Error upon 'make' command

[Pkaps25]

Hi, I just cloned the repo on a linux machine. Upon executing the setup instructions, I get this error with the command make inside of the danbing-tk directory:

g++ -std=c++11 -lpthread -O3 -o bin/danbing-tk src/aQueryFasta_thread.cpp /bin/ld: cannot open output file bin/danbing-tk: No such file or directory collect2: error: ld returned 1 exit status make: *** [bin/danbing-tk] Error 1

[joyeuxnoel8]

Hi,
Thanks for reporting the error. I've updated the Makefile. Let me know it there's still any error message.
Tsung-Yu

[Pkaps25]

Thank you, this fixed the error

[Pkaps25]

I'm experiencing another error when following the test instructions. I've replaced PREFIX in the bam.fofn file and in the config file, but it appears a file is missing from the test inputs. Could you clarify what the format of this input file should look like please.

OSError in line 11 of /local/workdir/pk445/vntr/danbing-tk/pipeline/GoodPanGenomeGraph.snakefile: /workdir/pk445/vntr/danbing-tk/test/input/genome.bam.tsv.bak not found. File "/local/workdir/pk445/vntr/danbing-tk/pipeline/GoodPanGenomeGraph.snakefile", line 11, in <module> File "/usr/lib64/python3.6/site-packages/numpy/lib/npyio.py", line 961, in loadtxt File "/usr/lib64/python3.6/site-packages/numpy/lib/_datasource.py", line 195, in open File "/usr/lib64/python3.6/site-packages/numpy/lib/_datasource.py", line 535, in open

[joyeuxnoel8]

Removed obsolete files and added the missing file. Now you just need to replace $PREFIX in goodPanGenomeGraph.json and input/genome.bam.tsv. Let me know if it works. Thanks!

[Pkaps25]

This fixed the error. I had to keep the genomes.txt file to avoid a different error, however.

[joyeuxnoel8]

Glad to know you were able to get it running! I now removed the dependency for genomes.txt.

[joyeuxnoel8]

Hello, I can't seem to find your comment on the page. I guess you've got it figured out; I'll make sure to fix that as well. Also, I'd like to let you know that I'm working on a release that will update the RPGG and the annotated VNTR set since it looks like you're trying to genotype samples.

…

On Sat, Jan 9, 2021 at 9:20 AM Pkaps25 ***@***.***> wrote: I have one more question about the command to align to the RPGG: samtools fasta ***@***.*** -n $SRS.bam | bam2pe -fai /dev/stdin | danbing-tk -gc 50 -k 21 -qs pan -fai /dev/stdin -o $OUT_PREFIX \ -p 24 -cth 45 -rth 0.5 There does not appear to be a danbing-tk command in PATH. Is the command danbing-tk referring to a specific script? Also, I am unfamiliar with the bam2pe tool. Which tool is this? Thank you for your help. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <https://urldefense.com/v3/__https://github.com/ChaissonLab/danbing-tk/discussions/1*discussioncomment-271449__;Iw!!LIr3w8kk_Xxm!8iBWZYQJF5XLJ6L3e1zodLtDPJjK96_kay4kXosJ4p4bAwHy0TSa02e3I4msY68$>, or unsubscribe <https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/AF4XDRBZX3KOAIX3ZJJFTX3SZCF6PANCNFSM4V3DIQCA__;!!LIr3w8kk_Xxm!8iBWZYQJF5XLJ6L3e1zodLtDPJjK96_kay4kXosJ4p4bAwHy0TSa02e3VcX9Ghg$> .

[joyeuxnoel8]

The only data I need to make the RPGG are the assembled genomes and the reference genome?

I probably didn't document this well, but the BAM files here are from SRS data matched with each genome and not from SRS or assemblies. Assembly bam files are used for liftover and are generated by the pipeline by aligning the specified reference to each assembly. I've updated the danbing-tk build section in README for clarity. If you do not have whole-genome SRS data, let me know. I will make the graph pruning step optional.

I notice that the pipeline expects two fasta files for each genome *.0.fa and *.1.fa. If I am using the RefSeq Genomes, is it acceptable to use the same fasta file for both *.0.fa and *.1.fa?

For testing purpose, this should be fine. And for un-phased assemblies, this is also the easy way to trick the program.

After creating the RPGG, I plan to align cfDNA reads to the graph.

This is cool! I look forward to the application.

[Pkaps25]

Thank you. I don't have the whole genome SRS data. If you could make the pruning optional that would be great.

For posterity, I tried simulating illumina short reads (40x and 80x) from each of the genomes and aligning those simulated reads back to their respective genomes to use as bam inputs. The output pan.tr.kmers file was still empty.

[joyeuxnoel8]

Hmm this is weird. Could you show an example of the paired-end reads?

[Pkaps25]

Apologies, please disregard that last comment. The above approach produces an output in the pan.tr.kmers file.

[joyeuxnoel8]

Glad to know this! Also the SRS data, or the pruning step, is optional now. Please check README for updated usage.