[2024-01-24 13:37:13,638] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:37:13,639] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:37:13,640] [INFO] DQC Reference Directory: /var/lib/cwl/stgf3a7009e-3da5-43b2-9b26-6c8c0c69e5b1/dqc_reference
[2024-01-24 13:37:14,855] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:37:14,856] [INFO] Task started: Prodigal
[2024-01-24 13:37:14,856] [INFO] Running command: gunzip -c /var/lib/cwl/stgdabb8938-f599-4990-94b9-a138015a5bdb/GCF_014610845.1_ASM1461084v1_genomic.fna.gz | prodigal -d GCF_014610845.1_ASM1461084v1_genomic.fna/cds.fna -a GCF_014610845.1_ASM1461084v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:34,817] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:34,817] [INFO] Task started: HMMsearch
[2024-01-24 13:37:34,817] [INFO] Running command: hmmsearch --tblout GCF_014610845.1_ASM1461084v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf3a7009e-3da5-43b2-9b26-6c8c0c69e5b1/dqc_reference/reference_markers.hmm GCF_014610845.1_ASM1461084v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:35,175] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:35,176] [INFO] Found 6/6 markers.
[2024-01-24 13:37:35,211] [INFO] Query marker FASTA was written to GCF_014610845.1_ASM1461084v1_genomic.fna/markers.fasta
[2024-01-24 13:37:35,212] [INFO] Task started: Blastn
[2024-01-24 13:37:35,212] [INFO] Running command: blastn -query GCF_014610845.1_ASM1461084v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf3a7009e-3da5-43b2-9b26-6c8c0c69e5b1/dqc_reference/reference_markers.fasta -out GCF_014610845.1_ASM1461084v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:35,841] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:35,845] [INFO] Selected 18 target genomes.
[2024-01-24 13:37:35,845] [INFO] Target genome list was writen to GCF_014610845.1_ASM1461084v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:35,854] [INFO] Task started: fastANI
[2024-01-24 13:37:35,854] [INFO] Running command: fastANI --query /var/lib/cwl/stgdabb8938-f599-4990-94b9-a138015a5bdb/GCF_014610845.1_ASM1461084v1_genomic.fna.gz --refList GCF_014610845.1_ASM1461084v1_genomic.fna/target_genomes.txt --output GCF_014610845.1_ASM1461084v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:51,167] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:51,168] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf3a7009e-3da5-43b2-9b26-6c8c0c69e5b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:51,168] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf3a7009e-3da5-43b2-9b26-6c8c0c69e5b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:51,181] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:37:51,182] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:51,182] [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
Maribacter arenosus	strain=CAU 1321	GCA_014610845.1	1854708	1854708	type	True	100.0	1375	1377	95	conclusive
Maribacter polysiphoniae	strain=DSM 23514	GCA_003148665.1	429344	429344	type	True	79.0363	613	1377	95	below_threshold
Maribacter polysiphoniae	strain=KCTC 22021	GCA_014673435.1	429344	429344	type	True	79.0075	597	1377	95	below_threshold
Maribacter luteus	strain=RZ05	GCA_009674825.1	2594478	2594478	type	True	78.8069	520	1377	95	below_threshold
Maribacter thermophilus	strain=HT7-2	GCA_001020565.1	1197874	1197874	type	True	77.419	132	1377	95	below_threshold
Maribacter aurantiacus	strain=KCTC 52409	GCA_005780245.1	1882343	1882343	type	True	77.075	125	1377	95	below_threshold
Maribacter flavus	strain=KCTC 42508	GCA_008386635.1	1658664	1658664	type	True	76.9775	138	1377	95	below_threshold
Saonia flava	strain=DSM 29762	GCA_011927795.1	523696	523696	type	True	76.9412	127	1377	95	below_threshold
Pelagihabitans pacificus	strain=TP-CH-4	GCA_009371985.2	2696054	2696054	type	True	76.73	139	1377	95	below_threshold
Arenibacter aquaticus	strain=GUO	GCA_003957295.1	2489054	2489054	type	True	76.6765	137	1377	95	below_threshold
Arenibacter arenosicollis	strain=BSSL-BM3	GCA_014397245.1	2762274	2762274	type	True	76.5413	160	1377	95	below_threshold
Arenibacter palladensis	strain=DSM 17539	GCA_900129275.1	237373	237373	type	True	76.5207	168	1377	95	below_threshold
Arenibacter algicola	strain=TG409	GCA_000733925.1	616991	616991	type	True	76.4664	164	1377	95	below_threshold
Muricauda beolgyonensis	strain=KCTC 23501	GCA_003992615.1	864064	864064	type	True	76.288	114	1377	95	below_threshold
Muricauda alvinocaridis	strain=SCR12	GCA_004916895.1	2530200	2530200	type	True	76.2467	113	1377	95	below_threshold
Aureibaculum luteum	strain=SM1352	GCA_003449015.1	1548456	1548456	type	True	76.1374	58	1377	95	below_threshold
Aestuariivivens marinum	strain=MT3-5-12	GCA_022662175.1	2913555	2913555	type	True	76.0842	53	1377	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:51,184] [INFO] DFAST Taxonomy check result was written to GCF_014610845.1_ASM1461084v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:51,184] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:51,184] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:51,185] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf3a7009e-3da5-43b2-9b26-6c8c0c69e5b1/dqc_reference/checkm_data
[2024-01-24 13:37:51,186] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:51,232] [INFO] Task started: CheckM
[2024-01-24 13:37:51,232] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014610845.1_ASM1461084v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014610845.1_ASM1461084v1_genomic.fna/checkm_input GCF_014610845.1_ASM1461084v1_genomic.fna/checkm_result
[2024-01-24 13:38:47,507] [INFO] Task succeeded: CheckM
[2024-01-24 13:38:47,508] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:38:47,530] [INFO] ===== Completeness check finished =====
[2024-01-24 13:38:47,530] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:38:47,531] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014610845.1_ASM1461084v1_genomic.fna/markers.fasta)
[2024-01-24 13:38:47,531] [INFO] Task started: Blastn
[2024-01-24 13:38:47,531] [INFO] Running command: blastn -query GCF_014610845.1_ASM1461084v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf3a7009e-3da5-43b2-9b26-6c8c0c69e5b1/dqc_reference/reference_markers_gtdb.fasta -out GCF_014610845.1_ASM1461084v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:38:48,427] [INFO] Task succeeded: Blastn
[2024-01-24 13:38:48,431] [INFO] Selected 19 target genomes.
[2024-01-24 13:38:48,431] [INFO] Target genome list was writen to GCF_014610845.1_ASM1461084v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:38:48,469] [INFO] Task started: fastANI
[2024-01-24 13:38:48,470] [INFO] Running command: fastANI --query /var/lib/cwl/stgdabb8938-f599-4990-94b9-a138015a5bdb/GCF_014610845.1_ASM1461084v1_genomic.fna.gz --refList GCF_014610845.1_ASM1461084v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014610845.1_ASM1461084v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:39:02,221] [INFO] Task succeeded: fastANI
[2024-01-24 13:39:02,241] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:39:02,241] [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_014610845.1	s__Maribacter_A arenosus	100.0	1375	1377	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003148665.1	s__Maribacter_A polysiphoniae	79.0185	616	1377	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_A	95.0	99.27	98.55	0.95	0.91	3	-
GCF_009674825.1	s__Maribacter_A luteus	78.7988	521	1377	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_014596745.1	s__Maribacter_A sp014596745	78.7726	570	1377	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018679695.1	s__Maribacter_A sp018679695	78.3441	350	1377	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_A	95.0	99.00	99.00	0.82	0.82	2	-
GCA_002749285.1	s__Maribacter_A sp002749285	78.2024	317	1377	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_000153165.2	s__Maribacter_A sp000153165	78.1071	364	1377	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013001935.1	s__Maribacter_A sp013001935	78.0792	235	1377	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_A	95.0	96.76	96.72	0.66	0.66	3	-
GCF_001020565.1	s__Maribacter thermophilus	77.419	132	1377	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011927795.1	s__Saonia flava	76.9594	126	1377	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Saonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003626755.1	s__Ulvibacterium marinum	76.7643	183	1377	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Ulvibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002699205.1	s__Muricauda sp002699205	76.6447	103	1377	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	99.91	99.91	0.89	0.89	2	-
GCF_014397245.1	s__Arenibacter arenosicollis	76.5413	160	1377	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102165.1	s__Cellulophaga baltica	76.5136	98	1377	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	97.62	97.40	0.90	0.89	7	-
GCF_000733925.1	s__Arenibacter algicola	76.4819	161	1377	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	98.04	97.34	0.85	0.81	5	-
GCF_900119145.1	s__Cellulophaga fucicola	76.4304	62	1377	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000186265.1	s__Cellulophaga algicola	76.3277	94	1377	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	98.35	98.34	0.88	0.87	3	-
GCF_009797025.1	s__Cellulophaga sp009797025	76.2895	99	1377	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004916895.1	s__Muricauda alvinocaridis	76.2621	112	1377	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:39:02,243] [INFO] GTDB search result was written to GCF_014610845.1_ASM1461084v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:39:02,243] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:39:02,247] [INFO] DFAST_QC result json was written to GCF_014610845.1_ASM1461084v1_genomic.fna/dqc_result.json
[2024-01-24 13:39:02,247] [INFO] DFAST_QC completed!
[2024-01-24 13:39:02,247] [INFO] Total running time: 0h1m49s