[2024-01-24 14:46:52,793] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:46:52,796] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:46:52,796] [INFO] DQC Reference Directory: /var/lib/cwl/stg4e91cba7-82be-4bc0-8e26-11c472a5af85/dqc_reference
[2024-01-24 14:46:55,362] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:46:55,365] [INFO] Task started: Prodigal
[2024-01-24 14:46:55,365] [INFO] Running command: gunzip -c /var/lib/cwl/stg2e4b2eef-be04-45de-8226-d51d25ae67f5/GCF_010671595.1_ASM1067159v1_genomic.fna.gz | prodigal -d GCF_010671595.1_ASM1067159v1_genomic.fna/cds.fna -a GCF_010671595.1_ASM1067159v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:47:12,988] [INFO] Task succeeded: Prodigal
[2024-01-24 14:47:12,989] [INFO] Task started: HMMsearch
[2024-01-24 14:47:12,989] [INFO] Running command: hmmsearch --tblout GCF_010671595.1_ASM1067159v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4e91cba7-82be-4bc0-8e26-11c472a5af85/dqc_reference/reference_markers.hmm GCF_010671595.1_ASM1067159v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:47:13,353] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:47:13,355] [INFO] Found 6/6 markers.
[2024-01-24 14:47:13,394] [INFO] Query marker FASTA was written to GCF_010671595.1_ASM1067159v1_genomic.fna/markers.fasta
[2024-01-24 14:47:13,395] [INFO] Task started: Blastn
[2024-01-24 14:47:13,395] [INFO] Running command: blastn -query GCF_010671595.1_ASM1067159v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4e91cba7-82be-4bc0-8e26-11c472a5af85/dqc_reference/reference_markers.fasta -out GCF_010671595.1_ASM1067159v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:14,011] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:14,014] [INFO] Selected 21 target genomes.
[2024-01-24 14:47:14,014] [INFO] Target genome list was writen to GCF_010671595.1_ASM1067159v1_genomic.fna/target_genomes.txt
[2024-01-24 14:47:14,046] [INFO] Task started: fastANI
[2024-01-24 14:47:14,046] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e4b2eef-be04-45de-8226-d51d25ae67f5/GCF_010671595.1_ASM1067159v1_genomic.fna.gz --refList GCF_010671595.1_ASM1067159v1_genomic.fna/target_genomes.txt --output GCF_010671595.1_ASM1067159v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:47:28,095] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:28,096] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4e91cba7-82be-4bc0-8e26-11c472a5af85/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:47:28,096] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4e91cba7-82be-4bc0-8e26-11c472a5af85/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:47:28,111] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:47:28,111] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:47:28,111] [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
Muriicola jejuensis	strain=KCTC 22299	GCA_010671595.1	504488	504488	type	True	100.0	1091	1092	95	conclusive
Muriicola marianensis	strain=CGMCC 1.12606	GCA_014638095.1	1324801	1324801	type	True	80.1316	682	1092	95	below_threshold
Muriicola soli	strain=MMS17-SY002	GCA_004139715.1	2507538	2507538	type	True	77.6464	317	1092	95	below_threshold
Poritiphilus flavus	strain=R33	GCA_009901585.1	2697053	2697053	type	True	76.858	131	1092	95	below_threshold
Robiginitalea sediminis	strain=O458	GCA_002198115.1	1982593	1982593	type	True	76.5801	139	1092	95	below_threshold
Muricauda maritima	strain=72	GCA_008017365.1	2306998	2306998	type	True	76.5693	69	1092	95	below_threshold
Muricauda maritima	strain=72	GCA_003584135.1	2306998	2306998	type	True	76.5693	69	1092	95	below_threshold
Robiginitalea biformata	strain=HTCC2501	GCA_000024125.1	252307	252307	type	True	76.5634	150	1092	95	below_threshold
Zeaxanthinibacter enoshimensis	strain=DSM 18435	GCA_004362865.1	392009	392009	type	True	76.5254	150	1092	95	below_threshold
Muricauda hadalis	strain=MT-229	GCA_007785775.2	2597517	2597517	type	True	76.5249	88	1092	95	below_threshold
Maribacter arenosus	strain=CAU 1321	GCA_014610845.1	1854708	1854708	type	True	76.5033	62	1092	95	below_threshold
Pelagihabitans pacificus	strain=TP-CH-4	GCA_009371985.2	2696054	2696054	type	True	76.4562	73	1092	95	below_threshold
Maribacter flavus	strain=KCTC 42508	GCA_008386635.1	1658664	1658664	type	True	76.3492	70	1092	95	below_threshold
Muricauda sediminis	strain=40Bstr401	GCA_010500845.1	2696468	2696468	type	True	76.3103	72	1092	95	below_threshold
Sinomicrobium weinanense	strain=FJxs	GCA_018863395.1	2842200	2842200	type	True	76.2284	63	1092	95	below_threshold
Sinomicrobium weinanense	strain=FJxs	GCA_014518365.1	2842200	2842200	type	True	76.0699	62	1092	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:47:28,113] [INFO] DFAST Taxonomy check result was written to GCF_010671595.1_ASM1067159v1_genomic.fna/tc_result.tsv
[2024-01-24 14:47:28,114] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:47:28,114] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:47:28,115] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4e91cba7-82be-4bc0-8e26-11c472a5af85/dqc_reference/checkm_data
[2024-01-24 14:47:28,118] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:47:28,154] [INFO] Task started: CheckM
[2024-01-24 14:47:28,155] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010671595.1_ASM1067159v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010671595.1_ASM1067159v1_genomic.fna/checkm_input GCF_010671595.1_ASM1067159v1_genomic.fna/checkm_result
[2024-01-24 14:48:20,014] [INFO] Task succeeded: CheckM
[2024-01-24 14:48:20,016] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:48:20,036] [INFO] ===== Completeness check finished =====
[2024-01-24 14:48:20,036] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:48:20,037] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010671595.1_ASM1067159v1_genomic.fna/markers.fasta)
[2024-01-24 14:48:20,037] [INFO] Task started: Blastn
[2024-01-24 14:48:20,037] [INFO] Running command: blastn -query GCF_010671595.1_ASM1067159v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4e91cba7-82be-4bc0-8e26-11c472a5af85/dqc_reference/reference_markers_gtdb.fasta -out GCF_010671595.1_ASM1067159v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:48:20,846] [INFO] Task succeeded: Blastn
[2024-01-24 14:48:20,849] [INFO] Selected 21 target genomes.
[2024-01-24 14:48:20,849] [INFO] Target genome list was writen to GCF_010671595.1_ASM1067159v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:48:20,864] [INFO] Task started: fastANI
[2024-01-24 14:48:20,864] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e4b2eef-be04-45de-8226-d51d25ae67f5/GCF_010671595.1_ASM1067159v1_genomic.fna.gz --refList GCF_010671595.1_ASM1067159v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010671595.1_ASM1067159v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:48:33,496] [INFO] Task succeeded: fastANI
[2024-01-24 14:48:33,518] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:48:33,518] [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_010671595.1	s__Muriicola jejuensis	100.0	1091	1092	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muriicola	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014638095.1	s__Muriicola marianensis	80.1316	682	1092	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muriicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004139715.1	s__Muriicola sp004139715	77.6464	317	1092	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muriicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013042315.1	s__Muriicola sp013042315	77.5975	230	1092	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muriicola	95.0	99.31	99.31	0.85	0.85	2	-
GCA_013042255.1	s__Muriicola sp013042255	77.1247	176	1092	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muriicola	95.0	98.63	98.55	0.78	0.75	6	-
GCA_009901585.1	s__R33 sp009901585	76.8595	130	1092	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__R33	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001683825.1	s__Zeaxanthinibacter sp001683825	76.7756	180	1092	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zeaxanthinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014243345.1	s__Robiginitalea sp014243345	76.5938	148	1092	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Robiginitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003584135.1	s__Muricauda sp003584135	76.5693	69	1092	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	100.00	100.00	0.99	0.99	2	-
GCF_002198115.1	s__Robiginitalea sediminis	76.5667	138	1092	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Robiginitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000024125.1	s__Robiginitalea biformata	76.5598	149	1092	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Robiginitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004362865.1	s__Zeaxanthinibacter enoshimensis	76.5383	149	1092	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zeaxanthinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014610845.1	s__Maribacter_A arenosus	76.5033	62	1092	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003992615.1	s__Muricauda beolgyonensis	76.4782	83	1092	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008386635.1	s__Maribacter flavus	76.3746	69	1092	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	96.59	96.59	0.88	0.88	2	-
GCF_003626755.1	s__Ulvibacterium marinum	76.3449	76	1092	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Ulvibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010500845.1	s__Muricauda sediminis	76.3103	72	1092	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018863395.1	s__Sinomicrobium sp014518365	76.2284	63	1092	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Sinomicrobium	95.0	100.00	100.00	0.99	0.99	2	-
GCA_013041785.1	s__Eudoraea sp013041785	76.0083	87	1092	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Eudoraea	95.0	97.28	95.79	0.83	0.71	4	-
--------------------------------------------------------------------------------
[2024-01-24 14:48:33,519] [INFO] GTDB search result was written to GCF_010671595.1_ASM1067159v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:48:33,520] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:48:33,523] [INFO] DFAST_QC result json was written to GCF_010671595.1_ASM1067159v1_genomic.fna/dqc_result.json
[2024-01-24 14:48:33,524] [INFO] DFAST_QC completed!
[2024-01-24 14:48:33,524] [INFO] Total running time: 0h1m41s