[2023-06-19 08:45:34,577] [INFO] DFAST_QC pipeline started.
[2023-06-19 08:45:34,581] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 08:45:34,581] [INFO] DQC Reference Directory: /var/lib/cwl/stg74d6c0de-e1d2-41a8-ae1c-0c1a90cea764/dqc_reference
[2023-06-19 08:45:36,563] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 08:45:36,564] [INFO] Task started: Prodigal
[2023-06-19 08:45:36,564] [INFO] Running command: gunzip -c /var/lib/cwl/stg23eab682-cae6-4c8b-a723-c485b75c51b9/GCA_013042715.1_ASM1304271v1_genomic.fna.gz | prodigal -d GCA_013042715.1_ASM1304271v1_genomic.fna/cds.fna -a GCA_013042715.1_ASM1304271v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 08:45:42,878] [INFO] Task succeeded: Prodigal
[2023-06-19 08:45:42,879] [INFO] Task started: HMMsearch
[2023-06-19 08:45:42,879] [INFO] Running command: hmmsearch --tblout GCA_013042715.1_ASM1304271v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg74d6c0de-e1d2-41a8-ae1c-0c1a90cea764/dqc_reference/reference_markers.hmm GCA_013042715.1_ASM1304271v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 08:45:43,160] [INFO] Task succeeded: HMMsearch
[2023-06-19 08:45:43,161] [INFO] Found 6/6 markers.
[2023-06-19 08:45:43,188] [INFO] Query marker FASTA was written to GCA_013042715.1_ASM1304271v1_genomic.fna/markers.fasta
[2023-06-19 08:45:43,188] [INFO] Task started: Blastn
[2023-06-19 08:45:43,188] [INFO] Running command: blastn -query GCA_013042715.1_ASM1304271v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg74d6c0de-e1d2-41a8-ae1c-0c1a90cea764/dqc_reference/reference_markers.fasta -out GCA_013042715.1_ASM1304271v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:45:43,862] [INFO] Task succeeded: Blastn
[2023-06-19 08:45:43,867] [INFO] Selected 32 target genomes.
[2023-06-19 08:45:43,868] [INFO] Target genome list was writen to GCA_013042715.1_ASM1304271v1_genomic.fna/target_genomes.txt
[2023-06-19 08:45:43,871] [INFO] Task started: fastANI
[2023-06-19 08:45:43,871] [INFO] Running command: fastANI --query /var/lib/cwl/stg23eab682-cae6-4c8b-a723-c485b75c51b9/GCA_013042715.1_ASM1304271v1_genomic.fna.gz --refList GCA_013042715.1_ASM1304271v1_genomic.fna/target_genomes.txt --output GCA_013042715.1_ASM1304271v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 08:46:02,256] [INFO] Task succeeded: fastANI
[2023-06-19 08:46:02,257] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg74d6c0de-e1d2-41a8-ae1c-0c1a90cea764/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 08:46:02,257] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg74d6c0de-e1d2-41a8-ae1c-0c1a90cea764/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 08:46:02,280] [INFO] Found 32 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 08:46:02,281] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 08:46:02,281] [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
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	77.9552	205	624	95	below_threshold
Winogradskyella litoriviva	strain=KMM6491	GCA_013249065.1	1220182	1220182	type	True	77.3271	163	624	95	below_threshold
Lacinutrix algicola	strain=AKS293	GCA_001418085.1	342954	342954	type	True	77.3135	160	624	95	below_threshold
Algibacter marinivivus	strain=ZY111	GCA_003143755.1	2100723	2100723	type	True	77.2533	153	624	95	below_threshold
Winogradskyella endarachnes	strain=HL2-2	GCA_009741275.1	2681965	2681965	type	True	77.2189	160	624	95	below_threshold
Psychroserpens jangbogonensis	strain=PAMC 27130	GCA_000797465.1	1484460	1484460	type	True	77.1963	153	624	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	77.1875	135	624	95	below_threshold
Arenitalea lutea	strain=CGMCC 1.12213	GCA_900141715.1	1178825	1178825	type	True	77.1801	144	624	95	below_threshold
Arenitalea lutea	strain=P7-3-5	GCA_000283015.1	1178825	1178825	type	True	77.1684	142	624	95	below_threshold
Hanstruepera flava	strain=NBU2984	GCA_023634025.1	2930218	2930218	type	True	77.1594	122	624	95	below_threshold
Olleya marilimosa	strain=CAM030	GCA_000518485.1	272164	272164	type	True	77.0419	162	624	95	below_threshold
Winogradskyella psychrotolerans	strain=RS-3	GCA_000427335.1	1344585	1344585	type	True	77.0318	137	624	95	below_threshold
Winogradskyella thalassocola	strain=DSM 15363	GCA_900099995.1	262004	262004	type	True	77.0081	135	624	95	below_threshold
Winogradskyella helgolandensis	strain=Z963	GCA_013404085.1	2697010	2697010	type	True	77.0033	149	624	95	below_threshold
Flavivirga rizhaonensis	strain=RZ03	GCA_004791695.1	2559571	2559571	type	True	76.994	140	624	95	below_threshold
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	76.9838	148	624	95	below_threshold
Lacinutrix mariniflava	strain=AKS432	GCA_001418015.1	342955	342955	type	True	76.9403	171	624	95	below_threshold
Seonamhaeicola maritimus	strain=1505	GCA_008056315.1	2591822	2591822	type	True	76.9251	157	624	95	below_threshold
Algibacter aestuarii	strain=KCTC 23449	GCA_006148925.1	912802	912802	type	True	76.9084	127	624	95	below_threshold
Olleya namhaensis	strain=DSM 28881	GCA_900114005.1	1144750	1144750	type	True	76.9077	134	624	95	below_threshold
Seonamhaeicola marinus	strain=B011	GCA_008085455.1	1912246	1912246	type	True	76.8875	116	624	95	below_threshold
Hyunsoonleella pacifica	strain=SW033	GCA_004310335.1	1080224	1080224	type	True	76.8766	132	624	95	below_threshold
Psychroserpens mesophilus	strain=JCM 13413	GCA_000826645.1	325473	325473	type	True	76.8716	134	624	95	below_threshold
Hyunsoonleella pacifica	strain=CGMCC 1.11009	GCA_014636335.1	1080224	1080224	type	True	76.8701	132	624	95	below_threshold
Algibacter alginicilyticus	strain=HZ22	GCA_001310225.1	1736674	1736674	type	True	76.8628	140	624	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	76.8311	123	624	95	below_threshold
Aestuariivivens marinum	strain=MT3-5-12	GCA_022662175.1	2913555	2913555	type	True	76.7876	101	624	95	below_threshold
Winogradskyella sediminis	strain=DSM 28134	GCA_003387355.1	1382466	1382466	type	True	76.7716	135	624	95	below_threshold
Algibacter lectus	strain=DSM 15365	GCA_900112395.1	221126	221126	type	True	76.7569	133	624	95	below_threshold
Winogradskyella jejuensis	strain=DSM 25330	GCA_900129745.1	1089305	1089305	type	True	76.5893	121	624	95	below_threshold
Winogradskyella ursingii	strain=HL4150	GCA_013403975.1	2686079	2686079	type	True	76.4933	94	624	95	below_threshold
Gelidibacter maritimus	strain=F6074	GCA_014062315.1	2761487	2761487	type	True	76.3609	61	624	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 08:46:02,285] [INFO] DFAST Taxonomy check result was written to GCA_013042715.1_ASM1304271v1_genomic.fna/tc_result.tsv
[2023-06-19 08:46:02,286] [INFO] ===== Taxonomy check completed =====
[2023-06-19 08:46:02,286] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 08:46:02,286] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg74d6c0de-e1d2-41a8-ae1c-0c1a90cea764/dqc_reference/checkm_data
[2023-06-19 08:46:02,288] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 08:46:02,319] [INFO] Task started: CheckM
[2023-06-19 08:46:02,319] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013042715.1_ASM1304271v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013042715.1_ASM1304271v1_genomic.fna/checkm_input GCA_013042715.1_ASM1304271v1_genomic.fna/checkm_result
[2023-06-19 08:46:27,648] [INFO] Task succeeded: CheckM
[2023-06-19 08:46:27,650] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 80.56%
Contamintation: 10.30%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-19 08:46:27,681] [INFO] ===== Completeness check finished =====
[2023-06-19 08:46:27,681] [INFO] ===== Start GTDB Search =====
[2023-06-19 08:46:27,681] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013042715.1_ASM1304271v1_genomic.fna/markers.fasta)
[2023-06-19 08:46:27,682] [INFO] Task started: Blastn
[2023-06-19 08:46:27,682] [INFO] Running command: blastn -query GCA_013042715.1_ASM1304271v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg74d6c0de-e1d2-41a8-ae1c-0c1a90cea764/dqc_reference/reference_markers_gtdb.fasta -out GCA_013042715.1_ASM1304271v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:46:28,613] [INFO] Task succeeded: Blastn
[2023-06-19 08:46:28,619] [INFO] Selected 24 target genomes.
[2023-06-19 08:46:28,619] [INFO] Target genome list was writen to GCA_013042715.1_ASM1304271v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 08:46:28,621] [INFO] Task started: fastANI
[2023-06-19 08:46:28,621] [INFO] Running command: fastANI --query /var/lib/cwl/stg23eab682-cae6-4c8b-a723-c485b75c51b9/GCA_013042715.1_ASM1304271v1_genomic.fna.gz --refList GCA_013042715.1_ASM1304271v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013042715.1_ASM1304271v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 08:46:41,656] [INFO] Task succeeded: fastANI
[2023-06-19 08:46:41,677] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 08:46:41,677] [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
GCA_013042715.1	s__Site-B15 sp013042715	100.0	613	624	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Site-B15	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_005047595.1	s__CAU-1491 sp005047595	77.9402	206	624	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__CAU-1491	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013151975.1	s__PRS1 sp013151975	77.6835	139	624	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__PRS1	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011777505.1	s__CAU-1491 sp011777505	77.64	200	624	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__CAU-1491	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004366715.1	s__Meridianimaribacter flavus	77.5079	185	624	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Meridianimaribacter	95.0	97.44	97.06	0.91	0.87	3	-
GCF_003610635.1	s__Ichthyenterobacterium magnum	77.4969	172	624	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Ichthyenterobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008084905.1	s__Xanthomarina maritima	77.4683	179	624	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860825.1	s__Oceanihabitans sp018860825	77.4207	195	624	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114265.1	s__Flaviramulus basaltis	77.3987	193	624	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flaviramulus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003650305.1	s__PRS1 sp003650305	77.3853	183	624	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__PRS1	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014641635.1	s__Aquaticitalea lipolytica	77.3788	191	624	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquaticitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013249065.1	s__Winogradskyella litoriviva	77.3448	162	624	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002741945.1	s__Wocania sp002741945	77.3334	166	624	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wocania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003443635.1	s__AU392 sp003443635	77.2741	171	624	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__AU392	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003143755.1	s__Algibacter_B sp003143755	77.2533	153	624	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000797465.1	s__Psychroserpens jangbogonensis	77.1963	153	624	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016864015.1	s__Oceanihabitans sp016864015	77.1945	182	624	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002162685.1	s__Psychroserpens sp002162685	77.1825	147	624	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016785945.1	s__Olleya sediminilitoris	77.1671	148	624	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	98.16	97.66	0.93	0.91	5	-
GCF_001971785.1	s__Seonamhaeicola sp001971785	77.1424	157	624	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Seonamhaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003386165.1	s__Winogradskyella eximia	77.0437	154	624	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000518485.1	s__Olleya marilimosa	77.0286	163	624	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	97.58	97.25	0.92	0.89	4	-
GCF_000826645.1	s__Psychroserpens mesophilus	76.8716	134	624	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005869935.1	s__Winogradskyella algicola	76.8174	139	624	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 08:46:41,680] [INFO] GTDB search result was written to GCA_013042715.1_ASM1304271v1_genomic.fna/result_gtdb.tsv
[2023-06-19 08:46:41,680] [INFO] ===== GTDB Search completed =====
[2023-06-19 08:46:41,686] [INFO] DFAST_QC result json was written to GCA_013042715.1_ASM1304271v1_genomic.fna/dqc_result.json
[2023-06-19 08:46:41,686] [INFO] DFAST_QC completed!
[2023-06-19 08:46:41,686] [INFO] Total running time: 0h1m7s