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WrightonLabCSU / DRAM

Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes
GNU General Public License v3.0
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returned non-zero exit status 1 #63

Closed nduan1 closed 3 years ago

nduan1 commented 3 years ago

Hi,

I got this error, could I have some suggestions? Thank you so much!

(DRAM) -bash-4.2$ DRAM-v.py annotate -i /lustre/haven/proj/UTK0124/ningd/whole_metagenome_2020/dram/virsorter12/M107/M107_virsort12_viralseqs.fa -v /lustre/haven/proj/UTK0124/ningd/whole_metagenome_2020/virsorter_test1/done_psi_v1/output_psi_M107/Metric_files/VIRSorter_affi-contigs.tab -o /lustre/haven/proj/UTK0124/ningd/whole_metagenome_2020/dram/virsorter12/M107/test_annotation --threads 1 2021-02-13 11:00:50.933895: Viral annotation started 0:00:01.816081: Retrieved database locations and descriptions 0:00:01.816280: Annotating VIRSorter_k127_1224637-cat_1 0:00:02.219924: Turning genes from prodigal to mmseqs2 db 0:00:07.580697: Getting hits from kofam Traceback (most recent call last): File "/lustre/haven/proj/UTK0124/conda2/envs/DRAM/bin/DRAM-v.py", line 7, in exec(compile(f.read(), file, 'exec')) File "/lustre/haven/proj/UTK0124/DRAM/scripts/DRAM-v.py", line 139, in args.func(**args_dict) File "/lustre/haven/proj/UTK0124/DRAM/mag_annotator/annotate_vgfs.py", line 361, in annotate_vgfs annotations = annotate_fastas(contig_locs, output_dir, db_locs_anno, db_handler, min_contig_size, prodigal_mode, File "/lustre/haven/proj/UTK0124/DRAM/mag_annotator/annotate_bins.py", line 922, in annotate_fastas annotations_list.append(annotate_fasta(fasta_loc, fasta_name, fasta_dir, db_locs, db_handler, min_contig_size, File "/lustre/haven/proj/UTK0124/DRAM/mag_annotator/annotate_bins.py", line 823, in annotate_fasta annotations = annotate_orfs(gene_faa, db_locs, tmp_dir, start_time, db_handler, custom_db_locs, bit_score_threshold, File "/lustre/haven/proj/UTK0124/DRAM/mag_annotator/annotate_bins.py", line 734, in annotate_orfs annotation_list.append(run_hmmscan_kofam(gene_faa, db_locs['kofam'], tmp_dir, File "/lustre/haven/proj/UTK0124/DRAM/mag_annotator/annotate_bins.py", line 236, in run_hmmscan_kofam run_process(['hmmsearch', '--domtblout', output, '--cpu', str(threads), kofam_hmm, gene_faa], verbose=verbose) File "/lustre/haven/proj/UTK0124/DRAM/mag_annotator/utils.py", line 38, in run_process return subprocess.run(command, check=check, shell=shell, stdout=subprocess.PIPE, File "/lustre/haven/proj/UTK0124/conda2/envs/DRAM/lib/python3.9/subprocess.py", line 524, in run raise CalledProcessError(retcode, process.args, subprocess.CalledProcessError: Command '['hmmsearch', '--domtblout', '/lustre/haven/proj/UTK0124/ningd/whole_metagenome_2020/dram/virsorter12/M107/test_annotation/working_dir/VIRSorter_k127_1224637-cat_1/tmp/kofam_profile.b6', '--cpu', '1', '/lustre/haven/proj/UTK0124/ningd/whole_metagenome_2020/dram/DRAM_data/kofam_profiles.hmm', '/lustre/haven/proj/UTK0124/ningd/whole_metagenome_2020/dram/virsorter12/M107/test_annotation/working_dir/VIRSorter_k127_1224637-cat_1/tmp/genes.faa']' returned non-zero exit status 1.

(DRAM) -bash-4.2$ DRAM-setup.py print_config KEGG db: None KOfam db: /lustre/haven/proj/UTK0124/ningd/whole_metagenome_2020/dram/DRAM_data/kofam_profiles.hmm KOfam KO list: /lustre/haven/proj/UTK0124/ningd/whole_metagenome_2020/dram/DRAM_data/kofam_ko_list.tsv UniRef db: None Pfam db: /lustre/haven/proj/UTK0124/ningd/whole_metagenome_2020/dram/DRAM_data/pfam.mmspro Pfam hmm dat: /lustre/haven/proj/UTK0124/ningd/whole_metagenome_2020/dram/DRAM_data/Pfam-A.hmm.dat.gz dbCAN db: /lustre/haven/proj/UTK0124/ningd/whole_metagenome_2020/dram/DRAM_data/dbCAN-HMMdb-V8.txt dbCAN family activities: /lustre/haven/proj/UTK0124/ningd/whole_metagenome_2020/dram/DRAM_data/CAZyDB.07312019.fam-activities.txt RefSeq Viral db: /lustre/haven/proj/UTK0124/ningd/whole_metagenome_2020/dram/DRAM_data/refseq_viral.20200926.mmsdb MEROPS peptidase db: /lustre/haven/proj/UTK0124/ningd/whole_metagenome_2020/dram/DRAM_data/peptidases.20200926.mmsdb VOGDB db: /lustre/haven/proj/UTK0124/ningd/whole_metagenome_2020/dram/DRAM_data/vog_latest_hmms.txt VOG annotations: /lustre/haven/proj/UTK0124/ningd/whole_metagenome_2020/dram/DRAM_data/vog_annotations_latest.tsv.gz Description db: /lustre/haven/proj/UTK0124/ningd/whole_metagenome_2020/dram/DRAM_data/description_db.sqlite Genome summary form: /lustre/haven/proj/UTK0124/ningd/whole_metagenome_2020/dram/DRAM_data/genome_summary_form.20200926.tsv Module step form: /lustre/haven/proj/UTK0124/ningd/whole_metagenome_2020/dram/DRAM_data/module_step_form.20200926.tsv ETC module database: /lustre/haven/proj/UTK0124/ningd/whole_metagenome_2020/dram/DRAM_data/etc_mdoule_database.20200926.tsv Function heatmap form: /lustre/haven/proj/UTK0124/ningd/whole_metagenome_2020/dram/DRAM_data/function_heatmap_form.20200926.tsv AMG database: /lustre/haven/proj/UTK0124/ningd/whole_metagenome_2020/dram/DRAM_data/amg_database.20200926.tsv

nduan1 commented 3 years ago

(DRAM-new) -bash-4.2$ DRAM-setup.py version 1.1.1

nduan1 commented 3 years ago

I ran this outside of DRAM hmmsearch --domtblout /lustre/haven/proj/UTK0124/ningd/whole_metagenome_2020/dram/test_annotation/working_dir/VIRSorter_k127_1224637-cat_1/tmp/kofam_profile.b6 --cpu 1 /lustre/haven/proj/UTK0124/ningd/whole_metagenome_2020/dram/DRAM_data/kofam_profiles.hmm /lustre/haven/proj/UTK0124/ningd/whole_metagenome_2020/dram/test_annotation/working_dir/VIRSorter_k127_1224637-cat_1/tmp/genes.faa

get this error info

Error: File existence/permissions problem in trying to open HMM file /lustre/haven/proj/UTK0124/ningd/whole_metagenome_2020/dram/DRAM_data/kofam_profiles.hmm. HMM file /lustre/haven/proj/UTK0124/ningd/whole_metagenome_2020/dram/DRAM_data/kofam_profiles.hmm not found (nor an .h3m binary

so I changed the file permission in DRAM_data by chmod u=rwx,g=r,o=r filename

It works!

Ning