[2023-06-07 21:13:40,806] [INFO] DFAST_QC pipeline started.
[2023-06-07 21:13:40,808] [INFO] DFAST_QC version: 0.5.7
[2023-06-07 21:13:40,809] [INFO] DQC Reference Directory: /var/lib/cwl/stg9ca19838-ec5e-49bd-93a1-a4d979699bbb/dqc_reference
[2023-06-07 21:13:42,874] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-07 21:13:42,875] [INFO] Task started: Prodigal
[2023-06-07 21:13:42,876] [INFO] Running command: gunzip -c /var/lib/cwl/stgd2692040-a5df-4537-b207-c01d27be74e0/GCA_947489385.1_ZE-Jul18-34_genomic.fna.gz | prodigal -d GCA_947489385.1_ZE-Jul18-34_genomic.fna/cds.fna -a GCA_947489385.1_ZE-Jul18-34_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-07 21:13:48,630] [INFO] Task succeeded: Prodigal
[2023-06-07 21:13:48,630] [INFO] Task started: HMMsearch
[2023-06-07 21:13:48,630] [INFO] Running command: hmmsearch --tblout GCA_947489385.1_ZE-Jul18-34_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9ca19838-ec5e-49bd-93a1-a4d979699bbb/dqc_reference/reference_markers.hmm GCA_947489385.1_ZE-Jul18-34_genomic.fna/protein.faa > /dev/null
[2023-06-07 21:13:48,838] [INFO] Task succeeded: HMMsearch
[2023-06-07 21:13:48,839] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgd2692040-a5df-4537-b207-c01d27be74e0/GCA_947489385.1_ZE-Jul18-34_genomic.fna.gz]
[2023-06-07 21:13:48,864] [INFO] Query marker FASTA was written to GCA_947489385.1_ZE-Jul18-34_genomic.fna/markers.fasta
[2023-06-07 21:13:48,864] [INFO] Task started: Blastn
[2023-06-07 21:13:48,864] [INFO] Running command: blastn -query GCA_947489385.1_ZE-Jul18-34_genomic.fna/markers.fasta -db /var/lib/cwl/stg9ca19838-ec5e-49bd-93a1-a4d979699bbb/dqc_reference/reference_markers.fasta -out GCA_947489385.1_ZE-Jul18-34_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 21:13:49,340] [INFO] Task succeeded: Blastn
[2023-06-07 21:13:49,349] [INFO] Selected 10 target genomes.
[2023-06-07 21:13:49,349] [INFO] Target genome list was writen to GCA_947489385.1_ZE-Jul18-34_genomic.fna/target_genomes.txt
[2023-06-07 21:13:49,350] [INFO] Task started: fastANI
[2023-06-07 21:13:49,351] [INFO] Running command: fastANI --query /var/lib/cwl/stgd2692040-a5df-4537-b207-c01d27be74e0/GCA_947489385.1_ZE-Jul18-34_genomic.fna.gz --refList GCA_947489385.1_ZE-Jul18-34_genomic.fna/target_genomes.txt --output GCA_947489385.1_ZE-Jul18-34_genomic.fna/fastani_result.tsv --threads 1
[2023-06-07 21:13:55,732] [INFO] Task succeeded: fastANI
[2023-06-07 21:13:55,732] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9ca19838-ec5e-49bd-93a1-a4d979699bbb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-07 21:13:55,733] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9ca19838-ec5e-49bd-93a1-a4d979699bbb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-07 21:13:55,735] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-07 21:13:55,735] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-07 21:13:55,736] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
--------------------------------------------------------------------------------
[2023-06-07 21:13:55,738] [INFO] DFAST Taxonomy check result was written to GCA_947489385.1_ZE-Jul18-34_genomic.fna/tc_result.tsv
[2023-06-07 21:13:55,739] [INFO] ===== Taxonomy check completed =====
[2023-06-07 21:13:55,739] [INFO] ===== Start completeness check using CheckM =====
[2023-06-07 21:13:55,739] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9ca19838-ec5e-49bd-93a1-a4d979699bbb/dqc_reference/checkm_data
[2023-06-07 21:13:55,743] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-07 21:13:55,770] [INFO] Task started: CheckM
[2023-06-07 21:13:55,770] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947489385.1_ZE-Jul18-34_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947489385.1_ZE-Jul18-34_genomic.fna/checkm_input GCA_947489385.1_ZE-Jul18-34_genomic.fna/checkm_result
[2023-06-07 21:14:18,874] [INFO] Task succeeded: CheckM
[2023-06-07 21:14:18,876] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 36.93%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-07 21:14:18,896] [INFO] ===== Completeness check finished =====
[2023-06-07 21:14:18,897] [INFO] ===== Start GTDB Search =====
[2023-06-07 21:14:18,897] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947489385.1_ZE-Jul18-34_genomic.fna/markers.fasta)
[2023-06-07 21:14:18,897] [INFO] Task started: Blastn
[2023-06-07 21:14:18,898] [INFO] Running command: blastn -query GCA_947489385.1_ZE-Jul18-34_genomic.fna/markers.fasta -db /var/lib/cwl/stg9ca19838-ec5e-49bd-93a1-a4d979699bbb/dqc_reference/reference_markers_gtdb.fasta -out GCA_947489385.1_ZE-Jul18-34_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 21:14:19,342] [INFO] Task succeeded: Blastn
[2023-06-07 21:14:19,347] [INFO] Selected 17 target genomes.
[2023-06-07 21:14:19,347] [INFO] Target genome list was writen to GCA_947489385.1_ZE-Jul18-34_genomic.fna/target_genomes_gtdb.txt
[2023-06-07 21:14:19,411] [INFO] Task started: fastANI
[2023-06-07 21:14:19,411] [INFO] Running command: fastANI --query /var/lib/cwl/stgd2692040-a5df-4537-b207-c01d27be74e0/GCA_947489385.1_ZE-Jul18-34_genomic.fna.gz --refList GCA_947489385.1_ZE-Jul18-34_genomic.fna/target_genomes_gtdb.txt --output GCA_947489385.1_ZE-Jul18-34_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-07 21:14:28,744] [INFO] Task succeeded: fastANI
[2023-06-07 21:14:28,750] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-07 21:14:28,750] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCA_014379625.1	s__Ferruginibacter sp014379625	76.4983	56	484	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014377975.1	s__Ferruginibacter sp014377975	76.4629	50	484	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-07 21:14:28,752] [INFO] GTDB search result was written to GCA_947489385.1_ZE-Jul18-34_genomic.fna/result_gtdb.tsv
[2023-06-07 21:14:28,753] [INFO] ===== GTDB Search completed =====
[2023-06-07 21:14:28,756] [INFO] DFAST_QC result json was written to GCA_947489385.1_ZE-Jul18-34_genomic.fna/dqc_result.json
[2023-06-07 21:14:28,756] [INFO] DFAST_QC completed!
[2023-06-07 21:14:28,756] [INFO] Total running time: 0h0m48s