[2024-01-24 13:31:32,174] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:32,176] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:32,176] [INFO] DQC Reference Directory: /var/lib/cwl/stgfc579bcf-325b-4628-8c0e-0bcf2f0ae221/dqc_reference
[2024-01-24 13:31:33,548] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:33,549] [INFO] Task started: Prodigal
[2024-01-24 13:31:33,549] [INFO] Running command: gunzip -c /var/lib/cwl/stg1070182b-ae30-4931-83bf-59ec4027e899/GCF_022921055.1_ASM2292105v1_genomic.fna.gz | prodigal -d GCF_022921055.1_ASM2292105v1_genomic.fna/cds.fna -a GCF_022921055.1_ASM2292105v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:12,955] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:12,956] [INFO] Task started: HMMsearch
[2024-01-24 13:32:12,956] [INFO] Running command: hmmsearch --tblout GCF_022921055.1_ASM2292105v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfc579bcf-325b-4628-8c0e-0bcf2f0ae221/dqc_reference/reference_markers.hmm GCF_022921055.1_ASM2292105v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:13,280] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:13,282] [INFO] Found 6/6 markers.
[2024-01-24 13:32:13,344] [INFO] Query marker FASTA was written to GCF_022921055.1_ASM2292105v1_genomic.fna/markers.fasta
[2024-01-24 13:32:13,344] [INFO] Task started: Blastn
[2024-01-24 13:32:13,344] [INFO] Running command: blastn -query GCF_022921055.1_ASM2292105v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfc579bcf-325b-4628-8c0e-0bcf2f0ae221/dqc_reference/reference_markers.fasta -out GCF_022921055.1_ASM2292105v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:14,023] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:14,026] [INFO] Selected 18 target genomes.
[2024-01-24 13:32:14,027] [INFO] Target genome list was writen to GCF_022921055.1_ASM2292105v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:14,038] [INFO] Task started: fastANI
[2024-01-24 13:32:14,038] [INFO] Running command: fastANI --query /var/lib/cwl/stg1070182b-ae30-4931-83bf-59ec4027e899/GCF_022921055.1_ASM2292105v1_genomic.fna.gz --refList GCF_022921055.1_ASM2292105v1_genomic.fna/target_genomes.txt --output GCF_022921055.1_ASM2292105v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:32,960] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:32,960] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfc579bcf-325b-4628-8c0e-0bcf2f0ae221/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:32,960] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfc579bcf-325b-4628-8c0e-0bcf2f0ae221/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:32,975] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:32:32,975] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:32:32,975] [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 telluris	strain=BT186	GCA_017313265.1	2816474	2816474	type	True	81.033	1118	2369	95	below_threshold
Hymenobacter norwichensis	strain=DSM 15439	GCA_000420705.1	223903	223903	type	True	80.6315	1090	2369	95	below_threshold
Hymenobacter duratus	strain=BT646	GCA_014698995.1	2771356	2771356	type	True	79.1669	734	2369	95	below_threshold
Hymenobacter psychrotolerans	strain=DSM 18569	GCA_900142395.1	344998	344998	type	True	79.1645	760	2369	95	below_threshold
Hymenobacter perfusus	strain=LMG 26000	GCA_003944765.1	1236770	1236770	type	True	78.8477	642	2369	95	below_threshold
Hymenobacter aquaticus	strain=JCM 31653	GCA_004765605.1	1867101	1867101	type	True	78.6814	669	2369	95	below_threshold
Hymenobacter gelipurpurascens	strain=DSM 11116	GCA_900187375.1	89968	89968	type	True	78.6701	631	2369	95	below_threshold
Hymenobacter swuensis	strain=DY53	GCA_000576555.1	1446467	1446467	type	True	78.5524	644	2369	95	below_threshold
Hymenobacter glacieicola	strain=CGMCC 1.12990	GCA_014640315.1	1562124	1562124	type	True	78.5037	651	2369	95	below_threshold
Hymenobacter wooponensis	strain=JCM 19491	GCA_004745865.1	1525360	1525360	type	True	78.3759	650	2369	95	below_threshold
Hymenobacter rigui	strain=KCTC 12533	GCA_003944715.1	334424	334424	type	True	78.3677	663	2369	95	below_threshold
Hymenobacter metallilatus	strain=9PBR-2	GCA_003944705.1	2493666	2493666	type	True	78.2957	563	2369	95	below_threshold
Hymenobacter sediminis	strain=ELS1360	GCA_003231285.1	2218621	2218621	type	True	78.2911	656	2369	95	below_threshold
Hymenobacter chitinivorans	strain=DSM 11115	GCA_002797555.1	89969	89969	type	True	78.2744	694	2369	95	below_threshold
Hymenobacter fodinae	strain=92R-1	GCA_004745825.1	2510796	2510796	type	True	78.2365	667	2369	95	below_threshold
Hymenobacter jejuensis	strain=17J68-5	GCA_006337165.1	2502781	2502781	type	True	77.8498	520	2369	95	below_threshold
Hymenobacter profundi	strain=M2	GCA_019334315.1	1982110	1982110	type	True	77.7915	525	2369	95	below_threshold
Hymenobacter edaphi	strain=NL	GCA_003258365.1	2211146	2211146	type	True	77.6657	555	2369	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:32,977] [INFO] DFAST Taxonomy check result was written to GCF_022921055.1_ASM2292105v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:32,978] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:32,978] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:32,978] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfc579bcf-325b-4628-8c0e-0bcf2f0ae221/dqc_reference/checkm_data
[2024-01-24 13:32:32,979] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:33,046] [INFO] Task started: CheckM
[2024-01-24 13:32:33,047] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022921055.1_ASM2292105v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022921055.1_ASM2292105v1_genomic.fna/checkm_input GCF_022921055.1_ASM2292105v1_genomic.fna/checkm_result
[2024-01-24 13:34:13,621] [INFO] Task succeeded: CheckM
[2024-01-24 13:34:13,623] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.62%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:34:13,648] [INFO] ===== Completeness check finished =====
[2024-01-24 13:34:13,648] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:34:13,649] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022921055.1_ASM2292105v1_genomic.fna/markers.fasta)
[2024-01-24 13:34:13,649] [INFO] Task started: Blastn
[2024-01-24 13:34:13,649] [INFO] Running command: blastn -query GCF_022921055.1_ASM2292105v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfc579bcf-325b-4628-8c0e-0bcf2f0ae221/dqc_reference/reference_markers_gtdb.fasta -out GCF_022921055.1_ASM2292105v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:34:14,552] [INFO] Task succeeded: Blastn
[2024-01-24 13:34:14,558] [INFO] Selected 18 target genomes.
[2024-01-24 13:34:14,559] [INFO] Target genome list was writen to GCF_022921055.1_ASM2292105v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:34:14,576] [INFO] Task started: fastANI
[2024-01-24 13:34:14,577] [INFO] Running command: fastANI --query /var/lib/cwl/stg1070182b-ae30-4931-83bf-59ec4027e899/GCF_022921055.1_ASM2292105v1_genomic.fna.gz --refList GCF_022921055.1_ASM2292105v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022921055.1_ASM2292105v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:34:32,687] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:32,709] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:34:32,709] [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_017313265.1	s__Hymenobacter sp017313265	81.0563	1114	2369	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000420705.1	s__Hymenobacter norwichensis	80.6417	1087	2369	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	79.3554	801	2369	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	79.1707	759	2369	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	79.1608	735	2369	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014333525.1	s__Hymenobacter sp014333525	79.131	723	2369	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	79.0408	697	2369	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	78.6665	632	2369	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	78.5513	644	2369	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013137895.1	s__Hymenobacter sp013137895	78.5498	586	2369	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	78.5219	648	2369	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004745865.1	s__Hymenobacter wooponensis	78.3959	646	2369	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	78.3618	664	2369	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	78.3019	561	2369	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	78.28	693	2369	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004745825.1	s__Hymenobacter sp004745825	78.2474	665	2369	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	77.8498	520	2369	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	97.30	97.30	0.94	0.94	2	-
GCF_001483135.1	s__Solirubrum puertoriconensis	77.5477	417	2369	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Solirubrum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:34:32,711] [INFO] GTDB search result was written to GCF_022921055.1_ASM2292105v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:34:32,711] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:34:32,716] [INFO] DFAST_QC result json was written to GCF_022921055.1_ASM2292105v1_genomic.fna/dqc_result.json
[2024-01-24 13:34:32,716] [INFO] DFAST_QC completed!
[2024-01-24 13:34:32,716] [INFO] Total running time: 0h3m1s