[2023-03-17 02:31:12,854] [INFO] DFAST_QC pipeline started.
[2023-03-17 02:31:12,854] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 02:31:12,854] [INFO] DQC Reference Directory: /var/lib/cwl/stg6b0c1879-0ae9-41cb-b918-a0956fb57af5/dqc_reference
[2023-03-17 02:31:14,378] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 02:31:14,379] [INFO] Task started: Prodigal
[2023-03-17 02:31:14,379] [INFO] Running command: cat /var/lib/cwl/stga4dcec95-c040-43c1-94a8-6645e228ae49/OceanDNA-b6291.fa | prodigal -d OceanDNA-b6291/cds.fna -a OceanDNA-b6291/protein.faa -g 11 -q > /dev/null
[2023-03-17 02:31:30,845] [INFO] Task succeeded: Prodigal
[2023-03-17 02:31:30,845] [INFO] Task started: HMMsearch
[2023-03-17 02:31:30,845] [INFO] Running command: hmmsearch --tblout OceanDNA-b6291/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6b0c1879-0ae9-41cb-b918-a0956fb57af5/dqc_reference/reference_markers.hmm OceanDNA-b6291/protein.faa > /dev/null
[2023-03-17 02:31:31,057] [INFO] Task succeeded: HMMsearch
[2023-03-17 02:31:31,058] [INFO] Found 6/6 markers.
[2023-03-17 02:31:31,079] [INFO] Query marker FASTA was written to OceanDNA-b6291/markers.fasta
[2023-03-17 02:31:31,079] [INFO] Task started: Blastn
[2023-03-17 02:31:31,079] [INFO] Running command: blastn -query OceanDNA-b6291/markers.fasta -db /var/lib/cwl/stg6b0c1879-0ae9-41cb-b918-a0956fb57af5/dqc_reference/reference_markers.fasta -out OceanDNA-b6291/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:31:31,682] [INFO] Task succeeded: Blastn
[2023-03-17 02:31:31,682] [INFO] Selected 29 target genomes.
[2023-03-17 02:31:31,683] [INFO] Target genome list was writen to OceanDNA-b6291/target_genomes.txt
[2023-03-17 02:31:31,695] [INFO] Task started: fastANI
[2023-03-17 02:31:31,695] [INFO] Running command: fastANI --query /var/lib/cwl/stga4dcec95-c040-43c1-94a8-6645e228ae49/OceanDNA-b6291.fa --refList OceanDNA-b6291/target_genomes.txt --output OceanDNA-b6291/fastani_result.tsv --threads 1
[2023-03-17 02:31:47,607] [INFO] Task succeeded: fastANI
[2023-03-17 02:31:47,608] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6b0c1879-0ae9-41cb-b918-a0956fb57af5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 02:31:47,608] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6b0c1879-0ae9-41cb-b918-a0956fb57af5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 02:31:47,623] [INFO] Found 29 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 02:31:47,624] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 02:31:47,624] [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	77.2592	240	816	95	below_threshold
Hanstruepera ponticola	strain=MM-14	GCA_012931685.1	2042995	2042995	type	True	76.5537	106	816	95	below_threshold
Seonamhaeicola marinus	strain=B011	GCA_008085455.1	1912246	1912246	type	True	76.5227	111	816	95	below_threshold
Olleya aquimaris	strain=DSM 24464	GCA_003259525.1	639310	639310	type	True	76.4776	103	816	95	below_threshold
Algibacter aestuarii	strain=KCTC 23449	GCA_006148925.1	912802	912802	type	True	76.4596	96	816	95	below_threshold
Bizionia myxarmorum	strain=ADA-4	GCA_008086205.1	291186	291186	type	True	76.4537	77	816	95	below_threshold
Seonamhaeicola maritimus	strain=1505	GCA_008056315.1	2591822	2591822	type	True	76.4057	119	816	95	below_threshold
Algibacter marinivivus	strain=ZY111	GCA_003143755.1	2100723	2100723	type	True	76.1861	128	816	95	below_threshold
Olleya marilimosa	strain=CAM030	GCA_000518485.1	272164	272164	type	True	76.1607	89	816	95	below_threshold
Algibacter mikhailovii	strain=KCTC 12710	GCA_014651495.1	425498	425498	type	True	76.1498	74	816	95	below_threshold
Oceanihabitans sediminis	strain=DSM 28133	GCA_003315315.1	1812012	1812012	type	True	76.143	84	816	95	below_threshold
Winogradskyella tangerina	strain=M1309	GCA_003260205.1	2023240	2023240	type	True	76.1426	74	816	95	below_threshold
Flavivirga rizhaonensis	strain=RZ03	GCA_004791695.1	2559571	2559571	type	True	76.1393	128	816	95	below_threshold
Oceanihabitans sediminis	strain=S9-10	GCA_003337215.1	1812012	1812012	type	True	76.1177	84	816	95	below_threshold
Winogradskyella litoriviva	strain=KMM6491	GCA_013249065.1	1220182	1220182	type	True	76.1142	102	816	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	76.0634	122	816	95	below_threshold
Winogradskyella endarachnes	strain=HL2-2	GCA_009741275.1	2681965	2681965	type	True	76.0199	107	816	95	below_threshold
Hyunsoonleella pacifica	strain=CGMCC 1.11009	GCA_014636335.1	1080224	1080224	type	True	76.0127	99	816	95	below_threshold
Bizionia echini	strain=DSM 23925	GCA_900115185.1	649333	649333	type	True	76.0036	84	816	95	below_threshold
Hyunsoonleella pacifica	strain=SW033	GCA_004310335.1	1080224	1080224	type	True	75.9817	101	816	95	below_threshold
Bizionia algoritergicola	strain=APA-1	GCA_008086165.1	291187	291187	type	True	75.9773	93	816	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014284085.1	538189	538189	type	True	75.93	112	816	95	below_threshold
Winogradskyella ludwigii	strain=HL116	GCA_013403985.1	2686076	2686076	type	True	75.8781	96	816	95	below_threshold
Winogradskyella helgolandensis	strain=Z963	GCA_013404085.1	2697010	2697010	type	True	75.8677	109	816	95	below_threshold
Mesonia phycicola	strain=DSM 21425	GCA_900141885.1	579105	579105	type	True	75.8616	59	816	95	below_threshold
Lacinutrix mariniflava	strain=AKS432	GCA_001418015.1	342955	342955	type	True	75.8391	96	816	95	below_threshold
Winogradskyella epiphytica	strain=KCTC 12220	GCA_014651315.1	262005	262005	type	True	75.8225	74	816	95	below_threshold
Winogradskyella epiphytica	strain=CECT 7945	GCA_003217215.1	262005	262005	type	True	75.8043	75	816	95	below_threshold
Winogradskyella sediminis	strain=DSM 28134	GCA_003387355.1	1382466	1382466	type	True	75.7932	94	816	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 02:31:47,624] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6291/tc_result.tsv
[2023-03-17 02:31:47,624] [INFO] ===== Taxonomy check completed =====
[2023-03-17 02:31:47,624] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 02:31:47,624] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6b0c1879-0ae9-41cb-b918-a0956fb57af5/dqc_reference/checkm_data
[2023-03-17 02:31:47,625] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 02:31:47,633] [INFO] Task started: CheckM
[2023-03-17 02:31:47,633] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6291/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6291/checkm_input OceanDNA-b6291/checkm_result
[2023-03-17 02:32:31,392] [INFO] Task succeeded: CheckM
[2023-03-17 02:32:31,393] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 56.60%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 02:32:31,395] [INFO] ===== Completeness check finished =====
[2023-03-17 02:32:31,395] [INFO] ===== Start GTDB Search =====
[2023-03-17 02:32:31,395] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6291/markers.fasta)
[2023-03-17 02:32:31,395] [INFO] Task started: Blastn
[2023-03-17 02:32:31,395] [INFO] Running command: blastn -query OceanDNA-b6291/markers.fasta -db /var/lib/cwl/stg6b0c1879-0ae9-41cb-b918-a0956fb57af5/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6291/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:32:32,255] [INFO] Task succeeded: Blastn
[2023-03-17 02:32:32,256] [INFO] Selected 28 target genomes.
[2023-03-17 02:32:32,256] [INFO] Target genome list was writen to OceanDNA-b6291/target_genomes_gtdb.txt
[2023-03-17 02:32:32,678] [INFO] Task started: fastANI
[2023-03-17 02:32:32,678] [INFO] Running command: fastANI --query /var/lib/cwl/stga4dcec95-c040-43c1-94a8-6645e228ae49/OceanDNA-b6291.fa --refList OceanDNA-b6291/target_genomes_gtdb.txt --output OceanDNA-b6291/fastani_result_gtdb.tsv --threads 1
[2023-03-17 02:32:47,352] [INFO] Task succeeded: fastANI
[2023-03-17 02:32:47,367] [INFO] Found 28 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 02:32:47,368] [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	77.3646	247	816	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	77.2592	240	816	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	77.1716	132	816	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__PRS1	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012931685.1	s__Pseudobizionia ponticola	76.5348	105	816	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Pseudobizionia	95.0	97.35	97.35	0.92	0.92	2	-
GCF_006148925.1	s__Algibacter_D aestuarii	76.4506	95	816	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003259525.1	s__Olleya aquimaris	76.4502	102	816	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008086205.1	s__Algorimicrobium myxarmorum	76.4423	76	816	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algorimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003650305.1	s__PRS1 sp003650305	76.3939	141	816	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__PRS1	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860825.1	s__Oceanihabitans sp018860825	76.2303	131	816	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	76.1938	128	816	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wocania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003143755.1	s__Algibacter_B sp003143755	76.1861	128	816	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_000518485.1	s__Olleya marilimosa	76.1476	88	816	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	97.58	97.25	0.92	0.89	4	-
GCA_000171875.1	s__Winogradskyella sp000171875	76.1171	123	816	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003260205.1	s__Winogradskyella tangerina	76.1022	73	816	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002682935.1	s__Winogradskyella sp002682935	76.1007	81	816	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002428965.1	s__Jejuia sp002428965	76.0897	103	816	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Jejuia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003550275.1	s__QXCW01 sp003550275	76.0649	82	816	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__QXCW01	95.0	98.16	98.16	0.93	0.93	2	-
GCF_014638915.1	s__Xanthomarina arctica	76.0596	88	816	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002722255.1	s__Winogradskyella sp002722255	75.9334	83	816	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	99.90	99.90	0.80	0.80	2	-
GCF_001280515.1	s__Mangrovimonas sp001280515	75.9138	76	816	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mangrovimonas	95.0	96.69	96.69	0.89	0.89	2	-
GCF_016785945.1	s__Olleya sediminilitoris	75.8987	88	816	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	98.16	97.66	0.93	0.91	5	-
GCF_003386165.1	s__Winogradskyella eximia	75.8465	109	816	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860565.1	s__Winogradskyella psychrotolerans_B	75.8413	99	816	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013404085.1	s__Winogradskyella helgolandensis	75.8292	107	816	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	98.14	98.14	0.94	0.94	2	-
GCA_013042245.1	s__Winogradskyella sp013042245	75.7982	70	816	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	99.97	99.97	0.95	0.95	2	-
GCF_900141885.1	s__Mesonia phycicola	75.7919	58	816	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002280395.1	s__Confluentibacter sp002280395	75.7326	50	816	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Confluentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008086175.1	s__Bizionia saleffrena	75.6432	67	816	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Bizionia	95.0	99.23	99.23	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2023-03-17 02:32:47,368] [INFO] GTDB search result was written to OceanDNA-b6291/result_gtdb.tsv
[2023-03-17 02:32:47,368] [INFO] ===== GTDB Search completed =====
[2023-03-17 02:32:47,371] [INFO] DFAST_QC result json was written to OceanDNA-b6291/dqc_result.json
[2023-03-17 02:32:47,371] [INFO] DFAST_QC completed!
[2023-03-17 02:32:47,371] [INFO] Total running time: 0h1m35s