[2023-03-15 03:25:37,028] [INFO] DFAST_QC pipeline started.
[2023-03-15 03:25:37,029] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 03:25:37,029] [INFO] DQC Reference Directory: /var/lib/cwl/stg3be61101-6c35-4b96-8f68-380bcdc816c6/dqc_reference
[2023-03-15 03:25:38,117] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 03:25:38,117] [INFO] Task started: Prodigal
[2023-03-15 03:25:38,117] [INFO] Running command: cat /var/lib/cwl/stgfac77004-4b1a-4e6d-b65b-5f460b43d1c8/OceanDNA-b11407.fa | prodigal -d OceanDNA-b11407/cds.fna -a OceanDNA-b11407/protein.faa -g 11 -q > /dev/null
[2023-03-15 03:25:47,849] [INFO] Task succeeded: Prodigal
[2023-03-15 03:25:47,849] [INFO] Task started: HMMsearch
[2023-03-15 03:25:47,849] [INFO] Running command: hmmsearch --tblout OceanDNA-b11407/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3be61101-6c35-4b96-8f68-380bcdc816c6/dqc_reference/reference_markers.hmm OceanDNA-b11407/protein.faa > /dev/null
[2023-03-15 03:25:48,011] [INFO] Task succeeded: HMMsearch
[2023-03-15 03:25:48,012] [INFO] Found 6/6 markers.
[2023-03-15 03:25:48,027] [INFO] Query marker FASTA was written to OceanDNA-b11407/markers.fasta
[2023-03-15 03:25:48,028] [INFO] Task started: Blastn
[2023-03-15 03:25:48,028] [INFO] Running command: blastn -query OceanDNA-b11407/markers.fasta -db /var/lib/cwl/stg3be61101-6c35-4b96-8f68-380bcdc816c6/dqc_reference/reference_markers.fasta -out OceanDNA-b11407/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:25:48,619] [INFO] Task succeeded: Blastn
[2023-03-15 03:25:48,620] [INFO] Selected 23 target genomes.
[2023-03-15 03:25:48,620] [INFO] Target genome list was writen to OceanDNA-b11407/target_genomes.txt
[2023-03-15 03:25:48,645] [INFO] Task started: fastANI
[2023-03-15 03:25:48,645] [INFO] Running command: fastANI --query /var/lib/cwl/stgfac77004-4b1a-4e6d-b65b-5f460b43d1c8/OceanDNA-b11407.fa --refList OceanDNA-b11407/target_genomes.txt --output OceanDNA-b11407/fastani_result.tsv --threads 1
[2023-03-15 03:26:01,736] [INFO] Task succeeded: fastANI
[2023-03-15 03:26:01,736] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3be61101-6c35-4b96-8f68-380bcdc816c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 03:26:01,736] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3be61101-6c35-4b96-8f68-380bcdc816c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 03:26:01,748] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 03:26:01,748] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 03:26:01,748] [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	77.7167	174	417	95	below_threshold
Winogradskyella ouciana	strain=ZXX205	GCA_009709615.1	2608631	2608631	type	True	77.5856	164	417	95	below_threshold
Winogradskyella tangerina	strain=M1309	GCA_003260205.1	2023240	2023240	type	True	77.5732	170	417	95	below_threshold
Winogradskyella flava	strain=KCTC 52348	GCA_014243395.1	1884876	1884876	type	True	77.4711	154	417	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014297365.1	538189	538189	type	True	77.2564	154	417	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014284085.1	538189	538189	type	True	77.2388	155	417	95	below_threshold
Winogradskyella litoriviva	strain=KMM6491	GCA_013249065.1	1220182	1220182	type	True	77.102	118	417	95	below_threshold
Winogradskyella undariae	strain=CCUG 63832	GCA_013285155.1	1285465	1285465	type	True	77.0172	118	417	95	below_threshold
Winogradskyella jejuensis	strain=DSM 25330	GCA_900129745.1	1089305	1089305	type	True	76.9399	112	417	95	below_threshold
Winogradskyella aurantia	strain=WNB302	GCA_002266855.1	1915063	1915063	type	True	76.9059	86	417	95	below_threshold
Winogradskyella endarachnes	strain=HL2-2	GCA_009741275.1	2681965	2681965	type	True	76.8617	135	417	95	below_threshold
Winogradskyella vidalii	strain=HL634	GCA_013403955.1	2615024	2615024	type	True	76.8461	118	417	95	below_threshold
Winogradskyella eckloniae	strain=EC29	GCA_013249045.1	1089306	1089306	type	True	76.7665	142	417	95	below_threshold
Winogradskyella thalassocola	strain=DSM 15363	GCA_900099995.1	262004	262004	type	True	76.7351	127	417	95	below_threshold
Arenitalea lutea	strain=CGMCC 1.12213	GCA_900141715.1	1178825	1178825	type	True	76.6727	80	417	95	below_threshold
Seonamhaeicola maritimus	strain=1505	GCA_008056315.1	2591822	2591822	type	True	76.4963	75	417	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	76.4612	68	417	95	below_threshold
Yeosuana marina	strain=JLT21	GCA_011762485.1	1565536	1565536	type	True	76.2281	73	417	95	below_threshold
Aestuariivivens insulae	strain=AH-MY3	GCA_022662195.1	1621988	1621988	type	True	76.1502	62	417	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 03:26:01,749] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11407/tc_result.tsv
[2023-03-15 03:26:01,749] [INFO] ===== Taxonomy check completed =====
[2023-03-15 03:26:01,749] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 03:26:01,749] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3be61101-6c35-4b96-8f68-380bcdc816c6/dqc_reference/checkm_data
[2023-03-15 03:26:01,750] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 03:26:01,754] [INFO] Task started: CheckM
[2023-03-15 03:26:01,754] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11407/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11407/checkm_input OceanDNA-b11407/checkm_result
[2023-03-15 03:26:30,909] [INFO] Task succeeded: CheckM
[2023-03-15 03:26:30,909] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 59.23%
Contamintation: 16.67%
Strain heterogeneity: 28.57%
--------------------------------------------------------------------------------
[2023-03-15 03:26:30,912] [INFO] ===== Completeness check finished =====
[2023-03-15 03:26:30,913] [INFO] ===== Start GTDB Search =====
[2023-03-15 03:26:30,913] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11407/markers.fasta)
[2023-03-15 03:26:30,914] [INFO] Task started: Blastn
[2023-03-15 03:26:30,914] [INFO] Running command: blastn -query OceanDNA-b11407/markers.fasta -db /var/lib/cwl/stg3be61101-6c35-4b96-8f68-380bcdc816c6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11407/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:26:31,759] [INFO] Task succeeded: Blastn
[2023-03-15 03:26:31,761] [INFO] Selected 22 target genomes.
[2023-03-15 03:26:31,761] [INFO] Target genome list was writen to OceanDNA-b11407/target_genomes_gtdb.txt
[2023-03-15 03:26:31,773] [INFO] Task started: fastANI
[2023-03-15 03:26:31,773] [INFO] Running command: fastANI --query /var/lib/cwl/stgfac77004-4b1a-4e6d-b65b-5f460b43d1c8/OceanDNA-b11407.fa --refList OceanDNA-b11407/target_genomes_gtdb.txt --output OceanDNA-b11407/fastani_result_gtdb.tsv --threads 1
[2023-03-15 03:26:44,789] [INFO] Task succeeded: fastANI
[2023-03-15 03:26:44,802] [INFO] Found 22 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 03:26:44,802] [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_002682935.1	s__Winogradskyella sp002682935	77.8992	154	417	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005869935.1	s__Winogradskyella algicola	77.7167	174	417	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	77.5732	170	417	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019203985.1	s__Winogradskyella sp019203985	77.4765	173	417	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	77.4737	154	417	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014243395.1	s__Winogradskyella flava	77.4711	154	417	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013213975.1	s__Winogradskyella sp013213975	77.4444	137	417	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000828715.1	s__Winogradskyella sp000828715	77.4144	155	417	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	77.2564	154	417	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_015645385.1	s__Winogradskyella sp015645385	77.2458	128	417	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013249065.1	s__Winogradskyella litoriviva	77.102	118	417	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002364335.1	s__Winogradskyella sp002364335	77.0536	138	417	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013285155.1	s__Winogradskyella undariae	77.0172	118	417	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	97.00	96.07	0.88	0.85	4	-
GCF_900129745.1	s__Winogradskyella jejuensis	76.9399	112	417	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002266855.1	s__Winogradskyella aurantia	76.9059	86	417	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	76.8994	137	417	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013249045.1	s__Winogradskyella eckloniae	76.7665	142	417	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	76.6719	125	417	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008056315.1	s__Seonamhaeicola maritimus	76.4963	75	417	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Seonamhaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016827605.1	s__Jejuia sp016827605	76.4612	68	417	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Jejuia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000789235.1	s__Wocania ichthyoenteri	76.1862	91	417	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wocania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003425985.1	s__Mariniflexile sp002848895	75.9032	61	417	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mariniflexile	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-15 03:26:44,803] [INFO] GTDB search result was written to OceanDNA-b11407/result_gtdb.tsv
[2023-03-15 03:26:44,803] [INFO] ===== GTDB Search completed =====
[2023-03-15 03:26:44,805] [INFO] DFAST_QC result json was written to OceanDNA-b11407/dqc_result.json
[2023-03-15 03:26:44,805] [INFO] DFAST_QC completed!
[2023-03-15 03:26:44,806] [INFO] Total running time: 0h1m8s