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apetkau / orthomcl-pipeline

Automates running of OrthoMCL software from http://orthomcl.org/common/downloads/software/v2.0/
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failing tests with t/test.pipeline.pl #39

Open huiyus16 opened 4 years ago

huiyus16 commented 4 years ago

Hi, I am trying to install orthomcl-pipeline and I successfully wrote the path of all programs into orthomcl-pipeline.conf. Here is the content of the file.

blast: F: 'm S' b: '100000' e: '1e-5' v: '100000' filter: max_percent_stop: '20' min_length: '10' mcl: inflation: '1.5' path: blastall: /usr/bin/blastall formatdb: /usr/bin/formatdb mcl: /home/huiyu/.linuxbrew/bin/mcl orthomcl: /home/huiyu/Desktop/orthomclSoftware-v2.0.9/bin scheduler: fork split: '4'

However, when i try to run the test, I had 7 of those 8 tests failed. Here is the report: $ perl t/test_pipeline.pl -m orthomcl.conf -s fork -t /tmp Test using scheduler fork

TESTING NON-COMPLIANT INPUT TESTING FULL PIPELINE RUN 4 README: Tests case of one gene (in 1.fasta) not present in any other files. /home/huiyu/orthomcl-pipeline/t/data/basic/4/groups/groups.txt contains entries (1|e 2|e 3|a) not in /tmp/orthomcl-pipeline.98cOZk/output/groups/groups.txt not ok 1 - Expected matched returned groups file

Failed test 'Expected matched returned groups file'

at t/test_pipeline.pl line 204.

TESTING FULL PIPELINE RUN 2 README: Test with split=2 of fasta files. /home/huiyu/orthomcl-pipeline/t/data/basic/2/groups/groups.txt contains entries (1|e 2|e 3|a) not in /tmp/orthomcl-pipeline.IcSyak/output/groups/groups.txt not ok 2 - Expected matched returned groups file

Failed test 'Expected matched returned groups file'

at t/test_pipeline.pl line 204.

TESTING FULL PIPELINE RUN 5 README: Tests case of one gene (in 1.fasta) not present in any other files but with a paralog in 1.fasta. /home/huiyu/orthomcl-pipeline/t/data/basic/5/groups/groups.txt contains entries (1|e 2|e 3|a) not in /tmp/orthomcl-pipeline.eOWOw9/output/groups/groups.txt not ok 3 - Expected matched returned groups file

Failed test 'Expected matched returned groups file'

at t/test_pipeline.pl line 204.

TESTING FULL PIPELINE RUN 3 README: Tests case of one gene (in 1.fasta and 2.fasta) not present in other files. /home/huiyu/orthomcl-pipeline/t/data/basic/3/groups/groups.txt contains entries (1|e 2|e 3|a) not in /tmp/orthomcl-pipeline.90SFfP/output/groups/groups.txt not ok 4 - Expected matched returned groups file

Failed test 'Expected matched returned groups file'

at t/test_pipeline.pl line 204.

TESTING FULL PIPELINE RUN 1 README: Test using with no splitting of fasta files. /home/huiyu/orthomcl-pipeline/t/data/basic/1/groups/groups.txt contains entries (1|d 2|e 3|a) not in /tmp/orthomcl-pipeline.NWIJa1/output/groups/groups.txt not ok 5 - Expected matched returned groups file

Failed test 'Expected matched returned groups file'

at t/test_pipeline.pl line 204.

TESTING COMPLIANT INPUT TESTING FULL PIPELINE RUN 1 README: Test non-compliant fasta input, no splitting. ok 6 - No compliant parameter successfully caught /home/huiyu/orthomcl-pipeline/t/data/compliant/1/groups/groups.txt contains entries (1|d 2|e 3|a) not in /tmp/orthomcl-pipeline.FqsGz5/output/groups/groups.txt not ok 7 - Pipeline succeeded with compliant parameter. Expected matched returned groups file

Failed test 'Pipeline succeeded with compliant parameter. Expected matched returned groups file'

at t/test_pipeline.pl line 239.

/home/huiyu/orthomcl-pipeline/t/data/compliant/1/groups/groups.txt contains entries (1|d 2|e 3|a) not in /tmp/orthomcl-pipeline.FqsGz5/output/groups/groups.txt not ok 8 - Pipeline succeeded with (default) compliant parameter. Expected matched returned groups file

Failed test 'Pipeline succeeded with (default) compliant parameter. Expected matched returned groups file'

at t/test_pipeline.pl line 248.

1..8

Looks like you failed 7 tests of 8.

Could someone please help me figure this out? Thank you so much! Huiyu

huiyus16 commented 4 years ago

Hi, I also found a closed issue in 2016 and tried to delete rmtree lines in test_pipeline.pl to get an output log. However, I didnt see a log file in the orthomcl-pipeline folder. Thank you!

Huiyu

apetkau commented 4 years ago

Hello @huiyus16 . Which version of BLAST do you have installed? The previous issue you referred to I believe is #7 and the solution there was to make sure to use BLAST 2.2.26.