[2023-03-17 11:57:19,284] [INFO] DFAST_QC pipeline started.
[2023-03-17 11:57:19,284] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 11:57:19,284] [INFO] DQC Reference Directory: /var/lib/cwl/stge0f35df0-5a5b-4d29-85e5-d2bd4f9c9f98/dqc_reference
[2023-03-17 11:57:20,886] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 11:57:20,887] [INFO] Task started: Prodigal
[2023-03-17 11:57:20,887] [INFO] Running command: cat /var/lib/cwl/stgec032130-4394-41c8-bcbe-f4e39a4ee7de/OceanDNA-b11359.fa | prodigal -d OceanDNA-b11359/cds.fna -a OceanDNA-b11359/protein.faa -g 11 -q > /dev/null
[2023-03-17 11:57:34,925] [INFO] Task succeeded: Prodigal
[2023-03-17 11:57:34,926] [INFO] Task started: HMMsearch
[2023-03-17 11:57:34,926] [INFO] Running command: hmmsearch --tblout OceanDNA-b11359/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge0f35df0-5a5b-4d29-85e5-d2bd4f9c9f98/dqc_reference/reference_markers.hmm OceanDNA-b11359/protein.faa > /dev/null
[2023-03-17 11:57:35,077] [INFO] Task succeeded: HMMsearch
[2023-03-17 11:57:35,077] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgec032130-4394-41c8-bcbe-f4e39a4ee7de/OceanDNA-b11359.fa]
[2023-03-17 11:57:35,092] [INFO] Query marker FASTA was written to OceanDNA-b11359/markers.fasta
[2023-03-17 11:57:35,092] [INFO] Task started: Blastn
[2023-03-17 11:57:35,092] [INFO] Running command: blastn -query OceanDNA-b11359/markers.fasta -db /var/lib/cwl/stge0f35df0-5a5b-4d29-85e5-d2bd4f9c9f98/dqc_reference/reference_markers.fasta -out OceanDNA-b11359/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:57:35,644] [INFO] Task succeeded: Blastn
[2023-03-17 11:57:35,644] [INFO] Selected 20 target genomes.
[2023-03-17 11:57:35,645] [INFO] Target genome list was writen to OceanDNA-b11359/target_genomes.txt
[2023-03-17 11:57:35,657] [INFO] Task started: fastANI
[2023-03-17 11:57:35,657] [INFO] Running command: fastANI --query /var/lib/cwl/stgec032130-4394-41c8-bcbe-f4e39a4ee7de/OceanDNA-b11359.fa --refList OceanDNA-b11359/target_genomes.txt --output OceanDNA-b11359/fastani_result.tsv --threads 1
[2023-03-17 11:57:47,428] [INFO] Task succeeded: fastANI
[2023-03-17 11:57:47,429] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge0f35df0-5a5b-4d29-85e5-d2bd4f9c9f98/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 11:57:47,429] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge0f35df0-5a5b-4d29-85e5-d2bd4f9c9f98/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 11:57:47,440] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 11:57:47,440] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 11:57:47,440] [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
Winogradskyella algicola	strain=IMCC33238	GCA_005869935.1	2575815	2575815	type	True	77.0667	111	720	95	below_threshold
Winogradskyella haliclonae	strain=CCM 8681	GCA_014635865.1	2048558	2048558	type	True	76.8281	110	720	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014284085.1	538189	538189	type	True	76.7326	133	720	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014297365.1	538189	538189	type	True	76.7326	133	720	95	below_threshold
Winogradskyella tangerina	strain=M1309	GCA_003260205.1	2023240	2023240	type	True	76.5986	87	720	95	below_threshold
Winogradskyella wandonensis	strain=CECT 8445	GCA_004346845.1	1442586	1442586	type	True	76.58	93	720	95	below_threshold
Winogradskyella ouciana	strain=ZXX205	GCA_009709615.1	2608631	2608631	type	True	76.5622	103	720	95	below_threshold
Winogradskyella helgolandensis	strain=Z963	GCA_013404085.1	2697010	2697010	type	True	76.5182	118	720	95	below_threshold
Winogradskyella sediminis	strain=DSM 28134	GCA_003387355.1	1382466	1382466	type	True	76.4842	108	720	95	below_threshold
Winogradskyella psychrotolerans	strain=RS-3	GCA_000427335.1	1344585	1344585	type	True	76.47	108	720	95	below_threshold
Winogradskyella vidalii	strain=HL634	GCA_013403955.1	2615024	2615024	type	True	76.4452	119	720	95	below_threshold
Winogradskyella undariae	strain=CCUG 63832	GCA_013285155.1	1285465	1285465	type	True	76.4436	116	720	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	76.3326	77	720	95	below_threshold
Winogradskyella marina	strain=F6397	GCA_015645385.1	2785530	2785530	type	True	76.2713	117	720	95	below_threshold
Winogradskyella flava	strain=KCTC 52348	GCA_014243395.1	1884876	1884876	type	True	76.2663	104	720	95	below_threshold
Winogradskyella thalassocola	strain=DSM 15363	GCA_900099995.1	262004	262004	type	True	76.2409	116	720	95	below_threshold
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	76.1964	109	720	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	76.15	89	720	95	below_threshold
Seonamhaeicola aphaedonensis	strain=CECT 8487	GCA_003386195.1	1461338	1461338	type	True	76.1312	82	720	95	below_threshold
Olleya aquimaris	strain=DSM 24464	GCA_003259525.1	639310	639310	type	True	76.0768	97	720	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 11:57:47,440] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11359/tc_result.tsv
[2023-03-17 11:57:47,440] [INFO] ===== Taxonomy check completed =====
[2023-03-17 11:57:47,441] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 11:57:47,441] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge0f35df0-5a5b-4d29-85e5-d2bd4f9c9f98/dqc_reference/checkm_data
[2023-03-17 11:57:47,441] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 11:57:47,445] [INFO] Task started: CheckM
[2023-03-17 11:57:47,445] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11359/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11359/checkm_input OceanDNA-b11359/checkm_result
[2023-03-17 11:58:26,020] [INFO] Task succeeded: CheckM
[2023-03-17 11:58:26,020] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 11:58:26,022] [INFO] ===== Completeness check finished =====
[2023-03-17 11:58:26,022] [INFO] ===== Start GTDB Search =====
[2023-03-17 11:58:26,022] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11359/markers.fasta)
[2023-03-17 11:58:26,022] [INFO] Task started: Blastn
[2023-03-17 11:58:26,022] [INFO] Running command: blastn -query OceanDNA-b11359/markers.fasta -db /var/lib/cwl/stge0f35df0-5a5b-4d29-85e5-d2bd4f9c9f98/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11359/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:58:26,799] [INFO] Task succeeded: Blastn
[2023-03-17 11:58:26,800] [INFO] Selected 20 target genomes.
[2023-03-17 11:58:26,800] [INFO] Target genome list was writen to OceanDNA-b11359/target_genomes_gtdb.txt
[2023-03-17 11:58:26,867] [INFO] Task started: fastANI
[2023-03-17 11:58:26,867] [INFO] Running command: fastANI --query /var/lib/cwl/stgec032130-4394-41c8-bcbe-f4e39a4ee7de/OceanDNA-b11359.fa --refList OceanDNA-b11359/target_genomes_gtdb.txt --output OceanDNA-b11359/fastani_result_gtdb.tsv --threads 1
[2023-03-17 11:58:37,931] [INFO] Task succeeded: fastANI
[2023-03-17 11:58:37,943] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 11:58:37,943] [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_002722255.1	s__Winogradskyella sp002722255	76.8817	113	720	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	99.90	99.90	0.80	0.80	2	-
GCF_014635865.1	s__Winogradskyella haliclonae	76.8495	109	720	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013042245.1	s__Winogradskyella sp013042245	76.8461	97	720	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	99.97	99.97	0.95	0.95	2	-
GCA_013213975.1	s__Winogradskyella sp013213975	76.83	101	720	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001971725.1	s__Winogradskyella sp001971725	76.7799	112	720	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	76.7515	110	720	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014297365.1	s__Winogradskyella echinorum	76.7496	132	720	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003610635.1	s__Ichthyenterobacterium magnum	76.7328	106	720	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Ichthyenterobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013213835.1	s__Winogradskyella sp013213835	76.698	118	720	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004346845.1	s__Winogradskyella wandonensis	76.58	93	720	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009709615.1	s__Winogradskyella ouciana	76.5622	103	720	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	97.22	97.22	0.91	0.91	2	-
GCA_003443635.1	s__AU392 sp003443635	76.5558	87	720	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__AU392	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002682935.1	s__Winogradskyella sp002682935	76.5387	105	720	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004366715.1	s__Meridianimaribacter flavus	76.5163	111	720	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Meridianimaribacter	95.0	97.44	97.06	0.91	0.87	3	-
GCF_014202195.1	s__Oceanihabitans iliipiscarium	76.4694	86	720	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013403955.1	s__Winogradskyella vidalii	76.4618	118	720	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860545.1	s__Winogradskyella psychrotolerans_A	76.2736	114	720	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425305.1	s__Psychroserpens burtonensis	76.129	107	720	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	99.48	99.48	0.94	0.94	2	-
GCA_002162685.1	s__Psychroserpens sp002162685	76.0573	125	720	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860825.1	s__Oceanihabitans sp018860825	75.7964	100	720	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 11:58:37,943] [INFO] GTDB search result was written to OceanDNA-b11359/result_gtdb.tsv
[2023-03-17 11:58:37,943] [INFO] ===== GTDB Search completed =====
[2023-03-17 11:58:37,945] [INFO] DFAST_QC result json was written to OceanDNA-b11359/dqc_result.json
[2023-03-17 11:58:37,945] [INFO] DFAST_QC completed!
[2023-03-17 11:58:37,945] [INFO] Total running time: 0h1m19s