[2024-01-25 18:10:35,920] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:10:35,922] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:10:35,922] [INFO] DQC Reference Directory: /var/lib/cwl/stga3a95085-54ad-4ebb-995b-c1a69a35ab02/dqc_reference
[2024-01-25 18:10:37,050] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:10:37,051] [INFO] Task started: Prodigal
[2024-01-25 18:10:37,051] [INFO] Running command: gunzip -c /var/lib/cwl/stgdc3d992f-3370-42f4-8938-d7ac0fb546ee/GCF_014333615.1_ASM1433361v1_genomic.fna.gz | prodigal -d GCF_014333615.1_ASM1433361v1_genomic.fna/cds.fna -a GCF_014333615.1_ASM1433361v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:11:00,968] [INFO] Task succeeded: Prodigal
[2024-01-25 18:11:00,968] [INFO] Task started: HMMsearch
[2024-01-25 18:11:00,968] [INFO] Running command: hmmsearch --tblout GCF_014333615.1_ASM1433361v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga3a95085-54ad-4ebb-995b-c1a69a35ab02/dqc_reference/reference_markers.hmm GCF_014333615.1_ASM1433361v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:11:01,207] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:11:01,208] [INFO] Found 6/6 markers.
[2024-01-25 18:11:01,248] [INFO] Query marker FASTA was written to GCF_014333615.1_ASM1433361v1_genomic.fna/markers.fasta
[2024-01-25 18:11:01,249] [INFO] Task started: Blastn
[2024-01-25 18:11:01,249] [INFO] Running command: blastn -query GCF_014333615.1_ASM1433361v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga3a95085-54ad-4ebb-995b-c1a69a35ab02/dqc_reference/reference_markers.fasta -out GCF_014333615.1_ASM1433361v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:11:01,826] [INFO] Task succeeded: Blastn
[2024-01-25 18:11:01,829] [INFO] Selected 17 target genomes.
[2024-01-25 18:11:01,829] [INFO] Target genome list was writen to GCF_014333615.1_ASM1433361v1_genomic.fna/target_genomes.txt
[2024-01-25 18:11:01,835] [INFO] Task started: fastANI
[2024-01-25 18:11:01,835] [INFO] Running command: fastANI --query /var/lib/cwl/stgdc3d992f-3370-42f4-8938-d7ac0fb546ee/GCF_014333615.1_ASM1433361v1_genomic.fna.gz --refList GCF_014333615.1_ASM1433361v1_genomic.fna/target_genomes.txt --output GCF_014333615.1_ASM1433361v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:11:20,959] [INFO] Task succeeded: fastANI
[2024-01-25 18:11:20,960] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga3a95085-54ad-4ebb-995b-c1a69a35ab02/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:11:20,960] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga3a95085-54ad-4ebb-995b-c1a69a35ab02/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:11:20,970] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:11:20,970] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:11:20,970] [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 citatus	strain=BT507	GCA_014333615.1	2763506	2763506	type	True	100.0	1672	1675	95	conclusive
Hymenobacter profundi	strain=M2	GCA_019334315.1	1982110	1982110	type	True	88.3036	1318	1675	95	below_threshold
Hymenobacter psychrotolerans	strain=DSM 18569	GCA_900142395.1	344998	344998	type	True	79.6436	708	1675	95	below_threshold
Hymenobacter aquaticus	strain=JCM 31653	GCA_004765605.1	1867101	1867101	type	True	79.5214	766	1675	95	below_threshold
Hymenobacter telluris	strain=BT186	GCA_017313265.1	2816474	2816474	type	True	79.4361	784	1675	95	below_threshold
Hymenobacter glacieicola	strain=CGMCC 1.12990	GCA_014640315.1	1562124	1562124	type	True	79.3598	709	1675	95	below_threshold
Hymenobacter piscis	strain=NST-14	GCA_018760735.1	2839984	2839984	type	True	79.351	778	1675	95	below_threshold
Hymenobacter perfusus	strain=LMG 26000	GCA_003944765.1	1236770	1236770	type	True	79.3393	763	1675	95	below_threshold
Hymenobacter daecheongensis	strain=DSM 21074	GCA_900141805.1	496053	496053	type	True	79.3123	681	1675	95	below_threshold
Hymenobacter guriensis	strain=BT594	GCA_015773195.1	2793065	2793065	type	True	79.1754	714	1675	95	below_threshold
Hymenobacter persicinus	strain=1-3-3-3	GCA_004167665.1	2025506	2025506	type	True	79.1529	677	1675	95	below_threshold
Hymenobacter chitinivorans	strain=DSM 11115	GCA_002797555.1	89969	89969	type	True	79.0725	759	1675	95	below_threshold
Hymenobacter metallicola	strain=9PBR-1	GCA_004745645.1	2563114	2563114	type	True	78.8761	710	1675	95	below_threshold
Hymenobacter armeniacus	strain=BT189	GCA_014699055.1	2771358	2771358	type	True	78.8704	654	1675	95	below_threshold
Hymenobacter elongatus	strain=JCM 17223	GCA_004745955.1	877208	877208	type	True	78.8505	582	1675	95	below_threshold
Hymenobacter cavernae	strain=CGMCC 1.15197	GCA_014641455.1	2044852	2044852	type	True	78.5655	699	1675	95	below_threshold
Hymenobacter jejuensis	strain=17J68-5	GCA_006337165.1	2502781	2502781	type	True	77.9481	578	1675	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:11:20,974] [INFO] DFAST Taxonomy check result was written to GCF_014333615.1_ASM1433361v1_genomic.fna/tc_result.tsv
[2024-01-25 18:11:20,974] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:11:20,974] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:11:20,975] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga3a95085-54ad-4ebb-995b-c1a69a35ab02/dqc_reference/checkm_data
[2024-01-25 18:11:20,975] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:11:21,037] [INFO] Task started: CheckM
[2024-01-25 18:11:21,038] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014333615.1_ASM1433361v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014333615.1_ASM1433361v1_genomic.fna/checkm_input GCF_014333615.1_ASM1433361v1_genomic.fna/checkm_result
[2024-01-25 18:12:23,524] [INFO] Task succeeded: CheckM
[2024-01-25 18:12:23,526] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:12:23,587] [INFO] ===== Completeness check finished =====
[2024-01-25 18:12:23,587] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:12:23,593] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014333615.1_ASM1433361v1_genomic.fna/markers.fasta)
[2024-01-25 18:12:23,593] [INFO] Task started: Blastn
[2024-01-25 18:12:23,593] [INFO] Running command: blastn -query GCF_014333615.1_ASM1433361v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga3a95085-54ad-4ebb-995b-c1a69a35ab02/dqc_reference/reference_markers_gtdb.fasta -out GCF_014333615.1_ASM1433361v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:12:24,456] [INFO] Task succeeded: Blastn
[2024-01-25 18:12:24,458] [INFO] Selected 18 target genomes.
[2024-01-25 18:12:24,459] [INFO] Target genome list was writen to GCF_014333615.1_ASM1433361v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:12:24,476] [INFO] Task started: fastANI
[2024-01-25 18:12:24,477] [INFO] Running command: fastANI --query /var/lib/cwl/stgdc3d992f-3370-42f4-8938-d7ac0fb546ee/GCF_014333615.1_ASM1433361v1_genomic.fna.gz --refList GCF_014333615.1_ASM1433361v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014333615.1_ASM1433361v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:12:47,152] [INFO] Task succeeded: fastANI
[2024-01-25 18:12:47,163] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:12:47,164] [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_014333615.1	s__Hymenobacter citatus	100.0	1672	1675	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_017589435.1	s__Hymenobacter defluvii	88.4171	1384	1675	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	96.38	96.38	0.86	0.86	2	-
GCF_000737515.1	s__Hymenobacter sp000737515	79.6942	763	1675	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004765605.1	s__Hymenobacter aquaticus	79.4937	769	1675	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199535.1	s__Hymenobacter latericoloratus	79.4364	751	1675	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_017313265.1	s__Hymenobacter sp017313265	79.4347	784	1675	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014640315.1	s__Hymenobacter glacieicola	79.3598	709	1675	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003944765.1	s__Hymenobacter perfusus	79.3357	763	1675	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	79.3149	680	1675	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014333525.1	s__Hymenobacter sp014333525	79.3105	699	1675	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015773195.1	s__Hymenobacter sp015773195	79.1616	717	1675	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004167665.1	s__Hymenobacter persicinus	79.1483	677	1675	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	79.1265	567	1675	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012273015.1	s__Hymenobacter sp012273015	79.1231	635	1675	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	97.59	97.59	0.91	0.91	2	-
GCF_003583925.1	s__Hymenobacter rubripertinctus	79.1122	690	1675	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	79.0781	757	1675	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	78.8797	710	1675	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006337165.1	s__Hymenobacter jejuensis	77.9594	576	1675	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	97.30	97.30	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:12:47,166] [INFO] GTDB search result was written to GCF_014333615.1_ASM1433361v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:12:47,167] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:12:47,170] [INFO] DFAST_QC result json was written to GCF_014333615.1_ASM1433361v1_genomic.fna/dqc_result.json
[2024-01-25 18:12:47,170] [INFO] DFAST_QC completed!
[2024-01-25 18:12:47,170] [INFO] Total running time: 0h2m11s