Closed signalbash closed 4 years ago
Hi there. Please replace the .fa suffix on your genome file to .fna, and the annotate pipeline should work. Let me know if that works for you
Thanks, Joel
Did that, and that resulted in this error File "/shared/homes/143470/enrichM/bin/../enrichm/annotate.py", line 152, in prep_genome os.symlink(gf, os.path.join(genome_directory, os.path.basename(gf))) NameError: name 'os' is not defined I cloned a copy of the enrichm repo and added import os into annotate.py
Now I get this error:
[143470@ermdc22 enrichm_test]$ enrichm annotate --output EAC.bins9.0.out --force --verbosity 5 --genome_files EAC.bin.9.fna --ko [2019-11-14 09:53:44 AM] INFO: Command: enrichm annotate --output EAC.bins9.0.out --force --verbosity 5 --genome_files EAC.bin.9.fna --ko [2019-11-14 09:53:44 AM] INFO: Running the annotate pipeline [2019-11-14 09:53:44 AM] INFO: Running pipeline: annotate [2019-11-14 09:53:44 AM] INFO: Setting up for genome annotation [2019-11-14 09:53:44 AM] INFO: Calling proteins for annotation [2019-11-14 09:53:44 AM] INFO: Preparing genomes for annotation [2019-11-14 09:53:44 AM] INFO: - Calling proteins for 1 genomes [2019-11-14 09:53:44 AM] DEBUG: ls EAC.bins9.0.out/genome_bin/.fna | sed 's/.fna//g' | grep -o '[^/]$' | parallel -j 5 prodigal -q -p meta -o /dev/null -d EAC.bins9.0.out/genome_genes/{}.fna -a EAC.bins9.0.out/genome_proteins/{}.faa -i EAC.bins9.0.out/genome_bin/{}.fna > /dev/null 2>&1 ls: cannot access EAC.bins9.0.out/genome_bin/EAC.bin.9.fna: Too many levels of symbolic links [2019-11-14 09:53:44 AM] DEBUG: Finished [2019-11-14 09:53:44 AM] ERROR: No files found with .fna suffix in input directory [2019-11-14 09:53:44 AM] INFO: Finished running EnrichM
Using enrichm-0.5.0 - where annotate.py uses cp instead of ln -s seems to have fixed it.
Working with enrichm 0.5.1
[143470@ermdc14 enrichm_test]$ enrichm annotate --output EAC.bins9.0.out --verbosity 5 --genome_files EAC.bin.9.fa --ko --force [2019-11-08 10:04:16 AM] INFO: Command: enrichm annotate --output EAC.bins9.0.out --verbosity 5 --genome_files EAC.bin.9.fa --ko [2019-11-08 10:04:16 AM] INFO: Running the annotate pipeline [2019-11-08 10:04:16 AM] INFO: Running pipeline: annotate [2019-11-08 10:04:16 AM] INFO: Setting up for genome annotation [2019-11-08 10:04:16 AM] INFO: Calling proteins for annotation [2019-11-08 10:04:16 AM] INFO: Preparing genomes for annotation [2019-11-08 10:04:16 AM] DEBUG: xargs --arg-file=/dev/stdin ln -s --target-directory=EAC.bins9.0.out/genome_bin ln: missing file operand Try `ln --help' for more information. [2019-11-08 10:04:16 AM] INFO: - Calling proteins for 0 genomes [2019-11-08 10:04:16 AM] DEBUG: ls EAC.bins9.0.out/genome_bin/.fna | sed 's/.fna//g' | grep -o '[^/]$' | parallel -j 5 prodigal -q -p meta -o /dev/null -d EAC.bins9.0.out/genome_genes/{}.fna -a EAC.bins9.0.out/genome_proteins/{}.faa -i EAC.bins9.0.out/genome_bin/{}.fna > /dev/null 2>&1 ls: cannot access EAC.bins9.0.out/genome_bin/*.fna: No such file or directory [2019-11-08 10:04:16 AM] DEBUG: Finished [2019-11-08 10:04:16 AM] ERROR: No files found with .fna suffix in input directory [2019-11-08 10:04:16 AM] INFO: Finished running EnrichM