[2024-01-24 15:17:49,825] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:17:49,827] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:17:49,827] [INFO] DQC Reference Directory: /var/lib/cwl/stga63a4d6f-9044-4ddf-be98-f0e5edbe354d/dqc_reference
[2024-01-24 15:17:51,532] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:17:51,534] [INFO] Task started: Prodigal
[2024-01-24 15:17:51,534] [INFO] Running command: gunzip -c /var/lib/cwl/stgebcfe7db-5c7c-4d0e-a59d-3f7ed877e411/GCF_003610635.1_ASM361063v1_genomic.fna.gz | prodigal -d GCF_003610635.1_ASM361063v1_genomic.fna/cds.fna -a GCF_003610635.1_ASM361063v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:18:00,130] [INFO] Task succeeded: Prodigal
[2024-01-24 15:18:00,131] [INFO] Task started: HMMsearch
[2024-01-24 15:18:00,131] [INFO] Running command: hmmsearch --tblout GCF_003610635.1_ASM361063v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga63a4d6f-9044-4ddf-be98-f0e5edbe354d/dqc_reference/reference_markers.hmm GCF_003610635.1_ASM361063v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:18:00,414] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:18:00,416] [INFO] Found 6/6 markers.
[2024-01-24 15:18:00,452] [INFO] Query marker FASTA was written to GCF_003610635.1_ASM361063v1_genomic.fna/markers.fasta
[2024-01-24 15:18:00,452] [INFO] Task started: Blastn
[2024-01-24 15:18:00,452] [INFO] Running command: blastn -query GCF_003610635.1_ASM361063v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga63a4d6f-9044-4ddf-be98-f0e5edbe354d/dqc_reference/reference_markers.fasta -out GCF_003610635.1_ASM361063v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:01,257] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:01,261] [INFO] Selected 24 target genomes.
[2024-01-24 15:18:01,262] [INFO] Target genome list was writen to GCF_003610635.1_ASM361063v1_genomic.fna/target_genomes.txt
[2024-01-24 15:18:01,274] [INFO] Task started: fastANI
[2024-01-24 15:18:01,275] [INFO] Running command: fastANI --query /var/lib/cwl/stgebcfe7db-5c7c-4d0e-a59d-3f7ed877e411/GCF_003610635.1_ASM361063v1_genomic.fna.gz --refList GCF_003610635.1_ASM361063v1_genomic.fna/target_genomes.txt --output GCF_003610635.1_ASM361063v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:18:16,748] [INFO] Task succeeded: fastANI
[2024-01-24 15:18:16,748] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga63a4d6f-9044-4ddf-be98-f0e5edbe354d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:18:16,749] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga63a4d6f-9044-4ddf-be98-f0e5edbe354d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:18:16,770] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 15:18:16,771] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 15:18:16,771] [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
Psychroserpens jangbogonensis	strain=PAMC 27130	GCA_000797465.1	1484460	1484460	type	True	79.1184	434	994	95	below_threshold
Psychroserpens mesophilus	strain=JCM 13413	GCA_000826645.1	325473	325473	type	True	78.8767	391	994	95	below_threshold
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	78.8209	417	994	95	below_threshold
Winogradskyella endarachnes	strain=HL2-2	GCA_009741275.1	2681965	2681965	type	True	78.5704	331	994	95	below_threshold
Winogradskyella litoriviva	strain=KMM6491	GCA_013249065.1	1220182	1220182	type	True	78.5662	350	994	95	below_threshold
Winogradskyella sediminis	strain=DSM 28134	GCA_003387355.1	1382466	1382466	type	True	78.5575	308	994	95	below_threshold
Winogradskyella costae	strain=Z3138	GCA_013403865.1	2697008	2697008	type	True	78.3056	305	994	95	below_threshold
Hanstruepera flava	strain=NBU2984	GCA_023634025.1	2930218	2930218	type	True	78.2678	268	994	95	below_threshold
Oceanihabitans sediminis	strain=DSM 28133	GCA_003315315.1	1812012	1812012	type	True	78.2481	278	994	95	below_threshold
Oceanihabitans sediminis	strain=S9-10	GCA_003337215.1	1812012	1812012	type	True	78.22	281	994	95	below_threshold
Winogradskyella undariae	strain=CCUG 63832	GCA_013285155.1	1285465	1285465	type	True	78.2091	325	994	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	78.1892	280	994	95	below_threshold
Hanstruepera ponticola	strain=MM-14	GCA_012931685.1	2042995	2042995	type	True	78.1686	264	994	95	below_threshold
Winogradskyella ludwigii	strain=HL116	GCA_013403985.1	2686076	2686076	type	True	78.1606	333	994	95	below_threshold
Winogradskyella eckloniae	strain=EC29	GCA_013249045.1	1089306	1089306	type	True	78.1603	312	994	95	below_threshold
Bizionia algoritergicola	strain=APA-1	GCA_008086165.1	291187	291187	type	True	78.0599	264	994	95	below_threshold
Winogradskyella vidalii	strain=HL634	GCA_013403955.1	2615024	2615024	type	True	77.9989	295	994	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	77.976	300	994	95	below_threshold
Lacinutrix jangbogonensis	strain=PAMC 27137	GCA_000797445.1	1469557	1469557	type	True	77.9739	311	994	95	below_threshold
Winogradskyella jejuensis	strain=DSM 25330	GCA_900129745.1	1089305	1089305	type	True	77.8205	240	994	95	below_threshold
Seonamhaeicola maritimus	strain=1505	GCA_008056315.1	2591822	2591822	type	True	77.7892	258	994	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	77.5947	287	994	95	below_threshold
Mariniflexile gromovii	strain=KCTC 12570	GCA_017814435.1	362523	362523	type	True	77.5097	262	994	95	below_threshold
Algibacter mikhailovii	strain=KCTC 12710	GCA_014651495.1	425498	425498	type	True	77.4103	229	994	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:18:16,772] [INFO] DFAST Taxonomy check result was written to GCF_003610635.1_ASM361063v1_genomic.fna/tc_result.tsv
[2024-01-24 15:18:16,773] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:18:16,773] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:18:16,773] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga63a4d6f-9044-4ddf-be98-f0e5edbe354d/dqc_reference/checkm_data
[2024-01-24 15:18:16,775] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:18:16,809] [INFO] Task started: CheckM
[2024-01-24 15:18:16,810] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003610635.1_ASM361063v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003610635.1_ASM361063v1_genomic.fna/checkm_input GCF_003610635.1_ASM361063v1_genomic.fna/checkm_result
[2024-01-24 15:18:47,307] [INFO] Task succeeded: CheckM
[2024-01-24 15:18:47,309] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:18:47,336] [INFO] ===== Completeness check finished =====
[2024-01-24 15:18:47,336] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:18:47,337] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003610635.1_ASM361063v1_genomic.fna/markers.fasta)
[2024-01-24 15:18:47,338] [INFO] Task started: Blastn
[2024-01-24 15:18:47,338] [INFO] Running command: blastn -query GCF_003610635.1_ASM361063v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga63a4d6f-9044-4ddf-be98-f0e5edbe354d/dqc_reference/reference_markers_gtdb.fasta -out GCF_003610635.1_ASM361063v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:48,370] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:48,375] [INFO] Selected 23 target genomes.
[2024-01-24 15:18:48,375] [INFO] Target genome list was writen to GCF_003610635.1_ASM361063v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:18:48,398] [INFO] Task started: fastANI
[2024-01-24 15:18:48,399] [INFO] Running command: fastANI --query /var/lib/cwl/stgebcfe7db-5c7c-4d0e-a59d-3f7ed877e411/GCF_003610635.1_ASM361063v1_genomic.fna.gz --refList GCF_003610635.1_ASM361063v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003610635.1_ASM361063v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:19:04,230] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:04,255] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:19:04,256] [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_003610635.1	s__Ichthyenterobacterium magnum	100.0	992	994	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Ichthyenterobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014641635.1	s__Aquaticitalea lipolytica	79.1673	458	994	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquaticitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000797465.1	s__Psychroserpens jangbogonensis	79.1196	433	994	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000826655.1	s__Psychroserpens damuponensis	79.0044	415	994	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002162685.1	s__Psychroserpens sp002162685	78.9724	459	994	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004366715.1	s__Meridianimaribacter flavus	78.9566	395	994	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Meridianimaribacter	95.0	97.44	97.06	0.91	0.87	3	-
GCF_000826645.1	s__Psychroserpens mesophilus	78.8818	390	994	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015319355.1	s__Psychroserpens luteus	78.7841	446	994	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014526325.1	s__Psychroserpens algicola	78.6659	422	994	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018222875.1	s__Psychroserpens sp018222875	78.6428	346	994	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009741275.1	s__Winogradskyella endarachnes	78.5773	331	994	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013249065.1	s__Winogradskyella litoriviva	78.5662	350	994	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114265.1	s__Flaviramulus basaltis	78.5181	382	994	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flaviramulus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422365.1	s__Mesoflavibacter zeaxanthinifaciens	78.4811	317	994	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesoflavibacter	95.0	97.07	97.05	0.91	0.91	3	-
GCA_001874145.1	s__Lacinutrix sp001874145	78.4431	335	994	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000171875.1	s__Winogradskyella sp000171875	78.4143	375	994	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001418105.1	s__Oceanihabitans himadriensis	78.3796	356	994	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000789235.1	s__Wocania ichthyoenteri	78.3266	377	994	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wocania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003337215.1	s__Oceanihabitans sediminis	78.2375	279	994	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013403985.1	s__Winogradskyella ludwigii	78.1502	335	994	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008086165.1	s__Algorimicrobium algoritergicola	78.0599	264	994	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algorimicrobium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000797445.1	s__Lacinutrix jangbogonensis	77.9776	312	994	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002441545.1	s__Yeosuana sp002441545	77.4412	248	994	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Yeosuana	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:19:04,257] [INFO] GTDB search result was written to GCF_003610635.1_ASM361063v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:19:04,258] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:19:04,262] [INFO] DFAST_QC result json was written to GCF_003610635.1_ASM361063v1_genomic.fna/dqc_result.json
[2024-01-24 15:19:04,262] [INFO] DFAST_QC completed!
[2024-01-24 15:19:04,262] [INFO] Total running time: 0h1m14s