Hi Luis,
thanks for implementing the log-file command.
I installed macrel 0.6.0 via miniconda in a dedicated environment:
conda install -c conda-forge -c defaults -c bioconda macrel=0.6.0
I checked the help function and generated the log file using --log-file path/log_samplename.txt. Only indicating the path to the sample results folder does not work.
Still, I get some error message which could maybe due to some problem in the new release?
My command was (using a bash script to iterate over samples):
#!/bin/bash
for F in /x/y/z/Input/*.fa; do
N=$(basename $F .fa) ;
macrel contigs --fasta $F --output /x/y/z/Outputs/Macrel_out/$N --log-file /x/y/z/Outputs/Macrel_out/$N/log_$N.txt --tag $N -t 10 ; gunzip /x/y/z/Outputs/Macrel_out/$N/$N.prediction.gz ;
done
Error message is (some module not found error):
Traceback (most recent call last):
File "/home/biwb2/miniconda3/envs/macrel-0.6.0/bin/macrel", line 11, in <module>
sys.exit(main())
File "/home/biwb2/miniconda3/envs/macrel-0.6.0/lib/python3.8/site-packages/macrel/main.py", line 338, in main
do_smorfs(args, tdir,logfile)
File "/home/biwb2/miniconda3/envs/macrel-0.6.0/lib/python3.8/site-packages/macrel/main.py", line 166, in do_smorfs
filter_smorfs(all_peptide_file, peptide_file, args.cluster, args.keep_fasta_headers)
File "/home/biwb2/miniconda3/envs/macrel-0.6.0/lib/python3.8/site-packages/macrel/filter_smorfs.py", line 7, in filter_smorfs
with open_output(ofile, mode='wt') as output:
File "/home/biwb2/miniconda3/envs/macrel-0.6.0/lib/python3.8/contextlib.py", line 113, in __enter__
return next(self.gen)
File "/home/biwb2/miniconda3/envs/macrel-0.6.0/lib/python3.8/site-packages/macrel/utils.py", line 9, in open_output
from atomicwrites import atomic_write
ModuleNotFoundError: No module named 'atomicwrites'
gzip: /x/y/z/Outputs/Macrel_out/samplename/samplename.prediction.gz: No such file or directory
Two files have been generated: the .all_orfs.faa and the log file. No prediction file was generated which is why unzipping it did not work.
the previous version of macrel was installed and run similarly and worked. Do you have any suggestion?
I guess I miss some python package (atomic writes) which should maybe included in the dependency list in order to install it upon macrel installation?
Cheers
Martin