failing tests with t/test_pipeline.pl

[ccodojunior]

Hi, I am trying to install OrthoMCL on my google colab environment.

I have successfully set up everything up to the orthomcl orthomcl-setup-database.pl step, but I had errors when trying to run the test_pipeline.pl, so I was hoping to get some advice about it.

When I tried to run !perl orthomcl-pipeline/t/test_pipeline.pl -m orthomcl.conf -s fork -t /tmp , I received error messages as below:

Test using scheduler fork

TESTING NON-COMPLIANT INPUT
TESTING FULL PIPELINE RUN 2
README:
Test with split=2 of fasta files.
Could not execute command /content/orthomcl-pipeline/t/../bin/orthomcl-pipeline --nocompliant --scheduler fork --yes -c /content/orthomcl-pipeline/t/data/basic/2/etc/orthomcl-pipeline.conf -i /content/orthomcl-pipeline/t/data/basic/2/input -o /tmp/orthomcl-pipeline.fEJpC0/output -m /tmp/orthomcl-pipeline.fEJpC0/orthomcl.config 2>/tmp/orthomcl-pipeline.fEJpC0/orthomcl-pipeline.err.log 1>/tmp/orthomcl-pipeline.fEJpC0/orthomcl-pipeline.out.log

The following are error log files:

!cat /tmp/orthomcl-pipeline.fEJpC0/orthomcl-pipeline.err.log

Error executing command: /content/orthomclSoftware-v2.0.9/bin/orthomclLoadBlast "/tmp/orthomcl-pipeline.fEJpC0/orthomcl.config" "/tmp/orthomcl-pipeline.fEJpC0/output/blast_load/similarSequences.txt" 1>/tmp/orthomcl-pipeline.fEJpC0/output/log/10.orthomclLoadBlast.out.log 2>/tmp/orthomcl-pipeline.fEJpC0/output/log/10.orthomclLoadBlast.err.log. See logs /tmp/orthomcl-pipeline.fEJpC0/output/log/10.orthomclLoadBlast.out.log and /tmp/orthomcl-pipeline.fEJpC0/output/log/10.orthomclLoadBlast.err.log

!cat /tmp/orthomcl-pipeline.fEJpC0/orthomcl-pipeline.err.log

DBD::mysql::st execute failed: Loading local data is disabled; this must be enabled on both the client and server sides at /content/orthomclSoftware-v2.0.9/bin/orthomclLoadBlast line 39, <F> line 12.

!cat /tmp/orthomcl-pipeline.fEJpC0/orthomcl-pipeline.out.log

Starting OrthoMCL pipeline on: Sun May 19 09:51:53 2024
Git commit: d0bacb3bd0f655406e09bc7fc3f776a40a57c75c


=Stage 1: Validate Files =
Validating 2.fasta ... 5 sequences
Validating 1.fasta ... 5 sequences
Validating 3.fasta ... 5 sequences
Validated 3 files
Stage 1 took 0.00 minutes 

=Stage 2: Validate Database=
Warning: some tables exist already in database dbi:mysql:orthomcl:localhost:mysql_local_infile, user=orthomcl, database_name=orthomcl. Do you want to remove (y/n)? Executing: 'drop database orthomcl'
Executing: 'create database orthomcl'
Successfully removed old database entries
Stage 2 took 0.02 minutes 


=Stage 3: Load OrthoMCL Database Schema=
/content/orthomclSoftware-v2.0.9/bin/orthomclInstallSchema "/tmp/orthomcl-pipeline.fEJpC0/orthomcl.config" "/tmp/orthomcl-pipeline.fEJpC0/output/log/orthomclSchema.log" 1>/tmp/orthomcl-pipeline.fEJpC0/output/log/3.loadschema.stdout.log 2>/tmp/orthomcl-pipeline.fEJpC0/output/log/3.loadschema.stderr.log
Stage 3 took 0.00 minutes 


=Stage 4: Adjust Fasta=
/content/orthomclSoftware-v2.0.9/bin/orthomclAdjustFasta 2 "/content/orthomcl-pipeline/t/data/basic/2/input/2.fasta" 1
/content/orthomclSoftware-v2.0.9/bin/orthomclAdjustFasta 1 "/content/orthomcl-pipeline/t/data/basic/2/input/1.fasta" 1
/content/orthomclSoftware-v2.0.9/bin/orthomclAdjustFasta 3 "/content/orthomcl-pipeline/t/data/basic/2/input/3.fasta" 1
Stage 4 took 0.00 minutes 


=Stage 5: Filter Fasta=
/content/orthomclSoftware-v2.0.9/bin/orthomclFilterFasta "/tmp/orthomcl-pipeline.fEJpC0/output/compliant_fasta" 10 20
Stage 5 took 0.00 minutes 


=Stage 6: Split Fasta=
splitting /tmp/orthomcl-pipeline.fEJpC0/output/blast_dir/goodProteins.fasta into 2 pieces
Stage 6 took 0.00 minutes 


=Stage 7: Format Database=
/content/blast-2.2.26/bin/formatdb -i "/tmp/orthomcl-pipeline.fEJpC0/output/blast_dir/goodProteins.fasta" -p "T" -l "/tmp/orthomcl-pipeline.fEJpC0/output/log/formatdb.log" 1>/tmp/orthomcl-pipeline.fEJpC0/output/log/7.format-stdout.log 2>/tmp/orthomcl-pipeline.fEJpC0/output/log/7.format-stderr.log
Stage 7 took 0.00 minutes 


=Stage 8: Perform Blast=
performing blastsexecuting /content/blast-2.2.26/bin/blastall -p "blastp" -i "/tmp/orthomcl-pipeline.fEJpC0/output/blast_dir/goodProteins.fasta.1" -m "8" -d "/tmp/orthomcl-pipeline.fEJpC0/output/blast_dir/goodProteins.fasta" -o "/tmp/orthomcl-pipeline.fEJpC0/output/blast_results/blast_results.1" -v "100000" -F "F" -e "1e-5" -b "100000" 1>/tmp/orthomcl-pipeline.fEJpC0/output/log/blast/8.stdout.blast.1 2>/tmp/orthomcl-pipeline.fEJpC0/output/log/blast/8.stderr.blast.1
executing /content/blast-2.2.26/bin/blastall -p "blastp" -i "/tmp/orthomcl-pipeline.fEJpC0/output/blast_dir/goodProteins.fasta.2" -m "8" -d "/tmp/orthomcl-pipeline.fEJpC0/output/blast_dir/goodProteins.fasta" -o "/tmp/orthomcl-pipeline.fEJpC0/output/blast_results/blast_results.2" -v "100000" -F "F" -e "1e-5" -b "100000" 1>/tmp/orthomcl-pipeline.fEJpC0/output/log/blast/8.stdout.blast.2 2>/tmp/orthomcl-pipeline.fEJpC0/output/log/blast/8.stderr.blast.2
Stage 8 took 0.02 minutes 
done


=Stage 9: Parse Blast Results=
cat /tmp/orthomcl-pipeline.fEJpC0/output/blast_results/blast_results.* > /tmp/orthomcl-pipeline.fEJpC0/output/blast_load/all.fasta
/content/orthomclSoftware-v2.0.9/bin/orthomclBlastParser "/tmp/orthomcl-pipeline.fEJpC0/output/blast_load/all.fasta" "/tmp/orthomcl-pipeline.fEJpC0/output/compliant_fasta" 1>/tmp/orthomcl-pipeline.fEJpC0/output/blast_load/similarSequences.txt 2>/tmp/orthomcl-pipeline.fEJpC0/output/log/9.parseBlast.log
Stage 9 took 0.00 minutes 


=Stage 10: Load Blast Results=
/content/orthomclSoftware-v2.0.9/bin/orthomclLoadBlast "/tmp/orthomcl-pipeline.fEJpC0/orthomcl.config" "/tmp/orthomcl-pipeline.fEJpC0/output/blast_load/similarSequences.txt" 1>/tmp/orthomcl-pipeline.fEJpC0/output/log/10.orthomclLoadBlast.out.log 2>/tmp/orthomcl-pipeline.fEJpC0/output/log/10.orthomclLoadBlast.err.log

Thank you for reading through all this. Looking forward to your reply,
Sarah