 11 steps (82%) done - -[Mon Sep 7 15:13:16 2020] -rule rearrange: - input: output/racon_polish_4.fa, script/start_gene.fa - output: output/B_assembly.fasta - jobid: 1 - -RuleException in line 1 of /data/user/huangf/Arginini/original/snakemake/rules/rearrangeStart.smk: -NameError: The name 'inout' is unknown in this context. Please make sure that you defined that variable. Also note that braces not used for variable access have to be escaped by repeating them, i.e. {{print $1}} - File "/data/user/huangf/snakemake/lib/python3.6/site-packages/snakemake/executors/__init__.py", line 115, in run_jobs - File "/data/user/huangf/snakemake/lib/python3.6/site-packages/snakemake/executors/__init__.py", line 402, in run - File "/data/user/huangf/snakemake/lib/python3.6/site-packages/snakemake/executors/__init__.py", line 203, in _run - File "/data/user/huangf/snakemake/lib/python3.6/site-packages/snakemake/executors/__init__.py", line 131, in _run - File "/data/user/huangf/snakemake/lib/python3.6/site-packages/snakemake/executors/__init__.py", line 137, in printjob diff --git a/.snakemake/log/2020-09-14T104916.819257.snakemake.log b/.snakemake/log/2020-09-14T104916.819257.snakemake.log deleted file mode 100644 index 6f65fd0..0000000 --- a/.snakemake/log/2020-09-14T104916.819257.snakemake.log +++ /dev/null @@ -1,61 +0,0 @@ -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 2 -Rules claiming more threads will be scaled down. -Job counts: - count jobs - 1 all - 1 polish_round1 - 1 polish_round2 - 1 polish_round3 - 1 polish_round4 - 5 - -[Mon Sep 14 10:49:16 2020] -rule polish_round1: - input: output/First_second_merge.fa, data/rawdata.fastq - output: output/racon_polish_1.fa - jobid: 4 - -[Mon Sep 14 10:55:55 2020] -Finished job 4. -1 of 5 steps (20%) done - -[Mon Sep 14 10:55:55 2020] -rule polish_round2: - input: output/racon_polish_1.fa, data/rawdata.fastq - output: output/racon_polish_2.fa - jobid: 3 - -[Mon Sep 14 11:02:35 2020] -Finished job 3. -2 of 5 steps (40%) done - -[Mon Sep 14 11:02:35 2020] -rule polish_round3: - input: output/racon_polish_2.fa, data/rawdata.fastq - output: output/racon_polish_3.fa - jobid: 2 - -[Mon Sep 14 11:09:13 2020] -Finished job 2. -3 of 5 steps (60%) done - -[Mon Sep 14 11:09:13 2020] -rule polish_round4: - input: output/racon_polish_3.fa, data/rawdata.fastq - output: output/merge_corrected_4.fasta - jobid: 1 - -Terminating processes on user request, this might take some time. -[Mon Sep 14 11:10:28 2020] -Error in rule polish_round4: - jobid: 1 - output: output/merge_corrected_4.fasta - shell: - minimap2 -ax map-ont output/racon_polish_3.fa data/rawdata.fastq > output/rawfq_merged_4.sam && racon data/rawdata.fastq output/rawfq_merged_4.sam output/racon_polish_3.fa > output/merge_corrected_4.fasta - (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!) - -Removing output files of failed job polish_round4 since they might be corrupted: -output/merge_corrected_4.fasta -Complete log: /data/user/huangf/Arginini/original/snakemake/.snakemake/log/2020-09-14T104916.819257.snakemake.log diff --git a/.snakemake/log/2021-01-17T155822.396144.snakemake.log b/.snakemake/log/2021-01-17T155822.396144.snakemake.log deleted file mode 100644 index e69de29..0000000 diff --git a/.snakemake/log/2021-01-17T155856.577273.snakemake.log b/.snakemake/log/2021-01-17T155856.577273.snakemake.log deleted file mode 100644 index e69de29..0000000 diff --git a/.snakemake/log/2021-01-17T155933.688080.snakemake.log b/.snakemake/log/2021-01-17T155933.688080.snakemake.log deleted file mode 100644 index e69de29..0000000 diff --git a/.snakemake/log/2021-01-17T162738.542780.snakemake.log b/.snakemake/log/2021-01-17T162738.542780.snakemake.log deleted file mode 100644 index e69de29..0000000 diff --git a/.snakemake/metadata/b3V0cHV0L0JlZ2luU2Vx b/.snakemake/metadata/b3V0cHV0L0JlZ2luU2Vx deleted file mode 100644 index 1ba54dd..0000000 --- a/.snakemake/metadata/b3V0cHV0L0JlZ2luU2Vx +++ /dev/null @@ -1 +0,0 @@ -{"version": null, "code": 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"endtime": 1599508211.3653595, "job_hash": -9223369104815058197, "conda_env": null, "container_img_url": null} \ No newline at end of file diff --git a/.snakemake/metadata/b3V0cHV0L0VuZEFsaWduLmZx b/.snakemake/metadata/b3V0cHV0L0VuZEFsaWduLmZx deleted file mode 100644 index 65bda51..0000000 --- a/.snakemake/metadata/b3V0cHV0L0VuZEFsaWduLmZx +++ /dev/null @@ -1 +0,0 @@ -{"version": null, "code": 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1599457169.014706, "endtime": 1599457170.2224395, "job_hash": -9223369104815058263, "conda_env": null, "container_img_url": null} \ No newline at end of file diff --git a/.snakemake/metadata/b3V0cHV0L0VuZFJlYWRzLmZh b/.snakemake/metadata/b3V0cHV0L0VuZFJlYWRzLmZh deleted file mode 100644 index 7198444..0000000 --- a/.snakemake/metadata/b3V0cHV0L0VuZFJlYWRzLmZh +++ /dev/null @@ -1 +0,0 @@ -{"version": null, "code": "gAMoQxJ0AGQBfA58EWQCjQMBAGQAUwBxAChYBQAAAGlucHV0cQFYBgAAAG91dHB1dHECWAYAAABwYXJhbXNxA1gJAAAAd2lsZGNhcmRzcQRYBwAAAHRocmVhZHNxBVgJAAAAcmVzb3VyY2VzcQZYAwAAAGxvZ3EHWAcAAAB2ZXJzaW9ucQhYBAAAAHJ1bGVxCVgJAAAAY29uZGFfZW52cQpYDQAAAGNvbnRhaW5lcl9pbWdxC1gQAAAAc2luZ3VsYXJpdHlfYXJnc3EMWA8AAAB1c2Vfc2luZ3VsYXJpdHlxDVgLAAAAZW52X21vZHVsZXNxDlgMAAAAYmVuY2hfcmVjb3JkcQ9YBQAAAGpvYmlkcRBYCAAAAGlzX3NoZWxscRFYDwAAAGJlbmNoX2l0ZXJhdGlvbnESWA8AAABjbGVhbnVwX3NjcmlwdHNxE1gKAAAAc2hhZG93X2RpcnEUWA0AAABlZGl0X25vdGVib29rcRV0cRZdcRcoTlhXAAAAY2F0IHtpbnB1dH0gPiB7b3V0cHV0LkVuZGZxfSAmJiBweXRob24gc2NyaXB0L2ZxX3RvX2ZhLnB5IHtvdXRwdXQuRW5kZnF9IHtvdXRwdXQuRW5kZmF9cRhoD2gShnEZZVgFAAAAc2hlbGxxGoVxG3RxHC4=", "rule": "merge_end_reads", "input": ["output/EndAlign.fq", "output/beginAlign.fq"], "log": [], "params": [], "shellcmd": "cat output/EndAlign.fq output/beginAlign.fq > output/EndReads.fq && python script/fq_to_fa.py output/EndReads.fq output/EndReads.fa", "incomplete": false, "starttime": 1599457170.227611, "endtime": 1599457170.4861834, "job_hash": 2932039717529, "conda_env": null, "container_img_url": null} \ No newline at end of file diff --git a/.snakemake/metadata/b3V0cHV0L0VuZFJlYWRzLmZx b/.snakemake/metadata/b3V0cHV0L0VuZFJlYWRzLmZx deleted file mode 100644 index 0598a35..0000000 --- a/.snakemake/metadata/b3V0cHV0L0VuZFJlYWRzLmZx +++ /dev/null @@ -1 +0,0 @@ -{"version": null, "code": "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", "rule": "merge_end_reads", "input": ["output/EndAlign.fq", "output/beginAlign.fq"], "log": [], "params": [], "shellcmd": "cat output/EndAlign.fq output/beginAlign.fq > output/EndReads.fq && python script/fq_to_fa.py output/EndReads.fq output/EndReads.fa", "incomplete": false, "starttime": 1599457170.227357, "endtime": 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"starttime": 1599507571.836405, "endtime": 1599508210.587438, "job_hash": -9223369104814927067, "conda_env": null, "container_img_url": null} \ No newline at end of file diff --git a/.snakemake/metadata/b3V0cHV0L3NlY29uZHJ1blNlcQ== b/.snakemake/metadata/b3V0cHV0L3NlY29uZHJ1blNlcQ== deleted file mode 100644 index 9300327..0000000 --- a/.snakemake/metadata/b3V0cHV0L3NlY29uZHJ1blNlcQ== +++ /dev/null @@ -1 +0,0 @@ -{"version": null, "code": 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a/.snakemake/metadata/b3V0cHV0L3Nob3J0X3RvX2xvbmcuc2Ft b/.snakemake/metadata/b3V0cHV0L3Nob3J0X3RvX2xvbmcuc2Ft deleted file mode 100644 index b99f1f0..0000000 --- a/.snakemake/metadata/b3V0cHV0L3Nob3J0X3RvX2xvbmcuc2Ft +++ /dev/null @@ -1 +0,0 @@ -{"version": null, "code": "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", "rule": "short_to_long", "input": ["output/filter_length.fa", "output/left_filter_length.fq"], "log": [], "params": ["'map-ont'"], "shellcmd": "\n minimap2 -ax map-ont output/filter_length.fa output/left_filter_length.fq > output/short_to_long.sam\n ", "incomplete": false, "starttime": 1612656005.308051, "endtime": 1612656013.5600655, "job_hash": -9223369104814778620, "conda_env": null, "container_img_url": null} \ No newline at end of file diff --git a/.snakemake/metadata/cmVhZF9sZW5fZGlzdHJidXRpb24xLnR4dA== b/.snakemake/metadata/cmVhZF9sZW5fZGlzdHJidXRpb24xLnR4dA== deleted file mode 100644 index dc33ef3..0000000 --- a/.snakemake/metadata/cmVhZF9sZW5fZGlzdHJidXRpb24xLnR4dA== +++ /dev/null @@ -1 +0,0 @@ -{"version": null, "code": "gASVSgEAAAAAAAAoQxJ0AGQBfA58EWQCjQMBAGQAUwCUKIwFaW5wdXSUjAZvdXRwdXSUjAZwYXJhbXOUjAl3aWxkY2FyZHOUjAd0aHJlYWRzlIwJcmVzb3VyY2VzlIwDbG9nlIwHdmVyc2lvbpSMBHJ1bGWUjAljb25kYV9lbnaUjA1jb250YWluZXJfaW1nlIwQc2luZ3VsYXJpdHlfYXJnc5SMD3VzZV9zaW5ndWxhcml0eZSMC2Vudl9tb2R1bGVzlIwMYmVuY2hfcmVjb3JklIwFam9iaWSUjAhpc19zaGVsbJSMD2JlbmNoX2l0ZXJhdGlvbpSMD2NsZWFudXBfc2NyaXB0c5SMCnNoYWRvd19kaXKUdJRdlChOjCFjYXQge2lucHV0fSB8IHNvcnQgLXJuID4ge291dHB1dH2UaA9oEoaUZYwFc2hlbGyUhZR0lC4=", "rule": "select_longread", "input": ["read_len_distrbution.txt"], "log": [], "params": [], "shellcmd": "cat read_len_distrbution.txt | sort -rn > read_len_distrbution1.txt", "incomplete": false, "starttime": 1597611220.741216, "endtime": 1597611220.749622, "job_hash": -5486902152089786271, "conda_env": null, "container_img_url": null} \ No newline at end of file From 4e31e26833565b070b6f3ca152a5d0fae0ac93e0 Mon Sep 17 00:00:00 2001 From: jdzm Date: Tue, 16 Dec 2025 14:07:00 +0100 Subject: [PATCH 03/14] added config yaml to gitignore, renamed file to template to allow editing without modifying git every time --- .gitignore | 3 +++ README.md | 1 + config.yaml => config-template.yaml | 0 3 files changed, 4 insertions(+) rename config.yaml => config-template.yaml (100%) diff --git a/.gitignore b/.gitignore index 6098fa9..eb40e70 100644 --- a/.gitignore +++ b/.gitignore @@ -4,6 +4,9 @@ final/ tmp/ input/ +# Project config file +config.yaml + # Snakemake folder .snakemake/ diff --git a/README.md b/README.md index 986b23b..ac5197f 100644 --- a/README.md +++ b/README.md @@ -54,6 +54,7 @@ conda activate B-assembler ## Write your configuation ###Provide sequence data in config.yaml file ``` +cp config-template.yaml config.yaml vi config.yaml ``` diff --git a/config.yaml b/config-template.yaml similarity index 100% rename from config.yaml rename to config-template.yaml From f2aa0d79879006a95c6c6d4c3650d45cc2124a2f Mon Sep 17 00:00:00 2001 From: jdzm Date: Tue, 16 Dec 2025 14:09:42 +0100 Subject: [PATCH 04/14] added thread parameter to config --- config-template.yaml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/config-template.yaml b/config-template.yaml index ef7bb47..280e6f0 100644 --- a/config-template.yaml +++ b/config-template.yaml @@ -14,3 +14,6 @@ readtype: ONT #nanopore:ONT, pacbio:pb # PATH sourceDir: PathToSourceDir outputDir: PathToOutputDir + +# Cores to use in pipeline +threads: 24 From b411153ab6cdf95df6f785752eca004893f919b8 Mon Sep 17 00:00:00 2001 From: jdzm Date: Tue, 16 Dec 2025 14:29:43 +0100 Subject: [PATCH 05/14] added threads parameter to all rules. some will use all the threads in config, some others half or 1 thread alone in rules requiring no multithreading --- rules/LongReadPolish.smk | 8 ++++++++ rules/LongReadSelectLongRead.smk | 8 ++++++++ rules/LongreadPolish_new.smk | 4 ++++ rules/firstround.smk | 6 ++++++ rules/hybridPolish.smk | 16 ++++++++++++++++ rules/hybridSelectLongRead.smk | 10 ++++++++++ rules/hybridSelectLongRead2.smk | 10 ++++++++++ rules/rearrangeStart.smk | 2 ++ rules/secondround.smk | 10 ++++++++++ rules/selectEndRead.smk | 6 ++++++ rules/tworoundMerge.smk | 4 ++++ 11 files changed, 84 insertions(+) diff --git a/rules/LongReadPolish.smk b/rules/LongReadPolish.smk index 47a9041..c2aa9b1 100644 --- a/rules/LongReadPolish.smk +++ b/rules/LongReadPolish.smk @@ -12,6 +12,8 @@ rule polish_round1: read=config['longread'] output: "output/racon_polish_1.fa" + threads: + config["threads"] params: type=par shell: @@ -24,6 +26,8 @@ rule polish_round2: read=config['longread'] output: "output/racon_polish_2.fa" + threads: + config["threads"] params: type=par shell: @@ -35,6 +39,8 @@ rule polish_round3: read=config['longread'] output: "output/racon_polish_3.fa" + threads: + config["threads"] params: type=par shell: @@ -46,6 +52,8 @@ rule polish_round4: read=config['longread'] output: "output/merge_corrected_4.fasta" + threads: + config["threads"] params: type=par shell: diff --git a/rules/LongReadSelectLongRead.smk b/rules/LongReadSelectLongRead.smk index 18b8054..b4caf55 100644 --- a/rules/LongReadSelectLongRead.smk +++ b/rules/LongReadSelectLongRead.smk @@ -12,6 +12,8 @@ rule select_longread: output: long="output/filter_length.fq", short="output/left_filter_length.fq" + threads: + 1 params: config['genomesize'] shell: @@ -23,6 +25,8 @@ rule fq_to_fa: "output/filter_length.fq" output: "output/filter_length.fa" + threads: + 1 shell: """ python scripts/FqToFa.py {input} {output} @@ -39,6 +43,8 @@ rule short_to_long: input: long = "output/filter_length.fa", short = "output/left_filter_length.fq" + threads: + config["threads"] output: "output/short_to_long.sam" params: @@ -52,6 +58,8 @@ rule longread_polish: long = 'output/filter_length.fa', short = 'output/left_filter_length.fq', sam = 'output/short_to_long.sam' + threads: + 1 output: "output/long_read_corrected.fasta" shell: diff --git a/rules/LongreadPolish_new.smk b/rules/LongreadPolish_new.smk index 7da3914..57f9348 100644 --- a/rules/LongreadPolish_new.smk +++ b/rules/LongreadPolish_new.smk @@ -12,6 +12,8 @@ rule polish_round1: read=config['longread'] output: "output/polished_1.fasta" + threads: + config["threads"] params: dir="output/", type=par @@ -26,6 +28,8 @@ rule rename: "output/polished_1.fasta" output: "output/B_assembly.fasta" + threads: + 1 shell: """ mv {input} {output} diff --git a/rules/firstround.smk b/rules/firstround.smk index d2f476e..39f2e59 100644 --- a/rules/firstround.smk +++ b/rules/firstround.smk @@ -13,6 +13,8 @@ rule first_assemble: "output/long_read_corrected.fasta" output: "output/assembly.fasta" + threads: + config["threads"] params: dir="output/", genoSize=config['genomesize'], @@ -27,6 +29,8 @@ rule select_longestContig: "output/assembly.fasta" output: "output/firstrun.fa" + threads: + 1 shell: """ python scripts/SelectPlasmidID_LongestContig.py {input} {output} @@ -39,6 +43,8 @@ rule rawfq_firstrun: output: bam = "output/rawfq-firstrun-srt.bam", bai = "output/rawfq-firstrun-srt.bam.bai" + threads: + config["threads"] params: type=mini shell: diff --git a/rules/hybridPolish.smk b/rules/hybridPolish.smk index c1d5ee1..447e331 100644 --- a/rules/hybridPolish.smk +++ b/rules/hybridPolish.smk @@ -6,6 +6,8 @@ rule bwa_1: output: bam="output/short_merge_srt_1.bam", bai="output/short_merge_srt_1.bam.bai" + threads: + config["threads"] conda: 'envs/bwa.yaml' shell: @@ -21,6 +23,8 @@ rule pilon_polish_1: bam = 'output/short_merge_srt_1.bam' output: "output/merge_pilon_corrected_1.fasta" + threads: + 1 params: output_prefix = 'merge_pilon_corrected_1', output_dir = 'output' @@ -36,6 +40,8 @@ rule bwa_2: output: bam="output/short_merge_srt_2.bam", bai="output/short_merge_srt_2.bam.bai" + threads: + config["threads"] conda: 'envs/bwa.yaml' shell: @@ -50,6 +56,8 @@ rule pilon_polish_2: bam = 'output/short_merge_srt_2.bam' output: "output/merge_pilon_corrected_2.fasta" + threads: + 1 params: output_prefix = 'merge_pilon_corrected_2', output_dir = 'output' @@ -65,6 +73,8 @@ rule bwa_3: output: bam="output/short_merge_srt_3.bam", bai="output/short_merge_srt_3.bam.bai" + threads: + config["threads"] conda: 'envs/bwa.yaml' shell: @@ -79,6 +89,8 @@ rule pilon_polish_3: bam = 'output/short_merge_srt_3.bam' output: "output/merge_pilon_corrected_3.fasta" + threads: + 1 params: output_prefix = 'merge_pilon_corrected_3', output_dir = 'output' @@ -94,6 +106,8 @@ rule bwa_4: output: bam="output/short_merge_srt_4.bam", bai="output/short_merge_srt_4.bam.bai" + threads: + config["threads"] conda: 'envs/bwa.yaml' shell: @@ -109,6 +123,8 @@ rule pilon_polish_4: bam = 'output/short_merge_srt_4.bam' output: "output/merge_corrected_4.fasta" + threads: + 1 params: output_prefix = 'merge_corrected_4', output_dir = 'output' diff --git a/rules/hybridSelectLongRead.smk b/rules/hybridSelectLongRead.smk index 5e5e601..fc06f48 100644 --- a/rules/hybridSelectLongRead.smk +++ b/rules/hybridSelectLongRead.smk @@ -3,6 +3,8 @@ rule longread_len: config['longread'] output: "output/read_len_distrbution_2.txt" + threads: + 1 shell: "python scripts/ReadLengthDistribution.py {input} {output}" @@ -13,6 +15,8 @@ rule select_longread: output: long="output/filter_length.fq", short="output/left_filter_length.fq" + threads: + 1 params: config['genomesize'] shell: @@ -23,6 +27,8 @@ rule select_longread: rule fq_to_fa: input: "output/filter_length.fq" + threads: + 1 output: "output/filter_length.fa" shell: @@ -36,6 +42,8 @@ rule bwa: short_1 = config['illumina']['R1'], short_2 = config['illumina']['R2'] output: + threads: + config["threads"] // 2 bam="output/short_read_long-srt.bam", bai="output/short_read_long-srt.bam.bai" conda: @@ -49,6 +57,8 @@ rule longread_polish: input: long = 'output/filter_length.fa', bam = 'output/short_read_long-srt.bam' + threads: + 1 output: "output/long_read_corrected.fasta" params: diff --git a/rules/hybridSelectLongRead2.smk b/rules/hybridSelectLongRead2.smk index 7fbca23..c23537f 100644 --- a/rules/hybridSelectLongRead2.smk +++ b/rules/hybridSelectLongRead2.smk @@ -3,6 +3,8 @@ rule longread_len: config['longread'] output: "output/read_len_distrbution_2.txt" + threads: + 1 shell: """ python scripts/ReadLengthDistribution.py {input} {output} @@ -14,6 +16,8 @@ rule select_longread: output: long="output/filter_length.fq", short="output/left_filter_length.fq" + threads: + 1 params: config['genomesize'] shell: @@ -23,6 +27,8 @@ rule select_longread: rule fq_to_fa: input: "output/filter_length.fq" + threads: + 1 output: "output/filter_length.fa" shell: @@ -41,6 +47,8 @@ rule short_to_long: input: long = "output/filter_length.fa", short = "output/left_filter_length.fq" + threads: + config["threads"] output: "output/short_to_long.sam" params: @@ -52,6 +60,8 @@ rule short_to_long: rule longread_polish: input: long = 'output/filter_length.fa', + threads: + 1 short = 'output/left_filter_length.fq', sam = 'output/short_to_long.sam' output: diff --git a/rules/rearrangeStart.smk b/rules/rearrangeStart.smk index 22688f8..11934b0 100644 --- a/rules/rearrangeStart.smk +++ b/rules/rearrangeStart.smk @@ -4,6 +4,8 @@ rule rearrange: startfa="scripts/start_gene.fa" output: "output/B_assembly.fasta" + threads: + 1 shell: """ python scripts/RearrangeStartPoint.py {input.assembly} {input.startfa} {output} diff --git a/rules/secondround.smk b/rules/secondround.smk index 823f93d..af4ac42 100644 --- a/rules/secondround.smk +++ b/rules/secondround.smk @@ -7,6 +7,8 @@ rule endReads_select: output: end="output/EndAlign.fq", begin="output/beginAlign.fq" + threads: + 1 shell: """ python scripts/ExtractEndReads.py {input.fa} {input.bam} {output.begin} {output.end} @@ -18,6 +20,8 @@ rule merge_end_reads: output: Endfq="output/EndReads.fq", Endfa="output/EndReads.fa" + threads: + 1 shell: """ cat {input} > {output.Endfq} && python scripts/FqToFa.py {output.Endfq} {output.Endfa} @@ -25,6 +29,8 @@ rule merge_end_reads: rule remove_dupl: input: "output/EndReads.fa" + threads: + 1 output: "output/EndReads_dupl_remove.fa" shell: @@ -43,6 +49,8 @@ resize=int(int(config['genomesize'])*0.4) rule second_assembly: input: "output/EndReads_dupl_remove.fa" + threads: + config["threads"] output: "output/secondrun/assembly.fasta" params: @@ -56,6 +64,8 @@ rule second_assembly: rule select_longContig: input: "output/secondrun/assembly.fasta" + threads: + 1 output: "output/secondrunOneline.fa" shell: diff --git a/rules/selectEndRead.smk b/rules/selectEndRead.smk index f2beaa4..8e04862 100644 --- a/rules/selectEndRead.smk +++ b/rules/selectEndRead.smk @@ -6,6 +6,8 @@ rule endReads_select: output: end="output/EndAlign.fq", begin="output/beginAlign.fq" + threads: + 1 shell: """ python scripts/ExtractEndReads.py {input.fa} {input.bam} {output.begin} {output.end} @@ -17,6 +19,8 @@ rule merge_end_reads: output: Endfq="output/EndReads.fq", Endfa="output/EndReads.fa" + threads: + 1 shell: """ cat {input} > {output.Endfq} && python scripts/FqToFa.py {output.Endfq} {output.Endfa} @@ -24,6 +28,8 @@ rule merge_end_reads: rule remove_dupl: input: "output/EndReads.fa" + threads: + 1 output: "output/EndReads_dupl_remove.fa" shell: diff --git a/rules/tworoundMerge.smk b/rules/tworoundMerge.smk index 4c1ac43..4a1d8c3 100644 --- a/rules/tworoundMerge.smk +++ b/rules/tworoundMerge.smk @@ -4,6 +4,8 @@ rule tworun_align: fir="output/firstrun.fa" output: "output/first_second.paf" + threads: + config["threads"] shell: """ minimap2 -cx asm20 {input.fir} {input.sec} > {output} @@ -15,6 +17,8 @@ rule merge: second="output/secondrunOneline.fa" output: merge="output/First_second_merge.fa" + threads: + 1 shell: """ python scripts/MergeTwoRun.py {input.paf} {input.first} {input.second} {output.merge} From 15e3399f3257bd219722f0a35d2101e2d6c88103 Mon Sep 17 00:00:00 2001 From: jdzm Date: Tue, 16 Dec 2025 14:34:40 +0100 Subject: [PATCH 06/14] added missing thread options to all minimap2 and flye calls --- rules/LongReadPolish.smk | 8 ++++---- rules/LongReadSelectLongRead.smk | 2 +- rules/LongreadPolish_new.smk | 2 +- rules/firstround.smk | 4 ++-- rules/hybridSelectLongRead2.smk | 2 +- rules/secondround.smk | 2 +- rules/tworoundMerge.smk | 2 +- 7 files changed, 11 insertions(+), 11 deletions(-) diff --git a/rules/LongReadPolish.smk b/rules/LongReadPolish.smk index c2aa9b1..e1bfbd5 100644 --- a/rules/LongReadPolish.smk +++ b/rules/LongReadPolish.smk @@ -18,7 +18,7 @@ rule polish_round1: type=par shell: """ - minimap2 -ax {params.type} {input.assembly} {input.read} > output/rawfq_merged.sam && racon {input.read} output/rawfq_merged.sam {input.assembly} > {output} + minimap2 -ax {params.type} -t {threads} {input.assembly} {input.read} > output/rawfq_merged.sam && racon {input.read} output/rawfq_merged.sam {input.assembly} > {output} """ rule polish_round2: input: @@ -31,7 +31,7 @@ rule polish_round2: params: type=par shell: - "minimap2 -ax {params.type} {input.assembly} {input.read} > output/rawfq_merged_2.sam && racon {input.read} output/rawfq_merged_2.sam {input.assembly} > {output}" + "minimap2 -ax {params.type} -t {threads} {input.assembly} {input.read} > output/rawfq_merged_2.sam && racon {input.read} output/rawfq_merged_2.sam {input.assembly} > {output}" rule polish_round3: input: @@ -44,7 +44,7 @@ rule polish_round3: params: type=par shell: - "minimap2 -ax {params.type} {input.assembly} {input.read} > output/rawfq_merged_3.sam && racon {input.read} output/rawfq_merged_3.sam {input.assembly} > {output}" + "minimap2 -ax {params.type} -t {threads} {input.assembly} {input.read} > output/rawfq_merged_3.sam && racon {input.read} output/rawfq_merged_3.sam {input.assembly} > {output}" rule polish_round4: input: @@ -57,6 +57,6 @@ rule polish_round4: params: type=par shell: - "minimap2 -ax {params.type} {input.assembly} {input.read} > output/rawfq_merged_4.sam && racon {input.read} output/rawfq_merged_4.sam {input.assembly} > {output}" + "minimap2 -ax {params.type} -t {threads} {input.assembly} {input.read} > output/rawfq_merged_4.sam && racon {input.read} output/rawfq_merged_4.sam {input.assembly} > {output}" diff --git a/rules/LongReadSelectLongRead.smk b/rules/LongReadSelectLongRead.smk index b4caf55..ac15719 100644 --- a/rules/LongReadSelectLongRead.smk +++ b/rules/LongReadSelectLongRead.smk @@ -51,7 +51,7 @@ rule short_to_long: type=par shell: """ - minimap2 -ax {params.type} {input.long} {input.short} > {output} + minimap2 -ax {params.type} -t {threads} {input.long} {input.short} > {output} """ rule longread_polish: input: diff --git a/rules/LongreadPolish_new.smk b/rules/LongreadPolish_new.smk index 57f9348..04febfe 100644 --- a/rules/LongreadPolish_new.smk +++ b/rules/LongreadPolish_new.smk @@ -20,7 +20,7 @@ rule polish_round1: shell: """ - flye --polish-target {input.assembly} {params.type} {input.read} --iterations 2 --out-dir {params.dir} + flye --polish-target {input.assembly} {params.type} {input.read} --iterations 2 --threads {threads} --out-dir {params.dir} """ rule rename: diff --git a/rules/firstround.smk b/rules/firstround.smk index 39f2e59..fc66429 100644 --- a/rules/firstround.smk +++ b/rules/firstround.smk @@ -21,7 +21,7 @@ rule first_assemble: type=par shell: """ - flye {params.type} {input} --min-overlap 3000 --genome-size {params.genoSize} --out-dir {params.dir} + flye {params.type} {input} --min-overlap 3000 --genome-size {params.genoSize} --threads {threads} --out-dir {params.dir} """ ##extract plasmid sequence rule select_longestContig: @@ -49,6 +49,6 @@ rule rawfq_firstrun: type=mini shell: """ - minimap2 -ax {params.type} {input.firstrun} {input.rawfq} | samtools view -Sb - | samtools sort - -o {output.bam} && samtools index {output.bam} > {output.bai} + minimap2 -ax {params.type} -t {threads} {input.firstrun} {input.rawfq} | samtools view -Sb - | samtools sort - -o {output.bam} && samtools index {output.bam} > {output.bai} """ diff --git a/rules/hybridSelectLongRead2.smk b/rules/hybridSelectLongRead2.smk index c23537f..aeb7459 100644 --- a/rules/hybridSelectLongRead2.smk +++ b/rules/hybridSelectLongRead2.smk @@ -55,7 +55,7 @@ rule short_to_long: type=par shell: """ - minimap2 -ax {params.type} {input.long} {input.short} > {output} + minimap2 -ax {params.type} -t {threads} {input.long} {input.short} > {output} """ rule longread_polish: input: diff --git a/rules/secondround.smk b/rules/secondround.smk index af4ac42..331ffee 100644 --- a/rules/secondround.smk +++ b/rules/secondround.smk @@ -59,7 +59,7 @@ rule second_assembly: size=resize shell: """ - flye {params.type} {input} --min-overlap 3000 --genome-size {params.size} --out-dir {params.dir} + flye {params.type} {input} --min-overlap 3000 --genome-size {params.size} --threads {threads} --out-dir {params.dir} """ rule select_longContig: input: diff --git a/rules/tworoundMerge.smk b/rules/tworoundMerge.smk index 4a1d8c3..bfb2c81 100644 --- a/rules/tworoundMerge.smk +++ b/rules/tworoundMerge.smk @@ -8,7 +8,7 @@ rule tworun_align: config["threads"] shell: """ - minimap2 -cx asm20 {input.fir} {input.sec} > {output} + minimap2 -cx asm20 -t {threads} {input.fir} {input.sec} > {output} """ rule merge: input: From 120fcadd4d77853b856cffd4522d2e8aa435a079 Mon Sep 17 00:00:00 2001 From: jdzm Date: Tue, 16 Dec 2025 15:05:11 +0100 Subject: [PATCH 07/14] added threads option to all samtools and minimap2 calls and reformatted some shell commands --- rules/firstround.smk | 6 +++++- rules/hybridPolish.smk | 26 +++++++++++++++++++++----- rules/hybridSelectLongRead.smk | 20 +++++++++++++------- 3 files changed, 39 insertions(+), 13 deletions(-) diff --git a/rules/firstround.smk b/rules/firstround.smk index fc66429..a5a5de1 100644 --- a/rules/firstround.smk +++ b/rules/firstround.smk @@ -49,6 +49,10 @@ rule rawfq_firstrun: type=mini shell: """ - minimap2 -ax {params.type} -t {threads} {input.firstrun} {input.rawfq} | samtools view -Sb - | samtools sort - -o {output.bam} && samtools index {output.bam} > {output.bai} + minimap2 -ax {params.type} -t {threads} {input.firstrun} {input.rawfq} | \ + samtools view -@ {threads} -Sb - | \ + samtools sort -@ {threads} - -o {output.bam} + + samtools index {output.bam} > {output.bai} """ diff --git a/rules/hybridPolish.smk b/rules/hybridPolish.smk index 447e331..17b6253 100644 --- a/rules/hybridPolish.smk +++ b/rules/hybridPolish.smk @@ -13,7 +13,11 @@ rule bwa_1: shell: """ bwa index {input.long}; - bwa mem -t 8 {input.long} {input.short_1} {input.short_2} |samtools view -Sb - | samtools sort - -o {output.bam}; + + bwa mem -t {threads} {input.long} {input.short_1} {input.short_2} | \ + samtools view -@ {threads} -Sb - | \ + samtools sort -@ {threads} - -o {output.bam} + samtools index {output.bam} """ @@ -47,7 +51,11 @@ rule bwa_2: shell: """ bwa index {input.long}; - bwa mem -t 8 {input.long} {input.short_1} {input.short_2} |samtools view -Sb - | samtools sort - -o {output.bam}; + + bwa mem -t {threads} {input.long} {input.short_1} {input.short_2} | \ + samtools view -@ {threads} -Sb - | \ + samtools sort -@ {threads} - -o {output.bam} + samtools index {output.bam} """ rule pilon_polish_2: @@ -80,7 +88,11 @@ rule bwa_3: shell: """ bwa index {input.long}; - bwa mem -t 8 {input.long} {input.short_1} {input.short_2} |samtools view -Sb - | samtools sort - -o {output.bam}; + + bwa mem -t {threads} {input.long} {input.short_1} {input.short_2} | \ + samtools view -@ {threads} -Sb - | \ + samtools sort -@ {threads} - -o {output.bam} + samtools index {output.bam} """ rule pilon_polish_3: @@ -113,9 +125,13 @@ rule bwa_4: shell: """ bwa index {input.long}; - bwa mem -t 8 {input.long} {input.short_1} {input.short_2} |samtools view -Sb - | samtools sort - -o {output.bam}; + + bwa mem -t {threads} {input.long} {input.short_1} {input.short_2} | \ + samtools view -@ {threads} -Sb - | \ + samtools sort -@ {threads} - -o {output.bam} + samtools index {output.bam} - """ + """ rule pilon_polish_4: input: diff --git a/rules/hybridSelectLongRead.smk b/rules/hybridSelectLongRead.smk index fc06f48..2d0780c 100644 --- a/rules/hybridSelectLongRead.smk +++ b/rules/hybridSelectLongRead.smk @@ -27,10 +27,10 @@ rule select_longread: rule fq_to_fa: input: "output/filter_length.fq" - threads: - 1 output: "output/filter_length.fa" + threads: + 1 shell: """ python scripts/FqToFa.py {input} {output} @@ -42,16 +42,22 @@ rule bwa: short_1 = config['illumina']['R1'], short_2 = config['illumina']['R2'] output: - threads: - config["threads"] // 2 bam="output/short_read_long-srt.bam", bai="output/short_read_long-srt.bam.bai" + threads: + config["threads"] conda: 'envs/bwa.yaml' shell: - 'bwa index {input.long};' - 'bwa mem -t 8 {input.long} {input.short_1} {input.short_2} | samtools view -Sb - | samtools sort - -o {output.bam};' - 'samtools index {output.bam}' + """ + bwa index {input.long}; + + bwa mem -t {threads} {input.long} {input.short_1} {input.short_2} | \ + samtools view -@ {threads} -Sb - | \ + samtools sort -@ {threads} - -o {output.bam} + + samtools index {output.bam} + """ rule longread_polish: input: From a7a6292e01fcf016c6138335c101271a4cf60499 Mon Sep 17 00:00:00 2001 From: jdzm Date: Tue, 16 Dec 2025 15:06:49 +0100 Subject: [PATCH 08/14] cosmetic reformatting --- rules/firstround.smk | 4 +++- rules/secondround.smk | 8 ++++---- rules/selectEndRead.smk | 2 ++ rules/tworoundMerge.smk | 1 + 4 files changed, 10 insertions(+), 5 deletions(-) diff --git a/rules/firstround.smk b/rules/firstround.smk index a5a5de1..e986fe9 100644 --- a/rules/firstround.smk +++ b/rules/firstround.smk @@ -21,7 +21,9 @@ rule first_assemble: type=par shell: """ - flye {params.type} {input} --min-overlap 3000 --genome-size {params.genoSize} --threads {threads} --out-dir {params.dir} + flye {params.type} {input} --min-overlap 3000 \ + --genome-size {params.genoSize} \ + --threads {threads} --out-dir {params.dir} """ ##extract plasmid sequence rule select_longestContig: diff --git a/rules/secondround.smk b/rules/secondround.smk index 331ffee..efb6c0e 100644 --- a/rules/secondround.smk +++ b/rules/secondround.smk @@ -49,10 +49,10 @@ resize=int(int(config['genomesize'])*0.4) rule second_assembly: input: "output/EndReads_dupl_remove.fa" - threads: - config["threads"] output: "output/secondrun/assembly.fasta" + threads: + config["threads"] params: dir="output/secondrun/", type=par, @@ -64,10 +64,10 @@ rule second_assembly: rule select_longContig: input: "output/secondrun/assembly.fasta" - threads: - 1 output: "output/secondrunOneline.fa" + threads: + 1 shell: """ python scripts/PrintOneLine.py {input} {output} diff --git a/rules/selectEndRead.smk b/rules/selectEndRead.smk index 8e04862..a19f6a3 100644 --- a/rules/selectEndRead.smk +++ b/rules/selectEndRead.smk @@ -12,6 +12,7 @@ rule endReads_select: """ python scripts/ExtractEndReads.py {input.fa} {input.bam} {output.begin} {output.end} """ + rule merge_end_reads: input: "output/EndAlign.fq", @@ -25,6 +26,7 @@ rule merge_end_reads: """ cat {input} > {output.Endfq} && python scripts/FqToFa.py {output.Endfq} {output.Endfa} """ + rule remove_dupl: input: "output/EndReads.fa" diff --git a/rules/tworoundMerge.smk b/rules/tworoundMerge.smk index bfb2c81..5d416a6 100644 --- a/rules/tworoundMerge.smk +++ b/rules/tworoundMerge.smk @@ -10,6 +10,7 @@ rule tworun_align: """ minimap2 -cx asm20 -t {threads} {input.fir} {input.sec} > {output} """ + rule merge: input: paf="output/first_second.paf", From 778618da67ef40f88f21bcbd74e4f7f9032e7a34 Mon Sep 17 00:00:00 2001 From: jdzm Date: Tue, 16 Dec 2025 15:16:16 +0100 Subject: [PATCH 09/14] added racon multithreading --- rules/LongReadSelectLongRead.smk | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/rules/LongReadSelectLongRead.smk b/rules/LongReadSelectLongRead.smk index ac15719..7a813e5 100644 --- a/rules/LongReadSelectLongRead.smk +++ b/rules/LongReadSelectLongRead.smk @@ -20,6 +20,7 @@ rule select_longread: """ python scripts/SelectLongRead.py {input.raw} {params} {output.long} {output.short} """ + rule fq_to_fa: input: "output/filter_length.fq" @@ -31,6 +32,7 @@ rule fq_to_fa: """ python scripts/FqToFa.py {input} {output} """ + ##longRead_correct par="" readType=config['readtype'] @@ -43,10 +45,10 @@ rule short_to_long: input: long = "output/filter_length.fa", short = "output/left_filter_length.fq" - threads: - config["threads"] output: "output/short_to_long.sam" + threads: + config["threads"] params: type=par shell: @@ -59,10 +61,10 @@ rule longread_polish: short = 'output/left_filter_length.fq', sam = 'output/short_to_long.sam' threads: - 1 + config["threads"] // 2 output: "output/long_read_corrected.fasta" shell: """ - racon {input.short} {input.sam} {input.long} > {output} + racon --threads {threads} {input.short} {input.sam} {input.long} > {output} """ From c68b1b858d3367310b1d04b9245a4af1a755dea8 Mon Sep 17 00:00:00 2001 From: jdzm Date: Tue, 16 Dec 2025 15:16:44 +0100 Subject: [PATCH 10/14] added racon multithreading and reorganized shell call --- rules/LongReadPolish.smk | 22 ++++++++++++++++++---- 1 file changed, 18 insertions(+), 4 deletions(-) diff --git a/rules/LongReadPolish.smk b/rules/LongReadPolish.smk index e1bfbd5..69575b2 100644 --- a/rules/LongReadPolish.smk +++ b/rules/LongReadPolish.smk @@ -18,8 +18,11 @@ rule polish_round1: type=par shell: """ - minimap2 -ax {params.type} -t {threads} {input.assembly} {input.read} > output/rawfq_merged.sam && racon {input.read} output/rawfq_merged.sam {input.assembly} > {output} + minimap2 -ax {params.type} -t {threads} {input.assembly} {input.read} > output/rawfq_merged.sam + + racon --threads {threads} {input.read} output/rawfq_merged.sam {input.assembly} > {output} """ + rule polish_round2: input: assembly="output/racon_polish_1.fa", @@ -31,7 +34,11 @@ rule polish_round2: params: type=par shell: - "minimap2 -ax {params.type} -t {threads} {input.assembly} {input.read} > output/rawfq_merged_2.sam && racon {input.read} output/rawfq_merged_2.sam {input.assembly} > {output}" + """ + minimap2 -ax {params.type} -t {threads} {input.assembly} {input.read} > output/rawfq_merged_2.sam + + racon --threads {threads} {input.read} output/rawfq_merged_2.sam {input.assembly} > {output} + """ rule polish_round3: input: @@ -44,7 +51,11 @@ rule polish_round3: params: type=par shell: - "minimap2 -ax {params.type} -t {threads} {input.assembly} {input.read} > output/rawfq_merged_3.sam && racon {input.read} output/rawfq_merged_3.sam {input.assembly} > {output}" + """ + minimap2 -ax {params.type} -t {threads} {input.assembly} {input.read} > output/rawfq_merged_3.sam + + racon --threads {threads} {input.read} output/rawfq_merged_3.sam {input.assembly} > {output} + """ rule polish_round4: input: @@ -57,6 +68,9 @@ rule polish_round4: params: type=par shell: - "minimap2 -ax {params.type} -t {threads} {input.assembly} {input.read} > output/rawfq_merged_4.sam && racon {input.read} output/rawfq_merged_4.sam {input.assembly} > {output}" + """ + minimap2 -ax {params.type} -t {threads} {input.assembly} {input.read} > output/rawfq_merged_4.sam + racon --threads {threads} {input.read} output/rawfq_merged_4.sam {input.assembly} > {output} + """ From b14fa135a51d6c7d4fd0ff75f4d278e6198ff996 Mon Sep 17 00:00:00 2001 From: jdzm Date: Tue, 16 Dec 2025 15:17:31 +0100 Subject: [PATCH 11/14] added multithreading to pilon --- rules/hybridPolish.smk | 27 ++++++++++++++++++++------- rules/hybridSelectLongRead.smk | 9 ++++++--- 2 files changed, 26 insertions(+), 10 deletions(-) diff --git a/rules/hybridPolish.smk b/rules/hybridPolish.smk index 17b6253..887e9cd 100644 --- a/rules/hybridPolish.smk +++ b/rules/hybridPolish.smk @@ -28,13 +28,16 @@ rule pilon_polish_1: output: "output/merge_pilon_corrected_1.fasta" threads: - 1 + config ["threads"] // 2 params: output_prefix = 'merge_pilon_corrected_1', output_dir = 'output' shell: """ - java -Xmx10G -jar script/pilon-1.23.jar --genome {input.long} --frags {input.bam} --fix all --output {params.output_prefix} --outdir {params.output_dir} + java -Xmx10G -jar script/pilon-1.23.jar --threads {threads} \ + --genome {input.long} --frags {input.bam} \ + --fix all --output {params.output_prefix} \ + --outdir {params.output_dir} """ rule bwa_2: input: @@ -65,13 +68,16 @@ rule pilon_polish_2: output: "output/merge_pilon_corrected_2.fasta" threads: - 1 + config ["threads"] // 2 params: output_prefix = 'merge_pilon_corrected_2', output_dir = 'output' shell: """ - java -Xmx10G -jar script/pilon-1.23.jar --genome {input.long} --frags {input.bam} --fix all --output {params.output_prefix} --outdir {params.output_dir} + java -Xmx10G -jar script/pilon-1.23.jar --threads {threads} \ + --genome {input.long} --frags {input.bam} \ + --fix all --output {params.output_prefix} \ + --outdir {params.output_dir} """ rule bwa_3: input: @@ -108,8 +114,12 @@ rule pilon_polish_3: output_dir = 'output' shell: """ - java -Xmx10G -jar script/pilon-1.23.jar --genome {input.long} --frags {input.bam} --fix all --output {params.output_prefix} --outdir {params.output_dir} + java -Xmx10G -jar script/pilon-1.23.jar --threads {threads} \ + --genome {input.long} --frags {input.bam} \ + --fix all --output {params.output_prefix} \ + --outdir {params.output_dir} """ + rule bwa_4: input: long = "output/merge_pilon_corrected_3.fasta", @@ -140,11 +150,14 @@ rule pilon_polish_4: output: "output/merge_corrected_4.fasta" threads: - 1 + config["threads"] // 2 params: output_prefix = 'merge_corrected_4', output_dir = 'output' shell: """ - java -Xmx10G -jar script/pilon-1.23.jar --genome {input.long} --frags {input.bam} --fix all --output {params.output_prefix} --outdir {params.output_dir} + java -Xmx10G -jar script/pilon-1.23.jar --threads {threads} \ + --genome {input.long} --frags {input.bam} \ + --fix all --output {params.output_prefix} \ + --outdir {params.output_dir} """ diff --git a/rules/hybridSelectLongRead.smk b/rules/hybridSelectLongRead.smk index 2d0780c..4730e3f 100644 --- a/rules/hybridSelectLongRead.smk +++ b/rules/hybridSelectLongRead.smk @@ -63,14 +63,17 @@ rule longread_polish: input: long = 'output/filter_length.fa', bam = 'output/short_read_long-srt.bam' - threads: - 1 output: "output/long_read_corrected.fasta" + threads: + config ["threads"] // 2 params: output_prefix = 'long_read_corrected', output_dir = 'output' shell: """ - java -Xmx10G -jar script/pilon-1.23.jar --genome {input.long} --frags {input.bam} --fix all --output {params.output_prefix} --outdir {params.output_dir} + java -Xmx10G -jar script/pilon-1.23.jar --threads {threads} \ + --genome {input.long} --frags {input.bam} \ + --fix all --output {params.output_prefix} \ + --outdir {params.output_dir} """ From bc00714d36df789a02f1572ed93a15165c9191a9 Mon Sep 17 00:00:00 2001 From: jdzm Date: Tue, 16 Dec 2025 15:17:48 +0100 Subject: [PATCH 12/14] added missing racon multithreading and missing space --- rules/LongreadPolish_new.smk | 1 - rules/hybridSelectLongRead2.smk | 18 +++++++++++------- 2 files changed, 11 insertions(+), 8 deletions(-) diff --git a/rules/LongreadPolish_new.smk b/rules/LongreadPolish_new.smk index 04febfe..ee3ea30 100644 --- a/rules/LongreadPolish_new.smk +++ b/rules/LongreadPolish_new.smk @@ -17,7 +17,6 @@ rule polish_round1: params: dir="output/", type=par - shell: """ flye --polish-target {input.assembly} {params.type} {input.read} --iterations 2 --threads {threads} --out-dir {params.dir} diff --git a/rules/hybridSelectLongRead2.smk b/rules/hybridSelectLongRead2.smk index aeb7459..39f44e5 100644 --- a/rules/hybridSelectLongRead2.smk +++ b/rules/hybridSelectLongRead2.smk @@ -9,6 +9,7 @@ rule longread_len: """ python scripts/ReadLengthDistribution.py {input} {output} """ + rule select_longread: input: raw=config['longread'], @@ -24,17 +25,19 @@ rule select_longread: """ python scripts/SelectLongRead.py {input.raw} {input.lenDis} {params} {output.long} {output.short} """ + rule fq_to_fa: input: "output/filter_length.fq" - threads: - 1 output: "output/filter_length.fa" + threads: + 1 shell: """ python scripts/FqToFa.py {input} {output} """ + ##longRead_correct par="" readType=config['readtype'] @@ -47,26 +50,27 @@ rule short_to_long: input: long = "output/filter_length.fa", short = "output/left_filter_length.fq" - threads: - config["threads"] output: "output/short_to_long.sam" + threads: + config["threads"] params: type=par shell: """ minimap2 -ax {params.type} -t {threads} {input.long} {input.short} > {output} """ + rule longread_polish: input: long = 'output/filter_length.fa', - threads: - 1 short = 'output/left_filter_length.fq', sam = 'output/short_to_long.sam' output: "output/long_read_corrected.fasta" + threads: + config ["threads"] // 2 shell: """ - racon {input.short} {input.sam} {input.long} > {output} + racon --threads {threads} {input.short} {input.sam} {input.long} > {output} """ From 4929c80ff97f2b788ea92073eda2a74f63cd42e8 Mon Sep 17 00:00:00 2001 From: jdzm Date: Tue, 16 Dec 2025 15:20:16 +0100 Subject: [PATCH 13/14] corrected ouput folder name in gitignore --- .gitignore | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.gitignore b/.gitignore index eb40e70..fd4e55d 100644 --- a/.gitignore +++ b/.gitignore @@ -1,5 +1,5 @@ # Output files -results/ +output/ final/ tmp/ input/ From 67173c034625f843ab4ba02a501c024a0883ced3 Mon Sep 17 00:00:00 2001 From: jdzm Date: Wed, 17 Dec 2025 17:21:34 +0100 Subject: [PATCH 14/14] Updated README with changes to threads parameter in config --- README.md | 15 ++++++--------- 1 file changed, 6 insertions(+), 9 deletions(-) diff --git a/README.md b/README.md index ac5197f..fdcecfd 100644 --- a/README.md +++ b/README.md @@ -38,13 +38,11 @@ Reasons to __not__ use B-assembler: # Installation ## Install from source - ``` git clone https://github.com/huang1990/B-assembler.git; cd B-assembler; ``` ## setup the environment - ``` conda env create -n B-assembler -f env.yaml conda activate B-assembler @@ -52,7 +50,7 @@ conda activate B-assembler **Note** It is important that you ensure all bioconda installed tools installed. ## Write your configuation -###Provide sequence data in config.yaml file +### Provide sequence data in config.yaml file ``` cp config-template.yaml config.yaml vi config.yaml @@ -68,8 +66,8 @@ Replace the YAML keys as appropriate. Keys are: | `readtype`| ONT or pb | Type of your long reads, ONT is for nanopore, pb is for pacbio| ## Engage the pipeline -Run the pipeline, you **must** specify `cores` to ensure that how many threads you give. -##Usage +Run the pipeline, you **must** specify `cores` to ensure that how many threads you give. The max number of cores to be used is limited by the parameter `threads` inside the `config.yaml` file. Please make sure that they both match. +## Usage ``` Usage: bash run_B-assembler.sh [output:PWD] @@ -85,11 +83,10 @@ output: output directory, current working directory by default ``` -##Examples +## Examples ``` bash run_B-assembler.sh 2 LongReadOnly ``` -# output - -The final assembly will be in the output directory, and the name of assembly: B-assembler.fasta +# output +The final assembly will be in the output directory, and the name of assembly: `B-assembler.fasta`