[2023-03-15 18:39:13,540] [INFO] DFAST_QC pipeline started.
[2023-03-15 18:39:13,540] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 18:39:13,540] [INFO] DQC Reference Directory: /var/lib/cwl/stg3cfa37fe-1892-44f7-b935-7bf8006c4662/dqc_reference
[2023-03-15 18:39:15,257] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 18:39:15,257] [INFO] Task started: Prodigal
[2023-03-15 18:39:15,257] [INFO] Running command: cat /var/lib/cwl/stge0227791-7c8c-4737-b568-51057a74d4bb/OceanDNA-b6298.fa | prodigal -d OceanDNA-b6298/cds.fna -a OceanDNA-b6298/protein.faa -g 11 -q > /dev/null
[2023-03-15 18:39:29,614] [INFO] Task succeeded: Prodigal
[2023-03-15 18:39:29,614] [INFO] Task started: HMMsearch
[2023-03-15 18:39:29,614] [INFO] Running command: hmmsearch --tblout OceanDNA-b6298/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3cfa37fe-1892-44f7-b935-7bf8006c4662/dqc_reference/reference_markers.hmm OceanDNA-b6298/protein.faa > /dev/null
[2023-03-15 18:39:29,834] [INFO] Task succeeded: HMMsearch
[2023-03-15 18:39:29,835] [INFO] Found 6/6 markers.
[2023-03-15 18:39:29,851] [INFO] Query marker FASTA was written to OceanDNA-b6298/markers.fasta
[2023-03-15 18:39:29,852] [INFO] Task started: Blastn
[2023-03-15 18:39:29,852] [INFO] Running command: blastn -query OceanDNA-b6298/markers.fasta -db /var/lib/cwl/stg3cfa37fe-1892-44f7-b935-7bf8006c4662/dqc_reference/reference_markers.fasta -out OceanDNA-b6298/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 18:39:30,544] [INFO] Task succeeded: Blastn
[2023-03-15 18:39:30,545] [INFO] Selected 27 target genomes.
[2023-03-15 18:39:30,545] [INFO] Target genome list was writen to OceanDNA-b6298/target_genomes.txt
[2023-03-15 18:39:30,568] [INFO] Task started: fastANI
[2023-03-15 18:39:30,568] [INFO] Running command: fastANI --query /var/lib/cwl/stge0227791-7c8c-4737-b568-51057a74d4bb/OceanDNA-b6298.fa --refList OceanDNA-b6298/target_genomes.txt --output OceanDNA-b6298/fastani_result.tsv --threads 1
[2023-03-15 18:39:48,623] [INFO] Task succeeded: fastANI
[2023-03-15 18:39:48,624] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3cfa37fe-1892-44f7-b935-7bf8006c4662/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 18:39:48,624] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3cfa37fe-1892-44f7-b935-7bf8006c4662/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 18:39:48,639] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 18:39:48,639] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 18:39:48,639] [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	78.2982	353	721	95	below_threshold
Lacinutrix himadriensis	strain=E4-9a	GCA_001418105.1	641549	641549	type	True	77.7901	227	721	95	below_threshold
Algibacter marinivivus	strain=ZY111	GCA_003143755.1	2100723	2100723	type	True	77.4351	216	721	95	below_threshold
Oceanihabitans sediminis	strain=DSM 28133	GCA_003315315.1	1812012	1812012	type	True	77.3416	188	721	95	below_threshold
Oceanihabitans sediminis	strain=S9-10	GCA_003337215.1	1812012	1812012	type	True	77.2684	186	721	95	below_threshold
Winogradskyella ludwigii	strain=HL116	GCA_013403985.1	2686076	2686076	type	True	77.2471	195	721	95	below_threshold
Psychroserpens mesophilus	strain=JCM 13413	GCA_000826645.1	325473	325473	type	True	77.2215	214	721	95	below_threshold
Flavivirga rizhaonensis	strain=RZ03	GCA_004791695.1	2559571	2559571	type	True	77.2052	199	721	95	below_threshold
Lacinutrix mariniflava	strain=AKS432	GCA_001418015.1	342955	342955	type	True	77.1841	213	721	95	below_threshold
Winogradskyella marina	strain=F6397	GCA_015645385.1	2785530	2785530	type	True	77.1838	185	721	95	below_threshold
Winogradskyella endarachnes	strain=HL2-2	GCA_009741275.1	2681965	2681965	type	True	77.1675	182	721	95	below_threshold
Algibacter alginicilyticus	strain=HZ22	GCA_001310225.1	1736674	1736674	type	True	77.1347	169	721	95	below_threshold
Hanstruepera neustonica	strain=JCM19743	GCA_002895005.1	1445657	1445657	type	True	77.0924	131	721	95	below_threshold
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	77.0848	206	721	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	77.0379	160	721	95	below_threshold
Bizionia argentinensis	strain=JUB59	GCA_000224335.2	456455	456455	type	True	77.0038	149	721	95	below_threshold
Seonamhaeicola maritimus	strain=1505	GCA_008056315.1	2591822	2591822	type	True	76.9923	160	721	95	below_threshold
Winogradskyella flava	strain=KCTC 52348	GCA_014243395.1	1884876	1884876	type	True	76.978	137	721	95	below_threshold
Mariniflexile fucanivorans	strain=DSM 18792	GCA_004341235.1	264023	264023	type	True	76.9714	185	721	95	below_threshold
Winogradskyella algicola	strain=IMCC33238	GCA_005869935.1	2575815	2575815	type	True	76.9289	149	721	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014297365.1	538189	538189	type	True	76.9034	206	721	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014284085.1	538189	538189	type	True	76.9034	206	721	95	below_threshold
Seonamhaeicola marinus	strain=B011	GCA_008085455.1	1912246	1912246	type	True	76.8928	148	721	95	below_threshold
Algibacter mikhailovii	strain=KCTC 12710	GCA_014651495.1	425498	425498	type	True	76.8863	145	721	95	below_threshold
Yeosuana aromativorans	strain=JCM 12862	GCA_014646655.1	288019	288019	type	True	76.7676	151	721	95	below_threshold
Aestuariivivens insulae	strain=AH-MY3	GCA_022662195.1	1621988	1621988	type	True	76.44	116	721	95	below_threshold
Joostella atrarenae	strain=M1-2	GCA_021764745.1	679257	679257	type	True	76.2679	73	721	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 18:39:48,640] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6298/tc_result.tsv
[2023-03-15 18:39:48,640] [INFO] ===== Taxonomy check completed =====
[2023-03-15 18:39:48,640] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 18:39:48,640] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3cfa37fe-1892-44f7-b935-7bf8006c4662/dqc_reference/checkm_data
[2023-03-15 18:39:48,641] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 18:39:48,645] [INFO] Task started: CheckM
[2023-03-15 18:39:48,645] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6298/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6298/checkm_input OceanDNA-b6298/checkm_result
[2023-03-15 18:40:27,758] [INFO] Task succeeded: CheckM
[2023-03-15 18:40:27,758] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 88.19%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 18:40:27,760] [INFO] ===== Completeness check finished =====
[2023-03-15 18:40:27,761] [INFO] ===== Start GTDB Search =====
[2023-03-15 18:40:27,761] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6298/markers.fasta)
[2023-03-15 18:40:27,762] [INFO] Task started: Blastn
[2023-03-15 18:40:27,762] [INFO] Running command: blastn -query OceanDNA-b6298/markers.fasta -db /var/lib/cwl/stg3cfa37fe-1892-44f7-b935-7bf8006c4662/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6298/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 18:40:28,702] [INFO] Task succeeded: Blastn
[2023-03-15 18:40:28,703] [INFO] Selected 24 target genomes.
[2023-03-15 18:40:28,704] [INFO] Target genome list was writen to OceanDNA-b6298/target_genomes_gtdb.txt
[2023-03-15 18:40:29,385] [INFO] Task started: fastANI
[2023-03-15 18:40:29,385] [INFO] Running command: fastANI --query /var/lib/cwl/stge0227791-7c8c-4737-b568-51057a74d4bb/OceanDNA-b6298.fa --refList OceanDNA-b6298/target_genomes_gtdb.txt --output OceanDNA-b6298/fastani_result_gtdb.tsv --threads 1
[2023-03-15 18:40:44,740] [INFO] Task succeeded: fastANI
[2023-03-15 18:40:44,754] [INFO] Found 24 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 18:40:44,754] [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_011777505.1	s__CAU-1491 sp011777505	78.7986	370	721	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_005047595.1	s__CAU-1491 sp005047595	78.3091	352	721	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_014638915.1	s__Xanthomarina arctica	77.9768	206	721	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003610635.1	s__Ichthyenterobacterium magnum	77.8931	252	721	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Ichthyenterobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001418105.1	s__Oceanihabitans himadriensis	77.7901	227	721	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013151975.1	s__PRS1 sp013151975	77.7835	190	721	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	77.7187	263	721	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquaticitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860825.1	s__Oceanihabitans sp018860825	77.6621	242	721	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008084905.1	s__Xanthomarina maritima	77.6361	245	721	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114265.1	s__Flaviramulus basaltis	77.5912	246	721	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flaviramulus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002162765.1	s__MAAR01 sp002162765	77.5754	199	721	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAAR01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004366715.1	s__Meridianimaribacter flavus	77.5431	224	721	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Meridianimaribacter	95.0	97.44	97.06	0.91	0.87	3	-
GCA_003650305.1	s__PRS1 sp003650305	77.5376	251	721	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__PRS1	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014202195.1	s__Oceanihabitans iliipiscarium	77.4895	237	721	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016744625.1	s__Winogradskyella sp016744625	77.4849	203	721	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003443635.1	s__AU392 sp003443635	77.449	233	721	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	77.4486	215	721	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003144015.1	s__Xanthomarina sp003144015	77.4381	229	721	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002741945.1	s__Wocania sp002741945	77.3867	222	721	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wocania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004791695.1	s__Flavivirga rizhaonensis	77.2174	198	721	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003386165.1	s__Winogradskyella eximia	77.1455	208	721	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860245.1	s__Tamlana_A agarivorans_A	77.0657	153	721	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tamlana_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013042715.1	s__Site-B15 sp013042715	76.935	150	721	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Site-B15	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000828715.1	s__Winogradskyella sp000828715	76.845	200	721	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 18:40:44,755] [INFO] GTDB search result was written to OceanDNA-b6298/result_gtdb.tsv
[2023-03-15 18:40:44,755] [INFO] ===== GTDB Search completed =====
[2023-03-15 18:40:44,757] [INFO] DFAST_QC result json was written to OceanDNA-b6298/dqc_result.json
[2023-03-15 18:40:44,757] [INFO] DFAST_QC completed!
[2023-03-15 18:40:44,758] [INFO] Total running time: 0h1m31s