[2024-01-24 12:14:48,383] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:48,385] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:48,385] [INFO] DQC Reference Directory: /var/lib/cwl/stgb6628b88-4c50-4a21-be0b-ed2b325aecee/dqc_reference
[2024-01-24 12:14:49,662] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:49,663] [INFO] Task started: Prodigal
[2024-01-24 12:14:49,664] [INFO] Running command: gunzip -c /var/lib/cwl/stga8b56088-f464-466c-8804-9cb09575e46c/GCF_003966335.1_ASM396633v1_genomic.fna.gz | prodigal -d GCF_003966335.1_ASM396633v1_genomic.fna/cds.fna -a GCF_003966335.1_ASM396633v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:15:02,450] [INFO] Task succeeded: Prodigal
[2024-01-24 12:15:02,450] [INFO] Task started: HMMsearch
[2024-01-24 12:15:02,450] [INFO] Running command: hmmsearch --tblout GCF_003966335.1_ASM396633v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb6628b88-4c50-4a21-be0b-ed2b325aecee/dqc_reference/reference_markers.hmm GCF_003966335.1_ASM396633v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:15:02,701] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:15:02,703] [INFO] Found 6/6 markers.
[2024-01-24 12:15:02,737] [INFO] Query marker FASTA was written to GCF_003966335.1_ASM396633v1_genomic.fna/markers.fasta
[2024-01-24 12:15:02,738] [INFO] Task started: Blastn
[2024-01-24 12:15:02,738] [INFO] Running command: blastn -query GCF_003966335.1_ASM396633v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb6628b88-4c50-4a21-be0b-ed2b325aecee/dqc_reference/reference_markers.fasta -out GCF_003966335.1_ASM396633v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:03,379] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:03,386] [INFO] Selected 13 target genomes.
[2024-01-24 12:15:03,387] [INFO] Target genome list was writen to GCF_003966335.1_ASM396633v1_genomic.fna/target_genomes.txt
[2024-01-24 12:15:03,392] [INFO] Task started: fastANI
[2024-01-24 12:15:03,393] [INFO] Running command: fastANI --query /var/lib/cwl/stga8b56088-f464-466c-8804-9cb09575e46c/GCF_003966335.1_ASM396633v1_genomic.fna.gz --refList GCF_003966335.1_ASM396633v1_genomic.fna/target_genomes.txt --output GCF_003966335.1_ASM396633v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:11,583] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:11,584] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb6628b88-4c50-4a21-be0b-ed2b325aecee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:11,584] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb6628b88-4c50-4a21-be0b-ed2b325aecee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:11,592] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:15:11,592] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:15:11,592] [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
Nonlabens ponticola	strain=MJ115	GCA_003966335.1	2496866	2496866	type	True	100.0	953	957	95	conclusive
Nonlabens agnitus	strain=JCM 17109	GCA_002994045.1	870484	870484	type	True	78.2241	313	957	95	below_threshold
Nonlabens marinus	strain=S1-08	GCA_000831385.1	930802	930802	type	True	78.1903	255	957	95	below_threshold
Nonlabens dokdonensis	strain=DSM 17205	GCA_003254015.1	328515	328515	type	True	77.9736	156	957	95	below_threshold
Nonlabens dokdonensis	strain=DSW-6	GCA_000332115.1	328515	328515	type	True	77.8743	156	957	95	below_threshold
Nonlabens antarcticus	strain=JCM 14068	GCA_015356755.1	392714	392714	type	True	77.526	218	957	95	below_threshold
Nonlabens spongiae	strain=JCM 13191	GCA_002117125.1	331648	331648	type	True	77.4063	134	957	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:11,595] [INFO] DFAST Taxonomy check result was written to GCF_003966335.1_ASM396633v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:11,596] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:11,596] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:11,596] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb6628b88-4c50-4a21-be0b-ed2b325aecee/dqc_reference/checkm_data
[2024-01-24 12:15:11,597] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:11,626] [INFO] Task started: CheckM
[2024-01-24 12:15:11,627] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003966335.1_ASM396633v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003966335.1_ASM396633v1_genomic.fna/checkm_input GCF_003966335.1_ASM396633v1_genomic.fna/checkm_result
[2024-01-24 12:15:50,772] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:50,773] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:50,794] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:50,794] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:50,794] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003966335.1_ASM396633v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:50,794] [INFO] Task started: Blastn
[2024-01-24 12:15:50,794] [INFO] Running command: blastn -query GCF_003966335.1_ASM396633v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb6628b88-4c50-4a21-be0b-ed2b325aecee/dqc_reference/reference_markers_gtdb.fasta -out GCF_003966335.1_ASM396633v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:51,580] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:51,583] [INFO] Selected 13 target genomes.
[2024-01-24 12:15:51,584] [INFO] Target genome list was writen to GCF_003966335.1_ASM396633v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:51,591] [INFO] Task started: fastANI
[2024-01-24 12:15:51,592] [INFO] Running command: fastANI --query /var/lib/cwl/stga8b56088-f464-466c-8804-9cb09575e46c/GCF_003966335.1_ASM396633v1_genomic.fna.gz --refList GCF_003966335.1_ASM396633v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003966335.1_ASM396633v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:58,346] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:58,357] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:15:58,357] [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
GCF_003966335.1	s__Nonlabens ponticola	100.0	954	957	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001413925.1	s__Nonlabens sp001413925	78.2983	315	957	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000831385.1	s__Nonlabens marinus	78.2552	256	957	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002994045.1	s__Nonlabens agnitus	78.2113	314	957	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101765.1	s__Nonlabens sp900101765	78.0068	296	957	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000332115.1	s__Nonlabens dokdonensis	77.7826	154	957	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002831625.1	s__Nonlabens sp002831625	77.7408	144	957	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012974865.1	s__Nonlabens sp012974865	77.5507	141	957	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002117125.1	s__Nonlabens spongiae	77.4063	134	957	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002162835.1	s__Nonlabens dokdonensis_B	77.307	143	957	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000755285.1	s__Nonlabens ulvanivorans_A	77.2458	146	957	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	97.55	97.55	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:15:58,359] [INFO] GTDB search result was written to GCF_003966335.1_ASM396633v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:58,359] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:58,362] [INFO] DFAST_QC result json was written to GCF_003966335.1_ASM396633v1_genomic.fna/dqc_result.json
[2024-01-24 12:15:58,363] [INFO] DFAST_QC completed!
[2024-01-24 12:15:58,363] [INFO] Total running time: 0h1m10s