Error: ln: missing file operand when running 'enrichm annotate'

[signalbash]

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

[geronimp]

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

[signalbash]

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

[signalbash]

Using enrichm-0.5.0 - where annotate.py uses cp instead of ln -s seems to have fixed it.