[2024-01-24 13:36:45,016] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:36:45,021] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:36:45,021] [INFO] DQC Reference Directory: /var/lib/cwl/stg9b9736ca-a4e7-4aea-a0d7-b4876f7708b7/dqc_reference
[2024-01-24 13:36:46,362] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:36:46,363] [INFO] Task started: Prodigal
[2024-01-24 13:36:46,363] [INFO] Running command: gunzip -c /var/lib/cwl/stg875d4714-0dae-4bcf-81ac-0a708d8a0334/GCF_013402795.1_ASM1340279v1_genomic.fna.gz | prodigal -d GCF_013402795.1_ASM1340279v1_genomic.fna/cds.fna -a GCF_013402795.1_ASM1340279v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:04,966] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:04,966] [INFO] Task started: HMMsearch
[2024-01-24 13:37:04,966] [INFO] Running command: hmmsearch --tblout GCF_013402795.1_ASM1340279v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9b9736ca-a4e7-4aea-a0d7-b4876f7708b7/dqc_reference/reference_markers.hmm GCF_013402795.1_ASM1340279v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:05,213] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:05,214] [INFO] Found 6/6 markers.
[2024-01-24 13:37:05,247] [INFO] Query marker FASTA was written to GCF_013402795.1_ASM1340279v1_genomic.fna/markers.fasta
[2024-01-24 13:37:05,248] [INFO] Task started: Blastn
[2024-01-24 13:37:05,248] [INFO] Running command: blastn -query GCF_013402795.1_ASM1340279v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9b9736ca-a4e7-4aea-a0d7-b4876f7708b7/dqc_reference/reference_markers.fasta -out GCF_013402795.1_ASM1340279v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:05,920] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:05,923] [INFO] Selected 24 target genomes.
[2024-01-24 13:37:05,924] [INFO] Target genome list was writen to GCF_013402795.1_ASM1340279v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:05,953] [INFO] Task started: fastANI
[2024-01-24 13:37:05,953] [INFO] Running command: fastANI --query /var/lib/cwl/stg875d4714-0dae-4bcf-81ac-0a708d8a0334/GCF_013402795.1_ASM1340279v1_genomic.fna.gz --refList GCF_013402795.1_ASM1340279v1_genomic.fna/target_genomes.txt --output GCF_013402795.1_ASM1340279v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:23,633] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:23,633] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9b9736ca-a4e7-4aea-a0d7-b4876f7708b7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:23,634] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9b9736ca-a4e7-4aea-a0d7-b4876f7708b7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:23,652] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:37:23,652] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:23,653] [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
Costertonia aggregata	strain=KCCM 42265	GCA_013402795.1	343403	343403	type	True	100.0	1301	1303	95	conclusive
Aequorivita iocasae	strain=KX20305	GCA_016757735.1	2803865	2803865	type	True	78.043	65	1303	95	below_threshold
Maribacter algarum	strain=RZ26	GCA_005885635.1	2578118	2578118	type	True	77.8027	181	1303	95	below_threshold
Cellulophaga algicola	strain=DSM 14237	GCA_000186265.1	59600	59600	type	True	77.1339	111	1303	95	below_threshold
Muricauda flava	strain=DSM 22638	GCA_900129665.1	570519	570519	type	True	77.063	110	1303	95	below_threshold
Muricauda lutimaris	strain=KCTC 22173	GCA_003581615.1	475082	475082	type	True	77.0462	108	1303	95	below_threshold
Maribacter polysiphoniae	strain=DSM 23514	GCA_003148665.1	429344	429344	type	True	77.0215	174	1303	95	below_threshold
Arenibacter algicola	strain=TG409	GCA_000733925.1	616991	616991	type	True	76.947	143	1303	95	below_threshold
Zobellia russellii	strain=KMM 3677	GCA_018728565.1	248907	248907	type	True	76.79	185	1303	95	below_threshold
Ulvibacterium marinum	strain=CCMM003	GCA_003626755.1	2419782	2419782	type	True	76.7884	175	1303	95	below_threshold
Arenibacter echinorum	strain=DSM 23522	GCA_003259375.1	440515	440515	type	True	76.7641	146	1303	95	below_threshold
Aggregatimonas sangjinii	strain=F202Z8	GCA_005943945.1	2583587	2583587	type	True	76.7138	170	1303	95	below_threshold
Kriegella aquimaris	strain=DSM 19886	GCA_900103215.1	192904	192904	type	True	76.6864	158	1303	95	below_threshold
Arenibacter arenosicollis	strain=BSSL-BM3	GCA_014397245.1	2762274	2762274	type	True	76.6383	154	1303	95	below_threshold
Zobellia amurskyensis	strain=KMM 3526	GCA_009725985.1	248905	248905	type	True	76.6357	166	1303	95	below_threshold
Arenibacter palladensis	strain=DSM 17539	GCA_900129275.1	237373	237373	type	True	76.5383	145	1303	95	below_threshold
Muricauda hymeniacidonis	strain=176CP4-71	GCA_004296335.1	2517819	2517819	type	True	76.4973	116	1303	95	below_threshold
Pelagihabitans pacificus	strain=TP-CH-4	GCA_009371985.2	2696054	2696054	type	True	76.4834	139	1303	95	below_threshold
Muricauda olearia	strain=CL-SS4	GCA_009184425.1	552546	552546	type	True	76.4562	124	1303	95	below_threshold
Cellulophaga fucicola	strain=DSM 24786	GCA_900119145.1	76595	76595	type	True	76.4268	95	1303	95	below_threshold
Maribacter orientalis	strain=DSM 16471	GCA_900109345.1	228957	228957	type	True	76.4216	149	1303	95	below_threshold
Arenibacter troitsensis	strain=DSM 19835	GCA_900177645.1	188872	188872	type	True	76.2101	159	1303	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:23,654] [INFO] DFAST Taxonomy check result was written to GCF_013402795.1_ASM1340279v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:23,655] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:23,655] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:23,655] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9b9736ca-a4e7-4aea-a0d7-b4876f7708b7/dqc_reference/checkm_data
[2024-01-24 13:37:23,656] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:23,696] [INFO] Task started: CheckM
[2024-01-24 13:37:23,697] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013402795.1_ASM1340279v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013402795.1_ASM1340279v1_genomic.fna/checkm_input GCF_013402795.1_ASM1340279v1_genomic.fna/checkm_result
[2024-01-24 13:38:18,864] [INFO] Task succeeded: CheckM
[2024-01-24 13:38:18,866] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:38:18,888] [INFO] ===== Completeness check finished =====
[2024-01-24 13:38:18,888] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:38:18,888] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013402795.1_ASM1340279v1_genomic.fna/markers.fasta)
[2024-01-24 13:38:18,889] [INFO] Task started: Blastn
[2024-01-24 13:38:18,889] [INFO] Running command: blastn -query GCF_013402795.1_ASM1340279v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9b9736ca-a4e7-4aea-a0d7-b4876f7708b7/dqc_reference/reference_markers_gtdb.fasta -out GCF_013402795.1_ASM1340279v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:38:19,637] [INFO] Task succeeded: Blastn
[2024-01-24 13:38:19,640] [INFO] Selected 22 target genomes.
[2024-01-24 13:38:19,640] [INFO] Target genome list was writen to GCF_013402795.1_ASM1340279v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:38:19,688] [INFO] Task started: fastANI
[2024-01-24 13:38:19,688] [INFO] Running command: fastANI --query /var/lib/cwl/stg875d4714-0dae-4bcf-81ac-0a708d8a0334/GCF_013402795.1_ASM1340279v1_genomic.fna.gz --refList GCF_013402795.1_ASM1340279v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013402795.1_ASM1340279v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:38:35,245] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:35,262] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:38:35,262] [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_013402795.1	s__Costertonia aggregata	100.0	1303	1303	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Costertonia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000186265.1	s__Cellulophaga algicola	77.1339	111	1303	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	98.35	98.34	0.88	0.87	3	-
GCA_002749285.1	s__Maribacter_A sp002749285	77.0976	85	1303	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_000733925.1	s__Arenibacter algicola	77.0488	144	1303	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	98.04	97.34	0.85	0.81	5	-
GCF_000973105.1	s__Zobellia galactanivorans	76.9834	168	1303	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zobellia	95.0	99.09	99.05	0.92	0.91	3	-
GCF_001447995.1	s__Maribacter dokdonensis	76.9498	150	1303	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	97.64	97.51	0.89	0.86	13	-
GCF_003201775.1	s__Arenibacter sp003201775	76.8491	144	1303	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018728565.1	s__Zobellia russellii	76.79	185	1303	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zobellia	95.0	97.51	97.51	0.91	0.91	2	-
GCF_003426735.1	s__Arenibacter sp003426735	76.7774	141	1303	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156625.1	s__Zobellia uliginosa	76.7692	167	1303	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zobellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003259375.1	s__Arenibacter echinorum	76.7641	146	1303	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860365.1	s__Arenibacter algicola_B	76.7478	147	1303	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103215.1	s__Kriegella aquimaris	76.6864	158	1303	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Kriegella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010993815.1	s__Muricauda sp010993815	76.6435	164	1303	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014397245.1	s__Arenibacter arenosicollis	76.6383	154	1303	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009725985.1	s__Zobellia amurskyensis	76.6357	166	1303	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zobellia	95.0	98.14	98.14	0.91	0.91	2	-
GCF_003385855.1	s__Muricauda sp003385855	76.5991	131	1303	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	97.98	97.98	0.89	0.89	2	-
GCA_009371985.2	s__TP-CH-4 sp009371985	76.4832	138	1303	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__TP-CH-4	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009184425.1	s__Muricauda olearia	76.4562	124	1303	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	96.52	96.52	0.87	0.87	2	-
GCF_900109345.1	s__Maribacter orientalis	76.4327	148	1303	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900119145.1	s__Cellulophaga fucicola	76.4268	95	1303	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013214065.1	s__DT-32 sp013214065	76.3175	81	1303	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__DT-32	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:38:35,264] [INFO] GTDB search result was written to GCF_013402795.1_ASM1340279v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:38:35,265] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:38:35,269] [INFO] DFAST_QC result json was written to GCF_013402795.1_ASM1340279v1_genomic.fna/dqc_result.json
[2024-01-24 13:38:35,269] [INFO] DFAST_QC completed!
[2024-01-24 13:38:35,269] [INFO] Total running time: 0h1m50s