domain_motif_annotation/InterProScan/split1/split1.interproscan.err metawibele characterize

Microbial community profiling MetaWIBELE
1

Hello,
I got an error when I sbatch a script. the details about the error and script as follow.
would you please give me some information or advice? Thanks!

一、THE ERROR

1、Task 27 failed
Name: interproscan____split1
Original error:
Failed to produce target `path/ouput_1/domain_motif_annotation/InterProScan/split1/split1.interproscan.txt’. Original exception: Traceback (most recent call last):
File “/usr/local/lib/python3.6/dist-packages/anadama2/runners.py”, line 220, in _get_task_result
targ_compares.append(list(target.compare()))
File “/usr/local/lib/python3.6/dist-packages/anadama2/tracked.py”, line 379, in compare
stat = os.stat(self.name)
FileNotFoundError: [Errno 2] No such file or directory: ‘path/ouput_1/domain_motif_annotation/InterProScan/split1/split1.interproscan.txt’

2、
I found some info in file (/ouput_1/domain_motif_annotation/InterProScan/split1/split1.interproscan.err) as follow:

ERROR - Command line failed with exit code: 126
Command: bin/phobius/1.01/phobius.pl /path/temp/node02_20220803_012518945_bz5s//jobPhobius/000000000001_000000001893.fasta

and I found that there is no file 000000000001_000000001893.fasta. in the path(/path/temp/node02_20220803_012518945_bz5s//jobPhobius/)

3、so
why is there no 000000000001_000000001893.fasta.?
and how can I fix it out ?

二、the slurm script

#!/bin/bash
#SBATCH -J cha_1
#SBATCH -N 1
#SBATCH -n 1

.sif file

SIF=/path/metawV3.sif
SINGULARITY=“singularity exec $SIF”

input files

INPUT_SEQUENCE=/path/demo_genecatalogs.centroid.faa
INPUT_COUNT=/path/demo_genecatalogs_counts.all.tsv
INPUT_METADATA=/path/demo_mgx_metadata.tsv
OUTPUT_DIR=/path/characterize/ouput_1

META_CHARACTERIZE=“metawibele characterize --input-sequence $INPUT_SEQUENCE
–input-count $INPUT_COUNT --input-metadata $INPUT_METADATA --output $OUTPUT_DIR”
singularity exec $SIF $META_CHARACTERIZE

2

Hi there,

Thanks for your interest in MetaWIBELE! Based on this message, it looks like something disordered during the InterProScan processing. To fix this issue, you could try the following on your system:

  1. Test whether the Interproscan dependency is well set on your system. E.g. ./interproscan.sh -i test_proteins.fasta -f tsv -appl phobius
  2. If the above command fails, you may want to debug the installation of Interproscane (e.g. Missing Input File When Using Phobius · Issue #54 · ebi-pf-team/interproscan · GitHub)
  3. If you can run Interproscan successfully, then test the individual task metawibele_interproscan_annotator and see whether it works on your system.

Hope these suggestions will help and let me know if you have any other questions.

Thanks!
Yancong

3

Hi! Similar error, did you ever figure this out?

4

this might be due to permissions,just chmod 755 phobius.pl