DRAM
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WrightonLabCSU
subprocess.CalledProcessError: mmseqs
Hello,
I am receiving a subprocess.CalledProcessError after running the following code: DRAM.py annotate -i '/scratch1/flores5/GF_fastq/02_ASSEMBLE/contigs/*.fa' -o annotation
33 fastas found
2021-07-06 00:54:28.962181: Annotation started
0:00:00.022096: Retrieved database locations and descriptions
0:00:00.022138: Annotating GF2_mjMb2B_input_S53_megahit.contigs
0:21:26.734696: Turning genes from prodigal to mmseqs2 db
Traceback (most recent call last):
File "/home/flores5/anaconda3/envs/DRAM/bin/DRAM.py", line 153, in
Any suggestions on how I can fix this?
Can you try running annotation/working_dir/GF2_mjMb2B_input_S53_megahit.contigs/tmp/genes.faa from the folder where you ran DRAM? It looks like maybe it can't find that file. Alternately how much RAM is available on this system? Processing the predicted genes file for mmseqs2 shouldn't take too much RAM but it could explain this issue.
Hi, I have the same issue as commented above: Once I run annotation/working_dir/GF2_mjMb2B_input_S53_megahit.contigs/tmp/genes.faa that's my output: zsh: no such file or directory: annotation/working_dir/GF2_mjMb2B_input_S53_megahit.contigs/tmp/genes.faa
How could I fix this?
Thank you very much for your help!
Hi @franztastic,
What is in the folder annotation/working_dir/GF2_mjMb2B_input_S53_megahit.contigs/tmp/? Were any errors or warning raised before this? Also what version of DRAM are you running (you can run DRAM-setup.py version to get this information).
Mike
Hi @shafferm, thank you very much for answering i have the same errors as @cflores10.
DRAM.py annotate -i './VirSorter/virsorter-out/Predicted_viral_sequences/*.fasta' -o annotation
6 fastas found
2021-09-02 19:41:36.916680: Annotation started
0:00:00.027491: Retrieved database locations and descriptions
0:00:00.027555: Annotating VIRSorter_cat-1
0:00:00.312119: Turning genes from prodigal to mmseqs2 db
0:00:02.330967: Getting hits from kofam
0:01:35.660939: Getting forward best hits from peptidase
Traceback (most recent call last):
File "/data/vpf/Laura/anaconda3/envs/DRAM/bin/DRAM.py", line 168, in
args.func(**args_dict)
File "/data/vpf/Laura/anaconda3/envs/DRAM/lib/python3.9/site-packages/mag_annotator/annotate_bins.py", line 967, in annotate_bins_cmd
annotate_bins(fasta_locs, output_dir, min_contig_size, prodigal_mode, trans_table, bit_score_threshold,
File "/data/vpf/Laura/anaconda3/envs/DRAM/lib/python3.9/site-packages/mag_annotator/annotate_bins.py", line 1006, in annotate_bins
all_annotations = annotate_fastas(fasta_locs, output_dir, db_locs, db_handler, min_contig_size, prodigal_mode,
File "/data/vpf/Laura/anaconda3/envs/DRAM/lib/python3.9/site-packages/mag_annotator/annotate_bins.py", line 944, in annotate_fastas
annotations_list.append(annotate_fasta(fasta_loc, fasta_name, fasta_dir, db_locs, db_handler, min_contig_size,
File "/data/vpf/Laura/anaconda3/envs/DRAM/lib/python3.9/site-packages/mag_annotator/annotate_bins.py", line 845, in annotate_fasta
annotations = annotate_orfs(gene_faa, db_locs, tmp_dir, start_time, db_handler, custom_db_locs, bit_score_threshold,
File "/data/vpf/Laura/anaconda3/envs/DRAM/lib/python3.9/site-packages/mag_annotator/annotate_bins.py", line 778, in annotate_orfs
annotation_list.append(do_blast_style_search(query_db, db_locs['peptidase'], tmp_dir,
File "/data/vpf/Laura/anaconda3/envs/DRAM/lib/python3.9/site-packages/mag_annotator/annotate_bins.py", line 663, in do_blast_style_search
forward_hits = get_best_hits(query_db, target_db, working_dir, 'gene', db_name, bit_score_threshold,
File "/data/vpf/Laura/anaconda3/envs/DRAM/lib/python3.9/site-packages/mag_annotator/annotate_bins.py", line 65, in get_best_hits
run_process(['mmseqs', 'search', query_db, target_db, query_target_db, tmp_dir, '--threads', str(threads)],
File "/data/vpf/Laura/anaconda3/envs/DRAM/lib/python3.9/site-packages/mag_annotator/utils.py", line 39, in run_process
return subprocess.run(command, check=check, shell=shell, stdout=subprocess.PIPE,
File "/data/vpf/Laura/anaconda3/envs/DRAM/lib/python3.9/subprocess.py", line 528, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['mmseqs', 'search', 'annotation/working_dir/VIRSorter_cat-1/tmp/gene.mmsdb', '/data/vpf/Laura/anaconda3/envs/DRAM_data/peptidases.20210825.mmsdb', 'annotation/working_dir/VIRSorter_cat-1/tmp/gene_peptidase.mmsdb', 'annotation/working_dir/VIRSorter_cat-1/tmp/tmp', '--threads', '10']' returned non-zero exit status 1.
Also I cannot find anything related to "annotation".
{1} $ DRAM-setup.py version (19:44:58) 1.2.4
That's my version!
Thank you very much for your help! Laura
So the problem is that this command mmseqs search annotation/working_dir/VIRSorter_cat-1/tmp/gene.mmsdb /data/vpf/Laura/anaconda3/envs/DRAM_data/peptidases.20210825.mmsdb annotation/working_dir/VIRSorter_cat-1/tmp/gene_peptidase.mmsdb annotation/working_dir/VIRSorter_cat-1/tmp/tmp --threads 10 is failing for an unknown reason. Typical causes are that a past run left some output files or some input file does not exist. You can try and fined the cause by running the above command in your working directory. Or running DRAM.py with the --verbose flag. One of these may produce a more informative error.
Hi, Is it possible that's because there's no "peptidases.20210825.mmsdb"? I have peptidases.20210830 instead... how could I get this other file? Thanks, Laura
I have uploaded the database config, so don't need an answer! Thank you! :)