[2024-01-24 15:18:19,596] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:19,598] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:19,598] [INFO] DQC Reference Directory: /var/lib/cwl/stga4983049-e6d4-4ff6-8599-c047b4589c9b/dqc_reference
[2024-01-24 15:18:20,787] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:20,788] [INFO] Task started: Prodigal
[2024-01-24 15:18:20,788] [INFO] Running command: gunzip -c /var/lib/cwl/stgd41d4cec-7c6d-42b9-9943-af9204d92d7d/GCF_004355185.1_ASM435518v1_genomic.fna.gz | prodigal -d GCF_004355185.1_ASM435518v1_genomic.fna/cds.fna -a GCF_004355185.1_ASM435518v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:18:46,838] [INFO] Task succeeded: Prodigal
[2024-01-24 15:18:46,838] [INFO] Task started: HMMsearch
[2024-01-24 15:18:46,838] [INFO] Running command: hmmsearch --tblout GCF_004355185.1_ASM435518v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga4983049-e6d4-4ff6-8599-c047b4589c9b/dqc_reference/reference_markers.hmm GCF_004355185.1_ASM435518v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:18:47,115] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:18:47,118] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgd41d4cec-7c6d-42b9-9943-af9204d92d7d/GCF_004355185.1_ASM435518v1_genomic.fna.gz]
[2024-01-24 15:18:47,169] [INFO] Query marker FASTA was written to GCF_004355185.1_ASM435518v1_genomic.fna/markers.fasta
[2024-01-24 15:18:47,170] [INFO] Task started: Blastn
[2024-01-24 15:18:47,170] [INFO] Running command: blastn -query GCF_004355185.1_ASM435518v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga4983049-e6d4-4ff6-8599-c047b4589c9b/dqc_reference/reference_markers.fasta -out GCF_004355185.1_ASM435518v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:47,794] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:47,798] [INFO] Selected 14 target genomes.
[2024-01-24 15:18:47,798] [INFO] Target genome list was writen to GCF_004355185.1_ASM435518v1_genomic.fna/target_genomes.txt
[2024-01-24 15:18:47,806] [INFO] Task started: fastANI
[2024-01-24 15:18:47,807] [INFO] Running command: fastANI --query /var/lib/cwl/stgd41d4cec-7c6d-42b9-9943-af9204d92d7d/GCF_004355185.1_ASM435518v1_genomic.fna.gz --refList GCF_004355185.1_ASM435518v1_genomic.fna/target_genomes.txt --output GCF_004355185.1_ASM435518v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:19:03,072] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:03,072] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga4983049-e6d4-4ff6-8599-c047b4589c9b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:19:03,073] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga4983049-e6d4-4ff6-8599-c047b4589c9b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:19:03,085] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:19:03,085] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:19:03,086] [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
Hymenobacter radiodurans	strain=17J36-26	GCA_004355185.1	2496028	2496028	type	True	100.0	1639	1639	95	conclusive
Hymenobacter qilianensis	strain=CGMCC 1.12720	GCA_014638675.1	1385715	1385715	type	True	86.1531	1369	1639	95	below_threshold
Hymenobacter qilianensis	strain=JCM 19763	GCA_014489555.1	1385715	1385715	type	True	86.1186	1382	1639	95	below_threshold
Hymenobacter roseosalivarius	strain=DSM 11622	GCA_900176135.1	89967	89967	type	True	83.8238	1140	1639	95	below_threshold
Hymenobacter metallicola	strain=9PBR-1	GCA_004745645.1	2563114	2563114	type	True	78.1914	559	1639	95	below_threshold
Hymenobacter daecheongensis	strain=DSM 21074	GCA_900141805.1	496053	496053	type	True	78.1483	534	1639	95	below_threshold
Hymenobacter telluris	strain=BT186	GCA_017313265.1	2816474	2816474	type	True	78.1199	523	1639	95	below_threshold
Hymenobacter guriensis	strain=BT594	GCA_015773195.1	2793065	2793065	type	True	78.1147	480	1639	95	below_threshold
Hymenobacter psychrotolerans	strain=DSM 18569	GCA_900142395.1	344998	344998	type	True	78.0961	521	1639	95	below_threshold
Hymenobacter duratus	strain=BT646	GCA_014698995.1	2771356	2771356	type	True	78.0504	500	1639	95	below_threshold
Hymenobacter cavernae	strain=CGMCC 1.15197	GCA_014641455.1	2044852	2044852	type	True	78.0089	531	1639	95	below_threshold
Hymenobacter fodinae	strain=92R-1	GCA_004745825.1	2510796	2510796	type	True	77.8761	516	1639	95	below_threshold
Hymenobacter jejuensis	strain=17J68-5	GCA_006337165.1	2502781	2502781	type	True	77.8389	538	1639	95	below_threshold
Hymenobacter armeniacus	strain=BT189	GCA_014699055.1	2771358	2771358	type	True	77.4587	424	1639	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:19:03,087] [INFO] DFAST Taxonomy check result was written to GCF_004355185.1_ASM435518v1_genomic.fna/tc_result.tsv
[2024-01-24 15:19:03,088] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:19:03,088] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:19:03,088] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga4983049-e6d4-4ff6-8599-c047b4589c9b/dqc_reference/checkm_data
[2024-01-24 15:19:03,089] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:19:03,137] [INFO] Task started: CheckM
[2024-01-24 15:19:03,137] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004355185.1_ASM435518v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004355185.1_ASM435518v1_genomic.fna/checkm_input GCF_004355185.1_ASM435518v1_genomic.fna/checkm_result
[2024-01-24 15:20:13,104] [INFO] Task succeeded: CheckM
[2024-01-24 15:20:13,105] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:20:13,135] [INFO] ===== Completeness check finished =====
[2024-01-24 15:20:13,135] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:20:13,136] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004355185.1_ASM435518v1_genomic.fna/markers.fasta)
[2024-01-24 15:20:13,136] [INFO] Task started: Blastn
[2024-01-24 15:20:13,136] [INFO] Running command: blastn -query GCF_004355185.1_ASM435518v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga4983049-e6d4-4ff6-8599-c047b4589c9b/dqc_reference/reference_markers_gtdb.fasta -out GCF_004355185.1_ASM435518v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:20:14,024] [INFO] Task succeeded: Blastn
[2024-01-24 15:20:14,028] [INFO] Selected 10 target genomes.
[2024-01-24 15:20:14,028] [INFO] Target genome list was writen to GCF_004355185.1_ASM435518v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:20:14,052] [INFO] Task started: fastANI
[2024-01-24 15:20:14,052] [INFO] Running command: fastANI --query /var/lib/cwl/stgd41d4cec-7c6d-42b9-9943-af9204d92d7d/GCF_004355185.1_ASM435518v1_genomic.fna.gz --refList GCF_004355185.1_ASM435518v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004355185.1_ASM435518v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:20:24,756] [INFO] Task succeeded: fastANI
[2024-01-24 15:20:24,772] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:20:24,773] [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_004355185.1	s__Hymenobacter radiodurans	100.0	1639	1639	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	96.17	96.17	0.96	0.96	2	conclusive
GCF_014333585.1	s__Hymenobacter sp014333585	87.17	1379	1639	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014489555.1	s__Hymenobacter qilianensis	86.1161	1384	1639	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	99.95	99.95	1.00	1.00	2	-
GCF_900176135.1	s__Hymenobacter roseosalivarius	83.8403	1138	1639	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004745645.1	s__Hymenobacter sp004745645	78.1846	560	1639	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900141805.1	s__Hymenobacter daecheongensis	78.1413	535	1639	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142395.1	s__Hymenobacter psychrotolerans	78.1115	518	1639	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001280305.1	s__Hymenobacter sp001280305	78.1016	461	1639	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018145755.1	s__Hymenobacter sp018145755	78.0366	502	1639	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_006337165.1	s__Hymenobacter jejuensis	77.8731	537	1639	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	97.30	97.30	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2024-01-24 15:20:24,775] [INFO] GTDB search result was written to GCF_004355185.1_ASM435518v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:20:24,776] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:20:24,780] [INFO] DFAST_QC result json was written to GCF_004355185.1_ASM435518v1_genomic.fna/dqc_result.json
[2024-01-24 15:20:24,780] [INFO] DFAST_QC completed!
[2024-01-24 15:20:24,780] [INFO] Total running time: 0h2m5s