[2024-01-25 17:35:35,614] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:35:35,627] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:35:35,628] [INFO] DQC Reference Directory: /var/lib/cwl/stg2e72862c-940e-4c22-88d7-c043b69aed81/dqc_reference
[2024-01-25 17:35:36,782] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:35:36,782] [INFO] Task started: Prodigal
[2024-01-25 17:35:36,782] [INFO] Running command: gunzip -c /var/lib/cwl/stgd2b89e56-14ce-448e-88c4-5b6fad38cd8d/GCF_027359925.1_ASM2735992v1_genomic.fna.gz | prodigal -d GCF_027359925.1_ASM2735992v1_genomic.fna/cds.fna -a GCF_027359925.1_ASM2735992v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:36:01,879] [INFO] Task succeeded: Prodigal
[2024-01-25 17:36:01,879] [INFO] Task started: HMMsearch
[2024-01-25 17:36:01,879] [INFO] Running command: hmmsearch --tblout GCF_027359925.1_ASM2735992v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2e72862c-940e-4c22-88d7-c043b69aed81/dqc_reference/reference_markers.hmm GCF_027359925.1_ASM2735992v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:36:02,111] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:36:02,113] [INFO] Found 6/6 markers.
[2024-01-25 17:36:02,151] [INFO] Query marker FASTA was written to GCF_027359925.1_ASM2735992v1_genomic.fna/markers.fasta
[2024-01-25 17:36:02,151] [INFO] Task started: Blastn
[2024-01-25 17:36:02,151] [INFO] Running command: blastn -query GCF_027359925.1_ASM2735992v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2e72862c-940e-4c22-88d7-c043b69aed81/dqc_reference/reference_markers.fasta -out GCF_027359925.1_ASM2735992v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:36:02,780] [INFO] Task succeeded: Blastn
[2024-01-25 17:36:02,784] [INFO] Selected 17 target genomes.
[2024-01-25 17:36:02,784] [INFO] Target genome list was writen to GCF_027359925.1_ASM2735992v1_genomic.fna/target_genomes.txt
[2024-01-25 17:36:02,795] [INFO] Task started: fastANI
[2024-01-25 17:36:02,795] [INFO] Running command: fastANI --query /var/lib/cwl/stgd2b89e56-14ce-448e-88c4-5b6fad38cd8d/GCF_027359925.1_ASM2735992v1_genomic.fna.gz --refList GCF_027359925.1_ASM2735992v1_genomic.fna/target_genomes.txt --output GCF_027359925.1_ASM2735992v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:36:25,684] [INFO] Task succeeded: fastANI
[2024-01-25 17:36:25,685] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2e72862c-940e-4c22-88d7-c043b69aed81/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:36:25,685] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2e72862c-940e-4c22-88d7-c043b69aed81/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:36:25,696] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:36:25,696] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:36:25,696] [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 psychrotolerans	strain=DSM 18569	GCA_900142395.1	344998	344998	type	True	84.2093	1101	1694	95	below_threshold
Hymenobacter duratus	strain=BT646	GCA_014698995.1	2771356	2771356	type	True	83.9213	1129	1694	95	below_threshold
Hymenobacter perfusus	strain=LMG 26000	GCA_003944765.1	1236770	1236770	type	True	83.7201	1055	1694	95	below_threshold
Hymenobacter swuensis	strain=DY53	GCA_000576555.1	1446467	1446467	type	True	83.1143	1043	1694	95	below_threshold
Hymenobacter piscis	strain=NST-14	GCA_018760735.1	2839984	2839984	type	True	83.1043	1072	1694	95	below_threshold
Hymenobacter rigui	strain=KCTC 12533	GCA_003944715.1	334424	334424	type	True	82.8693	1002	1694	95	below_threshold
Hymenobacter metallilatus	strain=9PBR-2	GCA_003944705.1	2493666	2493666	type	True	81.9579	980	1694	95	below_threshold
Hymenobacter daecheongensis	strain=DSM 21074	GCA_900141805.1	496053	496053	type	True	81.7931	928	1694	95	below_threshold
Hymenobacter telluris	strain=BT186	GCA_017313265.1	2816474	2816474	type	True	81.5517	1035	1694	95	below_threshold
Hymenobacter persicinus	strain=1-3-3-3	GCA_004167665.1	2025506	2025506	type	True	81.546	974	1694	95	below_threshold
Hymenobacter guriensis	strain=BT594	GCA_015773195.1	2793065	2793065	type	True	81.4948	929	1694	95	below_threshold
Hymenobacter glacieicola	strain=CGMCC 1.12990	GCA_014640315.1	1562124	1562124	type	True	81.3133	939	1694	95	below_threshold
Hymenobacter chitinivorans	strain=DSM 11115	GCA_002797555.1	89969	89969	type	True	80.8416	1026	1694	95	below_threshold
Hymenobacter gelipurpurascens	strain=DSM 11116	GCA_900187375.1	89968	89968	type	True	80.5098	878	1694	95	below_threshold
Hymenobacter metallicola	strain=9PBR-1	GCA_004745645.1	2563114	2563114	type	True	80.4079	919	1694	95	below_threshold
Hymenobacter armeniacus	strain=BT189	GCA_014699055.1	2771358	2771358	type	True	80.1038	857	1694	95	below_threshold
Hymenobacter fodinae	strain=92R-1	GCA_004745825.1	2510796	2510796	type	True	80.0632	795	1694	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:36:25,697] [INFO] DFAST Taxonomy check result was written to GCF_027359925.1_ASM2735992v1_genomic.fna/tc_result.tsv
[2024-01-25 17:36:25,698] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:36:25,698] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:36:25,698] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2e72862c-940e-4c22-88d7-c043b69aed81/dqc_reference/checkm_data
[2024-01-25 17:36:25,699] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:36:25,748] [INFO] Task started: CheckM
[2024-01-25 17:36:25,749] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_027359925.1_ASM2735992v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_027359925.1_ASM2735992v1_genomic.fna/checkm_input GCF_027359925.1_ASM2735992v1_genomic.fna/checkm_result
[2024-01-25 17:37:29,190] [INFO] Task succeeded: CheckM
[2024-01-25 17:37:29,191] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:37:29,213] [INFO] ===== Completeness check finished =====
[2024-01-25 17:37:29,213] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:37:29,214] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_027359925.1_ASM2735992v1_genomic.fna/markers.fasta)
[2024-01-25 17:37:29,214] [INFO] Task started: Blastn
[2024-01-25 17:37:29,214] [INFO] Running command: blastn -query GCF_027359925.1_ASM2735992v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2e72862c-940e-4c22-88d7-c043b69aed81/dqc_reference/reference_markers_gtdb.fasta -out GCF_027359925.1_ASM2735992v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:37:30,234] [INFO] Task succeeded: Blastn
[2024-01-25 17:37:30,236] [INFO] Selected 14 target genomes.
[2024-01-25 17:37:30,237] [INFO] Target genome list was writen to GCF_027359925.1_ASM2735992v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:37:30,243] [INFO] Task started: fastANI
[2024-01-25 17:37:30,244] [INFO] Running command: fastANI --query /var/lib/cwl/stgd2b89e56-14ce-448e-88c4-5b6fad38cd8d/GCF_027359925.1_ASM2735992v1_genomic.fna.gz --refList GCF_027359925.1_ASM2735992v1_genomic.fna/target_genomes_gtdb.txt --output GCF_027359925.1_ASM2735992v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:37:47,599] [INFO] Task succeeded: fastANI
[2024-01-25 17:37:47,608] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 17:37:47,608] [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_000737515.1	s__Hymenobacter sp000737515	91.3258	1341	1694	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	88.0896	1292	1694	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	84.2179	1098	1694	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018145755.1	s__Hymenobacter sp018145755	83.92	1130	1694	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003944765.1	s__Hymenobacter perfusus	83.7232	1054	1694	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	83.0898	1074	1694	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000576555.1	s__Hymenobacter swuensis	83.0806	1047	1694	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014250515.1	s__Hymenobacter sp014250515	83.0055	1047	1694	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003944715.1	s__Hymenobacter rigui	82.8333	1007	1694	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	81.9707	978	1694	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	81.6898	1013	1694	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	81.5287	978	1694	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	81.4898	930	1694	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	80.8595	1022	1694	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:37:47,610] [INFO] GTDB search result was written to GCF_027359925.1_ASM2735992v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:37:47,610] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:37:47,613] [INFO] DFAST_QC result json was written to GCF_027359925.1_ASM2735992v1_genomic.fna/dqc_result.json
[2024-01-25 17:37:47,614] [INFO] DFAST_QC completed!
[2024-01-25 17:37:47,614] [INFO] Total running time: 0h2m12s