Could not compute the factorizations

[ramadatta]

Hi,

I experience the following error: I have 16 gb ram, around 200K transcripts aligning on 24 chromosomes. May i please know, if it is the issue of memory. Thanks.

I am using pintron version: 1.3.3

[INFO ] 2016-03-14 14:09:51,054 - PIntron_____%PINTRON_VERSION%_____
[INFO ] 2016-03-14 14:09:51,054 - Copyright (C) 2010,2011 Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Raffaella Rizzi.
[INFO ] 2016-03-14 14:09:51,055 - This program is distributed under the terms of the GNU Affero General Public License (AGPL), either version 3 of the License, or (at your option) any later version.
[INFO ] 2016-03-14 14:09:51,055 - This program comes with ABSOLUTELY NO WARRANTY. See the GNU Affero General Public License for more details.
[INFO ] 2016-03-14 14:09:51,055 - This is free software, and you are welcome to redistribute it under the conditions specified by the license.
[INFO ] 2016-03-14 14:09:51,055 - Running: /home/prakkisr/bin/pintron -b /home/prakkisr/Documents/PIntron/bin -g /store1/home/prakkisr/NEW/Tilapia/6MTil_CollapsedIso_withMTil_Genome_Q1527_v2scaffolds_63ContaminantRemoved/SW_FW/Q1527_v2_scaffolds_63ContaminantRemoved.fasta -s sample_trans.fasta -n MozTilapia
[INFO ] 2016-03-14 14:09:51,055 - STEP 1: Checking executables and preparing input data...
[INFO ] 2016-03-14 14:10:04,712 - STEP 2: Pre-aligning transcript data...
Could not compute the factorizations 139
[ERROR ] 2016-03-14 14:10:14,181 - *** Fatal error caught during the execution of the pipeline! ***
Could not compute the factorizations
Traceback (most recent call last):
File "/home/prakkisr/bin/pintron", line 1017, in
pintron_pipeline(options)
File "/home/prakkisr/bin/pintron", line 884, in pintron_pipeline
output_file='raw-multifasta-out.txt')
File "/home/prakkisr/bin/pintron", line 773, in exec_system_command
raise PIntronError(error_comment)
PIntronError: Could not compute the factorizations

[gdv]

Thanks for your report.
It is likely to be due to memory usage.
Can you attach the logfiles produced by PIntron, so that we can further investigate the issue?

[ramadatta]

Hi, this is the content of my log file.

INFO:root:20160314-141507994:PIntron_____%PINTRON_VERSION%_____
INFO:root:20160314-141507994:Copyright (C) 2010,2011 Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Raffaella Rizzi.
INFO:root:20160314-141507994:This program is distributed under the terms of the GNU Affero General Public License (AGPL), either version 3 of the License, or (at your option) any later version.
INFO:root:20160314-141507995:This program comes with ABSOLUTELY NO WARRANTY. See the GNU Affero General Public License for more details.
INFO:root:20160314-141507995:This is free software, and you are welcome to redistribute it under the conditions specified by the license.
INFO:root:20160314-141507995:Running: /home/prakkisr/bin/pintron
INFO:root:20160314-141507995:STEP 1: Checking executables and preparing input data...
DEBUG:root:20160314-141507995:Using main program 'pintron' in dir '/home/prakkisr/Documents/PIntron/bin/pintron' (md5: 350bdf1530059e14185df9bcdc776808)
DEBUG:root:20160314-141507999:Using program 'est-fact' in dir '/home/prakkisr/Documents/PIntron/bin/est-fact' (md5: ba03671565959d0c6a02bcd3d5aba8e1)
DEBUG:root:20160314-1415082:Using program 'min-factorization' in dir '/home/prakkisr/Documents/PIntron/bin/min-factorization' (md5: 109b7da5108938b99eac04026ce5f377)
DEBUG:root:20160314-1415084:Using program 'intron-agreement' in dir '/home/prakkisr/Documents/PIntron/bin/intron-agreement' (md5: 53e20167291da8749a55f3d09e631dfd)
DEBUG:root:20160314-1415085:Using program 'compact-compositions' in dir '/home/prakkisr/Documents/PIntron/bin/compact-compositions' (md5: dc66e8fca806ecd8cf5ef0697dae04e9)
DEBUG:root:20160314-1415085:Using program 'maximal-transcripts' in dir '/home/prakkisr/Documents/PIntron/bin/maximal-transcripts' (md5: a2944fa0836d80c72b6adf7f28f8b02a)
DEBUG:root:20160314-1415086:Using program 'cds-annotation' in dir '/home/prakkisr/Documents/PIntron/bin/cds-annotation' (md5: b1aa10667d40b5cf55679d1525fdeeed)
DEBUG:root:20160314-1415086:Files "genomic.txt" and "genomic.txt" refer to the same file: skip copy.
DEBUG:root:20160314-1415086:Files "ests.txt" and "ests.txt" refer to the same file: skip copy.
INFO:root:20160314-1415086:STEP 2: Pre-aligning transcript data...
DEBUG:root:20160314-1415087:time.struct_time(tm_year=2016, tm_mon=3, tm_mday=14, tm_hour=14, tm_min=15, tm_sec=8, tm_wday=0, tm_yday=74, tm_isdst=0)
DEBUG:root:20160314-1415087:ulimit -t 3600 && ulimit -v 3072000 && /home/prakkisr/Documents/PIntron/bin/est-fact
ERROR:root:20160314-141516327:*** Fatal error caught during the execution of the pipeline! ***
Could not compute the factorizations
Traceback (most recent call last):
File "/home/prakkisr/bin/pintron", line 1017, in
pintron_pipeline(options)
File "/home/prakkisr/bin/pintron", line 884, in pintron_pipeline
output_file='raw-multifasta-out.txt')
File "/home/prakkisr/bin/pintron", line 773, in exec_system_command
raise PIntronError(error_comment)
PIntronError: Could not compute the factorizations

[rrizzi]

Hi, in order to understand your problem we need also the input files you used with PIntron (that is, the genomic file and the file of transcripts).
Please note that the input genomic sequence must be restricted to the gene locus and the input transcripts must originate from the gene you want to process.

[ramadatta]

I was using genome with 24 chromosomes (size around 550 Mb) and transcripts file was around 700 Mb in size. So, I need to predict the gene locus first and then align is it?

[gdv]

Yes, it would be much better to split the genome and the transcripts set
into parts.
We are implementing an automatic procedure for that step, but it's not
usable yet.

Gianluca Della Vedova
http://gianluca.dellavedova.org
Il 17/mar/2016 05:15, "Prakki Rama" notifications@github.com ha scritto:

I was using genome with 24 chromosomes (size around 550 Mb) and
transcripts file was around 700 Mb in size. So, I need to predict the gene
locus first and then align is it?

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