I am trying to run shortbred_identify.py but have been having lots of issues with getting this to run.
This my command.
module load anaconda3
conda activate /scratch/project/gut_oral_micro/shortbred
cd /scratch/project/gut_oral_micro
shortbred_identify.py --goi card_database_v4.0.0_all_prokka/card_database_v4.0.0_all.faa --ref uniref90.fasta.gz --markers RGI_4.0.0_markers.faa --tmpdir $TMPDIR --threads 32 --usearch /home/uqsleech/usearch6.1.544_i86linux32 --muscle /home/uqsleech/.conda/pkgs/muscle-3.8.31-0/bin/muscle --cdhit /home/uqsleech/.conda/pkgs/cd-hit-4.6.8-hfc679d8_2/bin/cd-hit --blastp /home/uqsleech/ncbi-blast-2.2.28+/bin/blastp --makeblastdb /home/uqsleech/ncbi-blast-2.2.28+/bin/makeblastdb
I had to add the biopython path to shortbred_identify.py to get that working.
I have also tried with --usearch usearch11.0.667_i86linux32
and --usearch /home/uqsleech/.conda/pkgs/usearch-12.0_beta-h9ee0642_1/bin/usearch with the same results
Currently I am getting the following error and warnings
Tested usearch. Appears to be working.
Tested blastp. Appears to be working.
Tested muscle returned a nonzero exit code (typically indicates failure). Please check to ensure the program is working. Will continue running.
Path for cdhit appears to be fine. This program returns an error [exit code=1] when tested and working properly, so ShortBRED does not check it.
Tested makeblastdb. Appears to be working.
Usearch cannot make a required database. Please check to make sure you have v6.0.307 of usearch or later installed.
With a final error of
Making BLAST database for the family consensus sequences...
Making BLAST database for the reference protein sequences...
Checking dependencies...
Checking to make sure that installed version of usearch can make databases...
Traceback (most recent call last):
File "/scratch/project/gut_oral_micro/shortbred/bin/shortbred_identify.py", line 297, in <module>
subprocess.check_call([
File "/sw/auto/rocky8c/epyc4/software/Anaconda3/2023.09-0/lib/python3.11/subprocess.py", line 413, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['/home/uqsleech/ncbi-blast-2.2.28+/bin/makeblastdb', '-in', 'uniref90.fasta.gz', '-out', '/scratch/temp/12250694/refdb/refdb', '-dbtype', 'prot', '-logfile', '/scratch/temp/12250694/refdb.log']' returned non-zero exit status 1.
Full log file is attached
slurm-12250694.txt (6.9 MB)