[2024-01-24 12:29:19,154] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:29:19,156] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:29:19,156] [INFO] DQC Reference Directory: /var/lib/cwl/stg3a3a42f2-24cf-403a-b05a-64807cb99ac6/dqc_reference
[2024-01-24 12:29:20,351] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:29:20,352] [INFO] Task started: Prodigal
[2024-01-24 12:29:20,353] [INFO] Running command: gunzip -c /var/lib/cwl/stg11b62ef4-14e6-4514-a8ee-67b778a43ea5/GCF_014698995.1_ASM1469899v1_genomic.fna.gz | prodigal -d GCF_014698995.1_ASM1469899v1_genomic.fna/cds.fna -a GCF_014698995.1_ASM1469899v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:29:47,289] [INFO] Task succeeded: Prodigal
[2024-01-24 12:29:47,289] [INFO] Task started: HMMsearch
[2024-01-24 12:29:47,290] [INFO] Running command: hmmsearch --tblout GCF_014698995.1_ASM1469899v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3a3a42f2-24cf-403a-b05a-64807cb99ac6/dqc_reference/reference_markers.hmm GCF_014698995.1_ASM1469899v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:29:47,601] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:29:47,603] [INFO] Found 6/6 markers.
[2024-01-24 12:29:47,649] [INFO] Query marker FASTA was written to GCF_014698995.1_ASM1469899v1_genomic.fna/markers.fasta
[2024-01-24 12:29:47,649] [INFO] Task started: Blastn
[2024-01-24 12:29:47,649] [INFO] Running command: blastn -query GCF_014698995.1_ASM1469899v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3a3a42f2-24cf-403a-b05a-64807cb99ac6/dqc_reference/reference_markers.fasta -out GCF_014698995.1_ASM1469899v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:29:48,296] [INFO] Task succeeded: Blastn
[2024-01-24 12:29:48,300] [INFO] Selected 17 target genomes.
[2024-01-24 12:29:48,301] [INFO] Target genome list was writen to GCF_014698995.1_ASM1469899v1_genomic.fna/target_genomes.txt
[2024-01-24 12:29:48,314] [INFO] Task started: fastANI
[2024-01-24 12:29:48,315] [INFO] Running command: fastANI --query /var/lib/cwl/stg11b62ef4-14e6-4514-a8ee-67b778a43ea5/GCF_014698995.1_ASM1469899v1_genomic.fna.gz --refList GCF_014698995.1_ASM1469899v1_genomic.fna/target_genomes.txt --output GCF_014698995.1_ASM1469899v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:30:06,670] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:06,670] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3a3a42f2-24cf-403a-b05a-64807cb99ac6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:30:06,671] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3a3a42f2-24cf-403a-b05a-64807cb99ac6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:30:06,688] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:30:06,688] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:30:06,688] [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 duratus	strain=BT646	GCA_014698995.1	2771356	2771356	type	True	100.0	1551	1551	95	conclusive
Hymenobacter psychrotolerans	strain=DSM 18569	GCA_900142395.1	344998	344998	type	True	86.3494	1195	1551	95	below_threshold
Hymenobacter perfusus	strain=LMG 26000	GCA_003944765.1	1236770	1236770	type	True	82.1138	930	1551	95	below_threshold
Hymenobacter swuensis	strain=DY53	GCA_000576555.1	1446467	1446467	type	True	81.6736	909	1551	95	below_threshold
Hymenobacter rigui	strain=KCTC 12533	GCA_003944715.1	334424	334424	type	True	81.5096	907	1551	95	below_threshold
Hymenobacter piscis	strain=NST-14	GCA_018760735.1	2839984	2839984	type	True	81.4933	878	1551	95	below_threshold
Hymenobacter telluris	strain=BT186	GCA_017313265.1	2816474	2816474	type	True	81.2054	970	1551	95	below_threshold
Hymenobacter metallilatus	strain=9PBR-2	GCA_003944705.1	2493666	2493666	type	True	81.1702	871	1551	95	below_threshold
Hymenobacter guriensis	strain=BT594	GCA_015773195.1	2793065	2793065	type	True	80.87	832	1551	95	below_threshold
Hymenobacter daecheongensis	strain=DSM 21074	GCA_900141805.1	496053	496053	type	True	80.8225	838	1551	95	below_threshold
Hymenobacter glacieicola	strain=CGMCC 1.12990	GCA_014640315.1	1562124	1562124	type	True	80.6016	830	1551	95	below_threshold
Hymenobacter gelipurpurascens	strain=DSM 11116	GCA_900187375.1	89968	89968	type	True	80.2381	821	1551	95	below_threshold
Hymenobacter chitinivorans	strain=DSM 11115	GCA_002797555.1	89969	89969	type	True	80.2027	881	1551	95	below_threshold
Hymenobacter metallicola	strain=9PBR-1	GCA_004745645.1	2563114	2563114	type	True	80.1673	799	1551	95	below_threshold
Hymenobacter amundsenii	strain=CCM 8682	GCA_002204745.1	2006685	2006685	type	True	80.0939	778	1551	95	below_threshold
Hymenobacter fodinae	strain=92R-1	GCA_004745825.1	2510796	2510796	type	True	79.6249	747	1551	95	below_threshold
Hymenobacter armeniacus	strain=BT189	GCA_014699055.1	2771358	2771358	type	True	79.285	716	1551	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:30:06,690] [INFO] DFAST Taxonomy check result was written to GCF_014698995.1_ASM1469899v1_genomic.fna/tc_result.tsv
[2024-01-24 12:30:06,690] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:30:06,690] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:30:06,691] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3a3a42f2-24cf-403a-b05a-64807cb99ac6/dqc_reference/checkm_data
[2024-01-24 12:30:06,691] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:30:06,742] [INFO] Task started: CheckM
[2024-01-24 12:30:06,742] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014698995.1_ASM1469899v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014698995.1_ASM1469899v1_genomic.fna/checkm_input GCF_014698995.1_ASM1469899v1_genomic.fna/checkm_result
[2024-01-24 12:31:16,672] [INFO] Task succeeded: CheckM
[2024-01-24 12:31:16,674] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:31:16,698] [INFO] ===== Completeness check finished =====
[2024-01-24 12:31:16,699] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:31:16,699] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014698995.1_ASM1469899v1_genomic.fna/markers.fasta)
[2024-01-24 12:31:16,699] [INFO] Task started: Blastn
[2024-01-24 12:31:16,700] [INFO] Running command: blastn -query GCF_014698995.1_ASM1469899v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3a3a42f2-24cf-403a-b05a-64807cb99ac6/dqc_reference/reference_markers_gtdb.fasta -out GCF_014698995.1_ASM1469899v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:17,602] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:17,607] [INFO] Selected 11 target genomes.
[2024-01-24 12:31:17,607] [INFO] Target genome list was writen to GCF_014698995.1_ASM1469899v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:31:17,617] [INFO] Task started: fastANI
[2024-01-24 12:31:17,617] [INFO] Running command: fastANI --query /var/lib/cwl/stg11b62ef4-14e6-4514-a8ee-67b778a43ea5/GCF_014698995.1_ASM1469899v1_genomic.fna.gz --refList GCF_014698995.1_ASM1469899v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014698995.1_ASM1469899v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:31:29,896] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:29,912] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:31:29,912] [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_018145755.1	s__Hymenobacter sp018145755	100.0	1551	1551	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_014250515.1	s__Hymenobacter sp014250515	92.2523	1356	1551	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	86.3397	1196	1551	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	84.367	1113	1551	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	83.7161	1093	1551	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	82.1292	927	1551	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018760735.1	s__Hymenobacter sp018760735	81.49	878	1551	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003944705.1	s__Hymenobacter metallilatus	81.1625	872	1551	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	80.9379	881	1551	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014640315.1	s__Hymenobacter glacieicola	80.6103	828	1551	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900187375.1	s__Hymenobacter gelipurpurascens	80.2588	818	1551	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 12:31:29,914] [INFO] GTDB search result was written to GCF_014698995.1_ASM1469899v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:31:29,915] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:31:29,918] [INFO] DFAST_QC result json was written to GCF_014698995.1_ASM1469899v1_genomic.fna/dqc_result.json
[2024-01-24 12:31:29,918] [INFO] DFAST_QC completed!
[2024-01-24 12:31:29,918] [INFO] Total running time: 0h2m11s