Empty output file in some genomes

[Daikuang]

Hello,

I tried to use this tool to predict prophage in different strains. It works in most strains. however, in some strains I can't get any results (with an empty output) and come out a problem as shown below. I am preety show that these genomes are good, and I can get results when I tried other tools. I will very appreciate help me to figure out what's the issue.

Thanks Dai

Traceback (most recent call last): File "/home/kuangdai/.local/bin/phigaro", line 8, in sys.exit(main()) File "/home/kuangdai/.local/lib/python3.8/site-packages/phigaro/cli/batch.py", line 246, in main task_output_file = run_tasks_chain(tasks) File "/home/kuangdai/.local/lib/python3.8/site-packages/phigaro/batch/runner.py", line 20, in run_tasks_chain task.run() File "/home/kuangdai/.local/lib/python3.8/site-packages/phigaro/batch/task/hmmer.py", line 27, in run self.hmmer( File "/home/kuangdai/.local/lib/python3.8/site-packages/sh.py", line 1520, in call return RunningCommand(cmd, call_args, stdin, stdout, stderr) File "/home/kuangdai/.local/lib/python3.8/site-packages/sh.py", line 784, in init self.wait() File "/home/kuangdai/.local/lib/python3.8/site-packages/sh.py", line 841, in wait self.handle_command_exit_code(exit_code) File "/home/kuangdai/.local/lib/python3.8/site-packages/sh.py", line 865, in handle_command_exit_code raise exc sh.SignalException_SIGSEGV:

RAN: /home/kuangdai/miniconda3/bin/hmmsearch --cpu 16 --notextw --tblout proc/hmmer/A255-6fe68ffa37454fa3bfce47431d78c54f.hmmer_out /home/kuangdai/.phigaro/pvog/allpvoghmms proc/prodigal/A255-6fe68ffa37454fa3bfce47431d78c54f.faa

STDOUT:

hmmsearch :: search profile(s) against a sequence database

HMMER 3.3.1 (Jul 2020); http://hmmer.org/

Copyright (C) 2020 Howard Hughes Medical Institute.

Freely distributed under the BSD open source license.

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query HMM file: /home/kuangdai/.phigaro/pvog/allpvoghmms

target sequence database: proc/prodigal/A255-6fe68ffa37454fa3bfce47431d78c54f.faa

per-seq hits tabular output: proc/hmmer/A255-6fe68ffa37454fa3bfce47431d78c54f.hmmer_out

max ASCII text line length: unlimited

number of worker threads: 16

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Query: VOG0001 [M=98] Scores for co... (12411522 more, please see e.stdout)

STDERR:

[PollyTikhonova]

Hello @Daikuang! Thank you very much for using our tool! Could you, please, send me the files/strains that cause the problems? You can send them privately to my email tikhonova.polly@mail.ru

[PollyTikhonova]

Dear @Daikuang , it seems as it's an internal hmmsearch v3.3.1 problem. I've tested different versions of it and run hmmsearch command itself - 3.3.2 and 3.2.1 and other really old versions work fine, while hmmsearch v3.3.1 corrupts at some point. According to bioconda files at anaconda server they were aware of this problem and tried to fix it but dropped the wrong version number (that's my speculations). So, I advise you just to upgrade or downgrade your hmmer. Please, do not hesitate to write me, if the problem will remain or you meet with other issues.

[Daikuang]

Thank you so much for your kind help and advice. I will try this soon.

Dai

At 2021-03-09 19:43:20, "Polina" notifications@github.com wrote:

Dear @Daikuang , it seems as it's an internal hmmsearch v3.3.1 problem. I've tested different versions of it and run hmmsearch command itself - 3.3.2 and 3.2.1 and other really old versions work fine, while hmmsearch v3.3.1 corrupts at some point. According to bioconda files at anaconda server they were aware of this problem and tried to fix it but dropped the wrong version number (that's my speculations). So, I advise you just to upgrade or downgrade your hmmer. Please, do not hesitate to write me, if the problem will remain or you meet with other issues.

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[miasungeunlee]

Dear @PollyTikhonova Thank you for developping this great tool ! @Daikuang Did you figure out the issue ? I have same issue, i downgraded my hmmer at 3.3.0 and there is still empty output directory created after run. When i run phigaro with test_data/Bacillus_anthracis_str_ames.fna, it worked fine.

Best wishes Mia