external program called by OrthoFinder returned an error code: 139

jinxbuddy commented 2 years ago

Hi David, I am currently running orthofinder on my pc and the program returns some errors iteratively. I am using orthofinder 2.5.4 on conda architecture right now.

Checking required programs are installed

Test can run "mcl -h" - ok Test can run "fastme -i /mnt/f/transcriptomics/sratoolkit.2.11.3-win64/bin/assembly/orthofinder_input_files/OrthoFinder/Results_Jan21_1/WorkingDirectory/SimpleTest.phy -o /mnt/f/transcriptomics/sratoolkit.2.11.3-win64/bin/assembly/orthofinder_input_files/OrthoFinder/Results_Jan21_1/WorkingDirectory/SimpleTest.tre" - ok

Dividing up work for BLAST for parallel processing

2022-01-21 18:00:54 : Creating diamond_ultra_sens database 1 of 22 2022-01-21 18:00:56 : Creating diamond_ultra_sens database 2 of 22 2022-01-21 18:00:58 : Creating diamond_ultra_sens database 3 of 22 2022-01-21 18:00:59 : Creating diamond_ultra_sens database 4 of 22 2022-01-21 18:01:01 : Creating diamond_ultra_sens database 5 of 22 2022-01-21 18:01:02 : Creating diamond_ultra_sens database 6 of 22 2022-01-21 18:01:04 : Creating diamond_ultra_sens database 7 of 22 2022-01-21 18:01:06 : Creating diamond_ultra_sens database 8 of 22 2022-01-21 18:01:06 : Creating diamond_ultra_sens database 9 of 22 2022-01-21 18:01:07 : Creating diamond_ultra_sens database 10 of 22 2022-01-21 18:01:08 : Creating diamond_ultra_sens database 11 of 22 2022-01-21 18:01:09 : Creating diamond_ultra_sens database 12 of 22 2022-01-21 18:01:11 : Creating diamond_ultra_sens database 13 of 22 2022-01-21 18:01:12 : Creating diamond_ultra_sens database 14 of 22 2022-01-21 18:01:12 : Creating diamond_ultra_sens database 15 of 22 2022-01-21 18:01:14 : Creating diamond_ultra_sens database 16 of 22 2022-01-21 18:01:16 : Creating diamond_ultra_sens database 17 of 22 2022-01-21 18:01:16 : Creating diamond_ultra_sens database 18 of 22 2022-01-21 18:01:17 : Creating diamond_ultra_sens database 19 of 22 2022-01-21 18:01:18 : Creating diamond_ultra_sens database 20 of 22 2022-01-21 18:01:19 : Creating diamond_ultra_sens database 21 of 22 2022-01-21 18:01:20 : Creating diamond_ultra_sens database 22 of 22

Running diamond_ultra_sens all-versus-all

Using 4 thread(s) 2022-01-21 18:01:21 : This may take some time.... 2022-01-21 18:01:21 : Done 0 of 484

ERROR: external program called by OrthoFinder returned an error code: 139 ERROR: external program called by OrthoFinder returned an error code: 139 ERROR: external program called by OrthoFinder returned an error code: 139

Command: diamond blastp -d /mnt/f/transcriptomics/sratoolkit.2.11.3-win64/bin/assembly/orthofinder_input_files/OrthoFinder/Results_Jan21_1/WorkingDirectory/diamond_ultra_sensDBSpecies2 -q /mnt/f/transcriptomics/sratoolkit.2.11.3-win64/bin/assembly/orthofinder_input_files/OrthoFinder/Results_Jan21_1/WorkingDirectory/Species14.fa -o /mnt/f/transcriptomics/sratoolkit.2.11.3-win64/bin/assembly/orthofinder_input_files/OrthoFinder/Results_Jan21_1/WorkingDirectory/Blast14_2.txt --ultra-sensitive -p 1 --quiet -e 0.001 --compress 1

Command: diamond blastp -d /mnt/f/transcriptomics/sratoolkit.2.11.3-win64/bin/assembly/orthofinder_input_files/OrthoFinder/Results_Jan21_1/WorkingDirectory/diamond_ultra_sensDBSpecies14 -q /mnt/f/transcriptomics/sratoolkit.2.11.3-win64/bin/assembly/orthofinder_input_files/OrthoFinder/Results_Jan21_1/WorkingDirectory/Species14.fa -o /mnt/f/transcriptomics/sratoolkit.2.11.3-win64/bin/assembly/orthofinder_input_files/OrthoFinder/Results_Jan21_1/WorkingDirectory/Blast14_14.txt --ultra-sensitive -p 1 --quiet -e 0.001 --compress 1

stdout

b'' stderr

b'Segmentation fault (core dumped)\n'

stdout

b'' stderr

b'Segmentation fault (core dumped)\n'

Command: diamond blastp -d /mnt/f/transcriptomics/sratoolkit.2.11.3-win64/bin/assembly/orthofinder_input_files/OrthoFinder/Results_Jan21_1/WorkingDirectory/diamond_ultra_sensDBSpecies2 -q /mnt/f/transcriptomics/sratoolkit.2.11.3-win64/bin/assembly/orthofinder_input_files/OrthoFinder/Results_Jan21_1/WorkingDirectory/Species2.fa -o /mnt/f/transcriptomics/sratoolkit.2.11.3-win64/bin/assembly/orthofinder_input_files/OrthoFinder/Results_Jan21_1/WorkingDirectory/Blast2_2.txt --ultra-sensitive -p 1 --quiet -e 0.001 --compress 1

stdout

b'' stderr

b'Segmentation fault (core dumped)\n'

ERROR: external program called by OrthoFinder returned an error code: 139

Command: diamond blastp -d /mnt/f/transcriptomics/sratoolkit.2.11.3-win64/bin/assembly/orthofinder_input_files/OrthoFinder/Results_Jan21_1/WorkingDirectory/diamond_ultra_sensDBSpecies14 -q /mnt/f/transcriptomics/sratoolkit.2.11.3-win64/bin/assembly/orthofinder_input_files/OrthoFinder/Results_Jan21_1/WorkingDirectory/Species2.fa -o /mnt/f/transcriptomics/sratoolkit.2.11.3-win64/bin/assembly/orthofinder_input_files/OrthoFinder/Results_Jan21_1/WorkingDirectory/Blast2_14.txt --ultra-sensitive -p 1 --quiet -e 0.001 --compress 1

stdout

b'' stderr

b'Segmentation fault (core dumped)\n'

davidemms commented 2 years ago

Hi

DIAMOND is crashing when 'blasting' some of your input files against each other (orthofinder uses the input proteomes but just renames the sequences with short IDs of the form iSpeices_iSeq). I'd suggest looking into what is causing the crash. You can run one of the problematic diamond commands it has printed, but without the '--quiet' flag and hopefully it will give you some meaningful information. Let me know what it says, it might be that I can put some pre-processing in OrthoFinder to prevent it from occurring, depending on what the error is.

Best wishes David

VectorFrankenstein commented 2 years ago

Hi @jinxbuddy,

Were you able to figure out what the issue was? I suspect I am currently facing this issue because I am only getting a partial output from one of my datasets. I am running my data on a remote machine that currently does not have error logging and I think my issue might be similar to this.

If you found a solution, could you let me know what?

Sincerely, Rijan

davidemms / OrthoFinder