[2024-01-24 15:26:04,875] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:26:04,877] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:26:04,877] [INFO] DQC Reference Directory: /var/lib/cwl/stgbcedb896-8c72-4f3d-aad2-464613e36cb0/dqc_reference
[2024-01-24 15:26:07,022] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:26:07,024] [INFO] Task started: Prodigal
[2024-01-24 15:26:07,024] [INFO] Running command: gunzip -c /var/lib/cwl/stgcbc7b41e-478d-44ea-b0e2-23934dbe8c90/GCF_004765605.1_ASM476560v1_genomic.fna.gz | prodigal -d GCF_004765605.1_ASM476560v1_genomic.fna/cds.fna -a GCF_004765605.1_ASM476560v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:26:38,735] [INFO] Task succeeded: Prodigal
[2024-01-24 15:26:38,736] [INFO] Task started: HMMsearch
[2024-01-24 15:26:38,736] [INFO] Running command: hmmsearch --tblout GCF_004765605.1_ASM476560v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbcedb896-8c72-4f3d-aad2-464613e36cb0/dqc_reference/reference_markers.hmm GCF_004765605.1_ASM476560v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:26:39,208] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:26:39,212] [INFO] Found 6/6 markers.
[2024-01-24 15:26:39,268] [INFO] Query marker FASTA was written to GCF_004765605.1_ASM476560v1_genomic.fna/markers.fasta
[2024-01-24 15:26:39,268] [INFO] Task started: Blastn
[2024-01-24 15:26:39,269] [INFO] Running command: blastn -query GCF_004765605.1_ASM476560v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbcedb896-8c72-4f3d-aad2-464613e36cb0/dqc_reference/reference_markers.fasta -out GCF_004765605.1_ASM476560v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:26:39,950] [INFO] Task succeeded: Blastn
[2024-01-24 15:26:39,954] [INFO] Selected 14 target genomes.
[2024-01-24 15:26:39,955] [INFO] Target genome list was writen to GCF_004765605.1_ASM476560v1_genomic.fna/target_genomes.txt
[2024-01-24 15:26:39,966] [INFO] Task started: fastANI
[2024-01-24 15:26:39,967] [INFO] Running command: fastANI --query /var/lib/cwl/stgcbc7b41e-478d-44ea-b0e2-23934dbe8c90/GCF_004765605.1_ASM476560v1_genomic.fna.gz --refList GCF_004765605.1_ASM476560v1_genomic.fna/target_genomes.txt --output GCF_004765605.1_ASM476560v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:26:58,110] [INFO] Task succeeded: fastANI
[2024-01-24 15:26:58,110] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbcedb896-8c72-4f3d-aad2-464613e36cb0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:26:58,111] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbcedb896-8c72-4f3d-aad2-464613e36cb0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:26:58,125] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:26:58,125] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:26:58,125] [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 aquaticus	strain=JCM 31653	GCA_004765605.1	1867101	1867101	type	True	100.0	1836	1836	95	conclusive
Hymenobacter chitinivorans	strain=DSM 11115	GCA_002797555.1	89969	89969	type	True	87.1661	1405	1836	95	below_threshold
Hymenobacter metallicola	strain=9PBR-1	GCA_004745645.1	2563114	2563114	type	True	85.6161	1335	1836	95	below_threshold
Hymenobacter persicinus	strain=1-3-3-3	GCA_004167665.1	2025506	2025506	type	True	83.6761	1139	1836	95	below_threshold
Hymenobacter elongatus	strain=JCM 17223	GCA_004745955.1	877208	877208	type	True	83.4444	1166	1836	95	below_threshold
Hymenobacter daecheongensis	strain=DSM 21074	GCA_900141805.1	496053	496053	type	True	82.9679	1051	1836	95	below_threshold
Hymenobacter piscis	strain=NST-14	GCA_018760735.1	2839984	2839984	type	True	81.7978	978	1836	95	below_threshold
Hymenobacter psychrotolerans	strain=DSM 18569	GCA_900142395.1	344998	344998	type	True	81.4908	967	1836	95	below_threshold
Hymenobacter perfusus	strain=LMG 26000	GCA_003944765.1	1236770	1236770	type	True	81.118	987	1836	95	below_threshold
Hymenobacter guriensis	strain=BT594	GCA_015773195.1	2793065	2793065	type	True	81.0598	974	1836	95	below_threshold
Hymenobacter metallilatus	strain=9PBR-2	GCA_003944705.1	2493666	2493666	type	True	80.5003	953	1836	95	below_threshold
Hymenobacter armeniacus	strain=BT189	GCA_014699055.1	2771358	2771358	type	True	80.0906	974	1836	95	below_threshold
Hymenobacter jejuensis	strain=17J68-5	GCA_006337165.1	2502781	2502781	type	True	78.7633	751	1836	95	below_threshold
Hymenobacter montanus	strain=BT664	GCA_014699115.1	2771359	2771359	type	True	78.7052	664	1836	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:26:58,127] [INFO] DFAST Taxonomy check result was written to GCF_004765605.1_ASM476560v1_genomic.fna/tc_result.tsv
[2024-01-24 15:26:58,128] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:26:58,128] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:26:58,128] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbcedb896-8c72-4f3d-aad2-464613e36cb0/dqc_reference/checkm_data
[2024-01-24 15:26:58,130] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:26:58,184] [INFO] Task started: CheckM
[2024-01-24 15:26:58,184] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004765605.1_ASM476560v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004765605.1_ASM476560v1_genomic.fna/checkm_input GCF_004765605.1_ASM476560v1_genomic.fna/checkm_result
[2024-01-24 15:28:18,150] [INFO] Task succeeded: CheckM
[2024-01-24 15:28:18,151] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:28:18,180] [INFO] ===== Completeness check finished =====
[2024-01-24 15:28:18,181] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:28:18,181] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004765605.1_ASM476560v1_genomic.fna/markers.fasta)
[2024-01-24 15:28:18,182] [INFO] Task started: Blastn
[2024-01-24 15:28:18,182] [INFO] Running command: blastn -query GCF_004765605.1_ASM476560v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbcedb896-8c72-4f3d-aad2-464613e36cb0/dqc_reference/reference_markers_gtdb.fasta -out GCF_004765605.1_ASM476560v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:28:19,191] [INFO] Task succeeded: Blastn
[2024-01-24 15:28:19,195] [INFO] Selected 11 target genomes.
[2024-01-24 15:28:19,195] [INFO] Target genome list was writen to GCF_004765605.1_ASM476560v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:28:19,204] [INFO] Task started: fastANI
[2024-01-24 15:28:19,205] [INFO] Running command: fastANI --query /var/lib/cwl/stgcbc7b41e-478d-44ea-b0e2-23934dbe8c90/GCF_004765605.1_ASM476560v1_genomic.fna.gz --refList GCF_004765605.1_ASM476560v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004765605.1_ASM476560v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:28:34,773] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:34,792] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:28:34,792] [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_004765605.1	s__Hymenobacter aquaticus	100.0	1836	1836	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_002797555.1	s__Hymenobacter chitinivorans	87.1494	1407	1836	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	85.6225	1334	1836	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	83.7084	1135	1836	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004745955.1	s__Hymenobacter elongatus	83.4205	1170	1836	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	82.955	1053	1836	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000737515.1	s__Hymenobacter sp000737515	82.0723	1038	1836	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	81.4823	968	1836	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	81.1258	986	1836	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	81.0445	975	1836	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	78.7522	753	1836	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 15:28:34,794] [INFO] GTDB search result was written to GCF_004765605.1_ASM476560v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:28:34,795] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:28:34,799] [INFO] DFAST_QC result json was written to GCF_004765605.1_ASM476560v1_genomic.fna/dqc_result.json
[2024-01-24 15:28:34,799] [INFO] DFAST_QC completed!
[2024-01-24 15:28:34,800] [INFO] Total running time: 0h2m30s