[2024-01-24 13:55:47,977] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:47,980] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:47,980] [INFO] DQC Reference Directory: /var/lib/cwl/stgd3fd53bb-edd4-4f01-bb1f-0986c45e1029/dqc_reference
[2024-01-24 13:55:49,229] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:49,229] [INFO] Task started: Prodigal
[2024-01-24 13:55:49,230] [INFO] Running command: gunzip -c /var/lib/cwl/stg1d31ae15-d5d7-4f88-8105-b22ec86894ae/GCF_022921095.1_ASM2292109v1_genomic.fna.gz | prodigal -d GCF_022921095.1_ASM2292109v1_genomic.fna/cds.fna -a GCF_022921095.1_ASM2292109v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:56:18,802] [INFO] Task succeeded: Prodigal
[2024-01-24 13:56:18,803] [INFO] Task started: HMMsearch
[2024-01-24 13:56:18,803] [INFO] Running command: hmmsearch --tblout GCF_022921095.1_ASM2292109v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd3fd53bb-edd4-4f01-bb1f-0986c45e1029/dqc_reference/reference_markers.hmm GCF_022921095.1_ASM2292109v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:56:19,098] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:56:19,099] [INFO] Found 6/6 markers.
[2024-01-24 13:56:19,143] [INFO] Query marker FASTA was written to GCF_022921095.1_ASM2292109v1_genomic.fna/markers.fasta
[2024-01-24 13:56:19,143] [INFO] Task started: Blastn
[2024-01-24 13:56:19,143] [INFO] Running command: blastn -query GCF_022921095.1_ASM2292109v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd3fd53bb-edd4-4f01-bb1f-0986c45e1029/dqc_reference/reference_markers.fasta -out GCF_022921095.1_ASM2292109v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:19,786] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:19,790] [INFO] Selected 16 target genomes.
[2024-01-24 13:56:19,790] [INFO] Target genome list was writen to GCF_022921095.1_ASM2292109v1_genomic.fna/target_genomes.txt
[2024-01-24 13:56:19,800] [INFO] Task started: fastANI
[2024-01-24 13:56:19,801] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d31ae15-d5d7-4f88-8105-b22ec86894ae/GCF_022921095.1_ASM2292109v1_genomic.fna.gz --refList GCF_022921095.1_ASM2292109v1_genomic.fna/target_genomes.txt --output GCF_022921095.1_ASM2292109v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:56:37,254] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:37,255] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd3fd53bb-edd4-4f01-bb1f-0986c45e1029/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:56:37,256] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd3fd53bb-edd4-4f01-bb1f-0986c45e1029/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:56:37,273] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:56:37,273] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:56:37,274] [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	86.2385	1371	1759	95	below_threshold
Hymenobacter profundi	strain=M2	GCA_019334315.1	1982110	1982110	type	True	85.9173	1277	1759	95	below_threshold
Hymenobacter psychrotolerans	strain=DSM 18569	GCA_900142395.1	344998	344998	type	True	79.0953	666	1759	95	below_threshold
Hymenobacter telluris	strain=BT186	GCA_017313265.1	2816474	2816474	type	True	78.9493	780	1759	95	below_threshold
Hymenobacter piscis	strain=NST-14	GCA_018760735.1	2839984	2839984	type	True	78.9463	674	1759	95	below_threshold
Hymenobacter aquaticus	strain=JCM 31653	GCA_004765605.1	1867101	1867101	type	True	78.8787	749	1759	95	below_threshold
Hymenobacter perfusus	strain=LMG 26000	GCA_003944765.1	1236770	1236770	type	True	78.8089	701	1759	95	below_threshold
Hymenobacter glacieicola	strain=CGMCC 1.12990	GCA_014640315.1	1562124	1562124	type	True	78.7178	667	1759	95	below_threshold
Hymenobacter guriensis	strain=BT594	GCA_015773195.1	2793065	2793065	type	True	78.6575	675	1759	95	below_threshold
Hymenobacter daecheongensis	strain=DSM 21074	GCA_900141805.1	496053	496053	type	True	78.6345	646	1759	95	below_threshold
Hymenobacter persicinus	strain=1-3-3-3	GCA_004167665.1	2025506	2025506	type	True	78.6021	646	1759	95	below_threshold
Hymenobacter chitinivorans	strain=DSM 11115	GCA_002797555.1	89969	89969	type	True	78.4544	699	1759	95	below_threshold
Hymenobacter metallicola	strain=9PBR-1	GCA_004745645.1	2563114	2563114	type	True	78.4355	649	1759	95	below_threshold
Hymenobacter gummosus	strain=KCTC 52166	GCA_003970915.1	1776032	1776032	type	True	78.294	714	1759	95	below_threshold
Hymenobacter armeniacus	strain=BT189	GCA_014699055.1	2771358	2771358	type	True	78.1259	625	1759	95	below_threshold
Hymenobacter cavernae	strain=CGMCC 1.15197	GCA_014641455.1	2044852	2044852	type	True	78.1184	644	1759	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:56:37,276] [INFO] DFAST Taxonomy check result was written to GCF_022921095.1_ASM2292109v1_genomic.fna/tc_result.tsv
[2024-01-24 13:56:37,276] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:56:37,277] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:56:37,277] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd3fd53bb-edd4-4f01-bb1f-0986c45e1029/dqc_reference/checkm_data
[2024-01-24 13:56:37,279] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:56:37,331] [INFO] Task started: CheckM
[2024-01-24 13:56:37,331] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022921095.1_ASM2292109v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022921095.1_ASM2292109v1_genomic.fna/checkm_input GCF_022921095.1_ASM2292109v1_genomic.fna/checkm_result
[2024-01-24 13:57:54,214] [INFO] Task succeeded: CheckM
[2024-01-24 13:57:54,215] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:57:54,247] [INFO] ===== Completeness check finished =====
[2024-01-24 13:57:54,248] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:57:54,248] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022921095.1_ASM2292109v1_genomic.fna/markers.fasta)
[2024-01-24 13:57:54,249] [INFO] Task started: Blastn
[2024-01-24 13:57:54,249] [INFO] Running command: blastn -query GCF_022921095.1_ASM2292109v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd3fd53bb-edd4-4f01-bb1f-0986c45e1029/dqc_reference/reference_markers_gtdb.fasta -out GCF_022921095.1_ASM2292109v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:55,211] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:55,215] [INFO] Selected 19 target genomes.
[2024-01-24 13:57:55,216] [INFO] Target genome list was writen to GCF_022921095.1_ASM2292109v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:57:55,249] [INFO] Task started: fastANI
[2024-01-24 13:57:55,249] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d31ae15-d5d7-4f88-8105-b22ec86894ae/GCF_022921095.1_ASM2292109v1_genomic.fna.gz --refList GCF_022921095.1_ASM2292109v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022921095.1_ASM2292109v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:15,246] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:15,264] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:58:15,265] [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	86.223	1373	1759	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017589435.1	s__Hymenobacter defluvii	85.9786	1370	1759	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	79.2127	714	1759	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	79.1053	664	1759	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017313265.1	s__Hymenobacter sp017313265	78.9499	782	1759	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	78.8873	747	1759	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	78.8266	698	1759	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	78.7258	619	1759	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	97.59	97.59	0.91	0.91	2	-
GCF_900141805.1	s__Hymenobacter daecheongensis	78.6279	647	1759	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	78.6241	642	1759	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	78.499	551	1759	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	78.4626	697	1759	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	78.4415	648	1759	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	78.3884	527	1759	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003583925.1	s__Hymenobacter rubripertinctus	78.3872	622	1759	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003970915.1	s__Solirubrum gummosum	78.2746	719	1759	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Solirubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014641455.1	s__Hymenobacter cavernae	78.1049	647	1759	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 13:58:15,266] [INFO] GTDB search result was written to GCF_022921095.1_ASM2292109v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:15,267] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:15,272] [INFO] DFAST_QC result json was written to GCF_022921095.1_ASM2292109v1_genomic.fna/dqc_result.json
[2024-01-24 13:58:15,273] [INFO] DFAST_QC completed!
[2024-01-24 13:58:15,273] [INFO] Total running time: 0h2m27s