[2024-01-24 10:47:24,450] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:24,455] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:24,456] [INFO] DQC Reference Directory: /var/lib/cwl/stgf7ba5854-d829-447a-bfbc-a61288d9ee85/dqc_reference
[2024-01-24 10:47:26,484] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:26,485] [INFO] Task started: Prodigal
[2024-01-24 10:47:26,485] [INFO] Running command: gunzip -c /var/lib/cwl/stg94634032-8a2b-435d-aa8b-15e444938c16/GCF_014489555.1_ASM1448955v1_genomic.fna.gz | prodigal -d GCF_014489555.1_ASM1448955v1_genomic.fna/cds.fna -a GCF_014489555.1_ASM1448955v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:53,163] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:53,164] [INFO] Task started: HMMsearch
[2024-01-24 10:47:53,164] [INFO] Running command: hmmsearch --tblout GCF_014489555.1_ASM1448955v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf7ba5854-d829-447a-bfbc-a61288d9ee85/dqc_reference/reference_markers.hmm GCF_014489555.1_ASM1448955v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:53,449] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:53,450] [INFO] Found 6/6 markers.
[2024-01-24 10:47:53,498] [INFO] Query marker FASTA was written to GCF_014489555.1_ASM1448955v1_genomic.fna/markers.fasta
[2024-01-24 10:47:53,499] [INFO] Task started: Blastn
[2024-01-24 10:47:53,499] [INFO] Running command: blastn -query GCF_014489555.1_ASM1448955v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf7ba5854-d829-447a-bfbc-a61288d9ee85/dqc_reference/reference_markers.fasta -out GCF_014489555.1_ASM1448955v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:54,129] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:54,136] [INFO] Selected 16 target genomes.
[2024-01-24 10:47:54,137] [INFO] Target genome list was writen to GCF_014489555.1_ASM1448955v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:54,144] [INFO] Task started: fastANI
[2024-01-24 10:47:54,144] [INFO] Running command: fastANI --query /var/lib/cwl/stg94634032-8a2b-435d-aa8b-15e444938c16/GCF_014489555.1_ASM1448955v1_genomic.fna.gz --refList GCF_014489555.1_ASM1448955v1_genomic.fna/target_genomes.txt --output GCF_014489555.1_ASM1448955v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:13,661] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:13,662] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf7ba5854-d829-447a-bfbc-a61288d9ee85/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:13,663] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf7ba5854-d829-447a-bfbc-a61288d9ee85/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:13,680] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 10:48:13,680] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:48:13,681] [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 qilianensis	strain=JCM 19763	GCA_014489555.1	1385715	1385715	type	True	100.0	1673	1673	95	conclusive
Hymenobacter qilianensis	strain=CGMCC 1.12720	GCA_014638675.1	1385715	1385715	type	True	99.9456	1661	1673	95	conclusive
Hymenobacter radiodurans	strain=17J36-26	GCA_004355185.1	2496028	2496028	type	True	86.1594	1390	1673	95	below_threshold
Hymenobacter roseosalivarius	strain=DSM 11622	GCA_900176135.1	89967	89967	type	True	84.6683	1155	1673	95	below_threshold
Hymenobacter psychrotolerans	strain=DSM 18569	GCA_900142395.1	344998	344998	type	True	78.7974	602	1673	95	below_threshold
Hymenobacter daecheongensis	strain=DSM 21074	GCA_900141805.1	496053	496053	type	True	78.7784	607	1673	95	below_threshold
Hymenobacter metallicola	strain=9PBR-1	GCA_004745645.1	2563114	2563114	type	True	78.7244	646	1673	95	below_threshold
Hymenobacter duratus	strain=BT646	GCA_014698995.1	2771356	2771356	type	True	78.4873	590	1673	95	below_threshold
Hymenobacter chitinivorans	strain=DSM 11115	GCA_002797555.1	89969	89969	type	True	78.4078	716	1673	95	below_threshold
Hymenobacter guriensis	strain=BT594	GCA_015773195.1	2793065	2793065	type	True	78.4048	545	1673	95	below_threshold
Hymenobacter telluris	strain=BT186	GCA_017313265.1	2816474	2816474	type	True	78.2788	621	1673	95	below_threshold
Hymenobacter cavernae	strain=CGMCC 1.15197	GCA_014641455.1	2044852	2044852	type	True	78.2143	588	1673	95	below_threshold
Hymenobacter norwichensis	strain=DSM 15439	GCA_000420705.1	223903	223903	type	True	78.0732	538	1673	95	below_threshold
Hymenobacter glacialis	strain=CCM 8648	GCA_001816165.1	1908236	1908236	type	True	77.8362	438	1673	95	below_threshold
Hymenobacter armeniacus	strain=BT189	GCA_014699055.1	2771358	2771358	type	True	77.6968	509	1673	95	below_threshold
Hymenobacter montanus	strain=BT664	GCA_014699115.1	2771359	2771359	type	True	77.1219	353	1673	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:13,682] [INFO] DFAST Taxonomy check result was written to GCF_014489555.1_ASM1448955v1_genomic.fna/tc_result.tsv
[2024-01-24 10:48:13,682] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:13,683] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:13,683] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf7ba5854-d829-447a-bfbc-a61288d9ee85/dqc_reference/checkm_data
[2024-01-24 10:48:13,684] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:13,732] [INFO] Task started: CheckM
[2024-01-24 10:48:13,732] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014489555.1_ASM1448955v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014489555.1_ASM1448955v1_genomic.fna/checkm_input GCF_014489555.1_ASM1448955v1_genomic.fna/checkm_result
[2024-01-24 10:49:24,303] [INFO] Task succeeded: CheckM
[2024-01-24 10:49:24,304] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:49:24,329] [INFO] ===== Completeness check finished =====
[2024-01-24 10:49:24,329] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:49:24,329] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014489555.1_ASM1448955v1_genomic.fna/markers.fasta)
[2024-01-24 10:49:24,330] [INFO] Task started: Blastn
[2024-01-24 10:49:24,330] [INFO] Running command: blastn -query GCF_014489555.1_ASM1448955v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf7ba5854-d829-447a-bfbc-a61288d9ee85/dqc_reference/reference_markers_gtdb.fasta -out GCF_014489555.1_ASM1448955v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:49:25,157] [INFO] Task succeeded: Blastn
[2024-01-24 10:49:25,161] [INFO] Selected 11 target genomes.
[2024-01-24 10:49:25,162] [INFO] Target genome list was writen to GCF_014489555.1_ASM1448955v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:49:25,171] [INFO] Task started: fastANI
[2024-01-24 10:49:25,172] [INFO] Running command: fastANI --query /var/lib/cwl/stg94634032-8a2b-435d-aa8b-15e444938c16/GCF_014489555.1_ASM1448955v1_genomic.fna.gz --refList GCF_014489555.1_ASM1448955v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014489555.1_ASM1448955v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:49:37,235] [INFO] Task succeeded: fastANI
[2024-01-24 10:49:37,249] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:49:37,249] [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_014489555.1	s__Hymenobacter qilianensis	100.0	1673	1673	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	99.95	99.95	1.00	1.00	2	conclusive
GCF_014333585.1	s__Hymenobacter sp014333585	89.3855	1405	1673	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004355185.1	s__Hymenobacter radiodurans	86.1594	1390	1673	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	96.17	96.17	0.96	0.96	2	-
GCF_900176135.1	s__Hymenobacter roseosalivarius	84.6683	1155	1673	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	78.779	607	1673	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	78.7308	645	1673	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002797555.1	s__Hymenobacter chitinivorans	78.4052	717	1673	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000801315.1	s__Hymenobacter sp000801315	78.3986	573	1673	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634355.1	s__Hymenobacter sp003634355	78.2582	507	1673	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000420705.1	s__Hymenobacter norwichensis	78.0627	539	1673	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001816165.1	s__Hymenobacter glacialis	77.8139	441	1673	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:49:37,250] [INFO] GTDB search result was written to GCF_014489555.1_ASM1448955v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:49:37,251] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:49:37,257] [INFO] DFAST_QC result json was written to GCF_014489555.1_ASM1448955v1_genomic.fna/dqc_result.json
[2024-01-24 10:49:37,257] [INFO] DFAST_QC completed!
[2024-01-24 10:49:37,257] [INFO] Total running time: 0h2m13s