[2023-03-17 23:31:12,156] [INFO] DFAST_QC pipeline started.
[2023-03-17 23:31:12,156] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 23:31:12,156] [INFO] DQC Reference Directory: /var/lib/cwl/stgd59b23b6-433f-49ce-9372-1d3749b50e9e/dqc_reference
[2023-03-17 23:31:13,282] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 23:31:13,283] [INFO] Task started: Prodigal
[2023-03-17 23:31:13,283] [INFO] Running command: cat /var/lib/cwl/stg223fc187-4d8e-41fe-8097-b93ff5d1000d/OceanDNA-b11404.fa | prodigal -d OceanDNA-b11404/cds.fna -a OceanDNA-b11404/protein.faa -g 11 -q > /dev/null
[2023-03-17 23:31:30,306] [INFO] Task succeeded: Prodigal
[2023-03-17 23:31:30,306] [INFO] Task started: HMMsearch
[2023-03-17 23:31:30,306] [INFO] Running command: hmmsearch --tblout OceanDNA-b11404/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd59b23b6-433f-49ce-9372-1d3749b50e9e/dqc_reference/reference_markers.hmm OceanDNA-b11404/protein.faa > /dev/null
[2023-03-17 23:31:30,485] [INFO] Task succeeded: HMMsearch
[2023-03-17 23:31:30,486] [INFO] Found 6/6 markers.
[2023-03-17 23:31:30,507] [INFO] Query marker FASTA was written to OceanDNA-b11404/markers.fasta
[2023-03-17 23:31:30,508] [INFO] Task started: Blastn
[2023-03-17 23:31:30,508] [INFO] Running command: blastn -query OceanDNA-b11404/markers.fasta -db /var/lib/cwl/stgd59b23b6-433f-49ce-9372-1d3749b50e9e/dqc_reference/reference_markers.fasta -out OceanDNA-b11404/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:31:31,117] [INFO] Task succeeded: Blastn
[2023-03-17 23:31:31,118] [INFO] Selected 20 target genomes.
[2023-03-17 23:31:31,118] [INFO] Target genome list was writen to OceanDNA-b11404/target_genomes.txt
[2023-03-17 23:31:31,130] [INFO] Task started: fastANI
[2023-03-17 23:31:31,130] [INFO] Running command: fastANI --query /var/lib/cwl/stg223fc187-4d8e-41fe-8097-b93ff5d1000d/OceanDNA-b11404.fa --refList OceanDNA-b11404/target_genomes.txt --output OceanDNA-b11404/fastani_result.tsv --threads 1
[2023-03-17 23:31:43,695] [INFO] Task succeeded: fastANI
[2023-03-17 23:31:43,696] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd59b23b6-433f-49ce-9372-1d3749b50e9e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 23:31:43,696] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd59b23b6-433f-49ce-9372-1d3749b50e9e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 23:31:43,707] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 23:31:43,707] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 23:31:43,707] [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	78.5505	338	891	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014297365.1	538189	538189	type	True	78.3089	336	891	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014284085.1	538189	538189	type	True	78.3089	336	891	95	below_threshold
Winogradskyella tangerina	strain=M1309	GCA_003260205.1	2023240	2023240	type	True	78.2679	332	891	95	below_threshold
Winogradskyella flava	strain=KCTC 52348	GCA_014243395.1	1884876	1884876	type	True	78.228	351	891	95	below_threshold
Winogradskyella ouciana	strain=ZXX205	GCA_009709615.1	2608631	2608631	type	True	78.18	358	891	95	below_threshold
Winogradskyella psychrotolerans	strain=RS-3	GCA_000427335.1	1344585	1344585	type	True	78.1154	246	891	95	below_threshold
Winogradskyella thalassocola	strain=DSM 15363	GCA_900099995.1	262004	262004	type	True	78.0529	260	891	95	below_threshold
Winogradskyella ludwigii	strain=HL116	GCA_013403985.1	2686076	2686076	type	True	77.9416	259	891	95	below_threshold
Winogradskyella marina	strain=F6397	GCA_015645385.1	2785530	2785530	type	True	77.9382	237	891	95	below_threshold
Winogradskyella wichelsiae	strain=Z738	GCA_013403925.1	2697007	2697007	type	True	77.8152	235	891	95	below_threshold
Winogradskyella litoriviva	strain=KMM6491	GCA_013249065.1	1220182	1220182	type	True	77.7709	271	891	95	below_threshold
Winogradskyella sediminis	strain=DSM 28134	GCA_003387355.1	1382466	1382466	type	True	77.7338	252	891	95	below_threshold
Winogradskyella jejuensis	strain=DSM 25330	GCA_900129745.1	1089305	1089305	type	True	77.6982	212	891	95	below_threshold
Winogradskyella wandonensis	strain=CECT 8445	GCA_004346845.1	1442586	1442586	type	True	77.6772	201	891	95	below_threshold
Winogradskyella endarachnes	strain=HL2-2	GCA_009741275.1	2681965	2681965	type	True	77.662	267	891	95	below_threshold
Winogradskyella vidalii	strain=HL634	GCA_013403955.1	2615024	2615024	type	True	77.636	219	891	95	below_threshold
Hyunsoonleella aquatilis	strain=SJ7	GCA_014270105.1	2762758	2762758	type	True	77.2091	70	891	95	below_threshold
Flavobacterium sediminilitoris	strain=YSM-43	GCA_023008245.1	2024526	2024526	type	True	75.7178	67	891	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 23:31:43,708] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11404/tc_result.tsv
[2023-03-17 23:31:43,708] [INFO] ===== Taxonomy check completed =====
[2023-03-17 23:31:43,708] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 23:31:43,708] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd59b23b6-433f-49ce-9372-1d3749b50e9e/dqc_reference/checkm_data
[2023-03-17 23:31:43,709] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 23:31:43,713] [INFO] Task started: CheckM
[2023-03-17 23:31:43,713] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11404/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11404/checkm_input OceanDNA-b11404/checkm_result
[2023-03-17 23:32:28,205] [INFO] Task succeeded: CheckM
[2023-03-17 23:32:28,205] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 23:32:28,208] [INFO] ===== Completeness check finished =====
[2023-03-17 23:32:28,208] [INFO] ===== Start GTDB Search =====
[2023-03-17 23:32:28,208] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11404/markers.fasta)
[2023-03-17 23:32:28,209] [INFO] Task started: Blastn
[2023-03-17 23:32:28,209] [INFO] Running command: blastn -query OceanDNA-b11404/markers.fasta -db /var/lib/cwl/stgd59b23b6-433f-49ce-9372-1d3749b50e9e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11404/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:32:29,114] [INFO] Task succeeded: Blastn
[2023-03-17 23:32:29,115] [INFO] Selected 20 target genomes.
[2023-03-17 23:32:29,115] [INFO] Target genome list was writen to OceanDNA-b11404/target_genomes_gtdb.txt
[2023-03-17 23:32:29,326] [INFO] Task started: fastANI
[2023-03-17 23:32:29,326] [INFO] Running command: fastANI --query /var/lib/cwl/stg223fc187-4d8e-41fe-8097-b93ff5d1000d/OceanDNA-b11404.fa --refList OceanDNA-b11404/target_genomes_gtdb.txt --output OceanDNA-b11404/fastani_result_gtdb.tsv --threads 1
[2023-03-17 23:32:42,733] [INFO] Task succeeded: fastANI
[2023-03-17 23:32:42,744] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 23:32:42,744] [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_013213975.1	s__Winogradskyella sp013213975	99.758	828	891	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002722255.1	s__Winogradskyella sp002722255	78.7064	280	891	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	99.90	99.90	0.80	0.80	2	-
GCF_005869935.1	s__Winogradskyella algicola	78.5385	339	891	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	78.4661	327	891	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	78.3539	317	891	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	78.3059	344	891	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	78.2987	337	891	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003260205.1	s__Winogradskyella tangerina	78.2679	332	891	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000171875.1	s__Winogradskyella sp000171875	78.2431	348	891	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003335675.1	s__Winogradskyella sp003335675	78.2387	273	891	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	78.228	351	891	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	78.1824	359	891	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	97.22	97.22	0.91	0.91	2	-
GCA_013213835.1	s__Winogradskyella sp013213835	78.1643	286	891	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016744625.1	s__Winogradskyella sp016744625	78.063	319	891	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013403915.1	s__Winogradskyella pacifica	77.8491	266	891	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	97.90	97.90	0.94	0.94	2	-
GCF_013403865.1	s__Winogradskyella costae	77.8308	234	891	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	77.7693	269	891	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002163855.1	s__Winogradskyella sp002163855	77.5623	232	891	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	99.88	99.82	0.99	0.99	3	-
GCF_004366715.1	s__Meridianimaribacter flavus	77.2211	176	891	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Meridianimaribacter	95.0	97.44	97.06	0.91	0.87	3	-
GCF_004310335.1	s__Jejuia pacifica	77.1798	128	891	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Jejuia	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-17 23:32:42,746] [INFO] GTDB search result was written to OceanDNA-b11404/result_gtdb.tsv
[2023-03-17 23:32:42,746] [INFO] ===== GTDB Search completed =====
[2023-03-17 23:32:42,748] [INFO] DFAST_QC result json was written to OceanDNA-b11404/dqc_result.json
[2023-03-17 23:32:42,749] [INFO] DFAST_QC completed!
[2023-03-17 23:32:42,749] [INFO] Total running time: 0h1m31s