ANN Macrel release 0.6.0

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Luis Pedro Coelho

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Oct 12, 2020, 4:48:30 AM10/12/20
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Dear List,

We released macrel 0.6.0 over the weekend. Upgrading is from conda (https://anaconda.org/bioconda/macrel)

The classifications do not change compared to 0.5.0, so results should be identical to 0.5.0, but the UX is improved (including implementing a --log-file command line argument as suggested by Martin Klapper on this mailing-list; Thanks Martin!)

List of changes:
https://macrel.readthedocs.io/en/latest/whatsnew/

HTH,
Luis

Luis Pedro Coelho | Fudan University | http://luispedro.org
https://orcid.org/0000-0002-9280-7885

Martin Klapper

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Oct 16, 2020, 4:18:26 AM10/16/20
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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

Luis Pedro Coelho

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Oct 16, 2020, 6:27:55 AM10/16/20
to Martin Klapper, ampsphere-users
Thanks for the feedback.

Yes, the package is missing atomicwrites. For the moment, you can just install atomicwrites (`conda install atomicwrites`) into the same environment and it will fix it for you. 

I also created a PR on the conda package and it will eventually (probably within 24-48 hours) be merged for everyone else too (https://github.com/bioconda/bioconda-recipes/pull/24885)

Best
Luis

Luis Pedro Coelho | Fudan University | http://luispedro.org


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Martin Klapper

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Oct 28, 2020, 8:32:37 AM10/28/20
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Hi Luis,
I repeated the installation of the latest Macrel release 0.6.0, but the module atomic writes is still not installed.
Will try to add it manually now.
Best, Martin

Luis Pedro Coelho

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Oct 28, 2020, 11:12:13 AM10/28/20
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Unfortunately, it seems that atomicwrites causes issues on Mac OSX (https://github.com/bioconda/bioconda-recipes/pull/24885)

I have just released a new version of macrel (version 0.6.1), which makes atomicwrites into an optional dependency. If present, it uses it, but it will still work well:


Now, it should take a few hours for bioconda to pick it up...

Best
Luis

Luis Pedro Coelho | Fudan University | http://luispedro.org


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