[2023-03-18 00:21:56,064] [INFO] DFAST_QC pipeline started.
[2023-03-18 00:21:56,065] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 00:21:56,065] [INFO] DQC Reference Directory: /var/lib/cwl/stga58b9bcd-e9ce-4c9d-92b0-795b59a6cb97/dqc_reference
[2023-03-18 00:21:57,150] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 00:21:57,150] [INFO] Task started: Prodigal
[2023-03-18 00:21:57,150] [INFO] Running command: cat /var/lib/cwl/stgdcc31e45-6f3a-4cd2-8948-31f0ba5f6e40/OceanDNA-b11401.fa | prodigal -d OceanDNA-b11401/cds.fna -a OceanDNA-b11401/protein.faa -g 11 -q > /dev/null
[2023-03-18 00:22:15,086] [INFO] Task succeeded: Prodigal
[2023-03-18 00:22:15,087] [INFO] Task started: HMMsearch
[2023-03-18 00:22:15,087] [INFO] Running command: hmmsearch --tblout OceanDNA-b11401/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga58b9bcd-e9ce-4c9d-92b0-795b59a6cb97/dqc_reference/reference_markers.hmm OceanDNA-b11401/protein.faa > /dev/null
[2023-03-18 00:22:15,296] [INFO] Task succeeded: HMMsearch
[2023-03-18 00:22:15,297] [INFO] Found 6/6 markers.
[2023-03-18 00:22:15,316] [INFO] Query marker FASTA was written to OceanDNA-b11401/markers.fasta
[2023-03-18 00:22:15,317] [INFO] Task started: Blastn
[2023-03-18 00:22:15,317] [INFO] Running command: blastn -query OceanDNA-b11401/markers.fasta -db /var/lib/cwl/stga58b9bcd-e9ce-4c9d-92b0-795b59a6cb97/dqc_reference/reference_markers.fasta -out OceanDNA-b11401/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:22:15,919] [INFO] Task succeeded: Blastn
[2023-03-18 00:22:15,919] [INFO] Selected 17 target genomes.
[2023-03-18 00:22:15,920] [INFO] Target genome list was writen to OceanDNA-b11401/target_genomes.txt
[2023-03-18 00:22:15,926] [INFO] Task started: fastANI
[2023-03-18 00:22:15,926] [INFO] Running command: fastANI --query /var/lib/cwl/stgdcc31e45-6f3a-4cd2-8948-31f0ba5f6e40/OceanDNA-b11401.fa --refList OceanDNA-b11401/target_genomes.txt --output OceanDNA-b11401/fastani_result.tsv --threads 1
[2023-03-18 00:22:26,051] [INFO] Task succeeded: fastANI
[2023-03-18 00:22:26,051] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga58b9bcd-e9ce-4c9d-92b0-795b59a6cb97/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 00:22:26,051] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga58b9bcd-e9ce-4c9d-92b0-795b59a6cb97/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 00:22:26,061] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 00:22:26,061] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 00:22:26,061] [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 tangerina	strain=M1309	GCA_003260205.1	2023240	2023240	type	True	81.1152	640	878	95	below_threshold
Winogradskyella algicola	strain=IMCC33238	GCA_005869935.1	2575815	2575815	type	True	78.1894	326	878	95	below_threshold
Winogradskyella ouciana	strain=ZXX205	GCA_009709615.1	2608631	2608631	type	True	77.9396	331	878	95	below_threshold
Winogradskyella flava	strain=KCTC 52348	GCA_014243395.1	1884876	1884876	type	True	77.7956	316	878	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014284085.1	538189	538189	type	True	77.6504	284	878	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014297365.1	538189	538189	type	True	77.6391	285	878	95	below_threshold
Winogradskyella litoriviva	strain=KMM6491	GCA_013249065.1	1220182	1220182	type	True	77.2701	240	878	95	below_threshold
Winogradskyella schleiferi	strain=Z215	GCA_013394655.1	2686078	2686078	type	True	77.1102	226	878	95	below_threshold
Winogradskyella psychrotolerans	strain=RS-3	GCA_000427335.1	1344585	1344585	type	True	77.1011	215	878	95	below_threshold
Winogradskyella thalassocola	strain=DSM 15363	GCA_900099995.1	262004	262004	type	True	77.0922	242	878	95	below_threshold
Winogradskyella vidalii	strain=HL634	GCA_013403955.1	2615024	2615024	type	True	77.0263	213	878	95	below_threshold
Winogradskyella haliclonae	strain=CCM 8681	GCA_014635865.1	2048558	2048558	type	True	76.8914	178	878	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	76.6331	96	878	95	below_threshold
Aestuariivivens insulae	strain=AH-MY3	GCA_022662195.1	1621988	1621988	type	True	76.4288	79	878	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	76.3834	119	878	95	below_threshold
Hyunsoonleella aquatilis	strain=SJ7	GCA_014270105.1	2762758	2762758	type	True	76.2295	70	878	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 00:22:26,062] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11401/tc_result.tsv
[2023-03-18 00:22:26,062] [INFO] ===== Taxonomy check completed =====
[2023-03-18 00:22:26,062] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 00:22:26,062] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga58b9bcd-e9ce-4c9d-92b0-795b59a6cb97/dqc_reference/checkm_data
[2023-03-18 00:22:26,063] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 00:22:26,067] [INFO] Task started: CheckM
[2023-03-18 00:22:26,067] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11401/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11401/checkm_input OceanDNA-b11401/checkm_result
[2023-03-18 00:23:13,375] [INFO] Task succeeded: CheckM
[2023-03-18 00:23:13,375] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 00:23:13,378] [INFO] ===== Completeness check finished =====
[2023-03-18 00:23:13,378] [INFO] ===== Start GTDB Search =====
[2023-03-18 00:23:13,378] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11401/markers.fasta)
[2023-03-18 00:23:13,378] [INFO] Task started: Blastn
[2023-03-18 00:23:13,378] [INFO] Running command: blastn -query OceanDNA-b11401/markers.fasta -db /var/lib/cwl/stga58b9bcd-e9ce-4c9d-92b0-795b59a6cb97/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11401/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:23:14,240] [INFO] Task succeeded: Blastn
[2023-03-18 00:23:14,241] [INFO] Selected 22 target genomes.
[2023-03-18 00:23:14,241] [INFO] Target genome list was writen to OceanDNA-b11401/target_genomes_gtdb.txt
[2023-03-18 00:23:14,263] [INFO] Task started: fastANI
[2023-03-18 00:23:14,263] [INFO] Running command: fastANI --query /var/lib/cwl/stgdcc31e45-6f3a-4cd2-8948-31f0ba5f6e40/OceanDNA-b11401.fa --refList OceanDNA-b11401/target_genomes_gtdb.txt --output OceanDNA-b11401/fastani_result_gtdb.tsv --threads 1
[2023-03-18 00:23:27,774] [INFO] Task succeeded: fastANI
[2023-03-18 00:23:27,786] [INFO] Found 22 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 00:23:27,787] [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_003260205.1	s__Winogradskyella tangerina	81.1188	640	878	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	78.3932	290	878	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002722255.1	s__Winogradskyella sp002722255	78.3189	260	878	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	78.1894	326	878	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	78.0971	293	878	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	77.9396	331	878	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	97.22	97.22	0.91	0.91	2	-
GCA_013213975.1	s__Winogradskyella sp013213975	77.8695	297	878	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	77.8588	300	878	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	77.8081	316	878	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	77.647	283	878	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_016744625.1	s__Winogradskyella sp016744625	77.6211	289	878	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	77.608	300	878	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	77.5677	285	878	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013213835.1	s__Winogradskyella sp013213835	77.5482	245	878	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	77.2426	222	878	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003386165.1	s__Winogradskyella eximia	77.1834	234	878	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013394655.1	s__Winogradskyella schleiferi	77.1106	224	878	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900099995.1	s__Winogradskyella thalassocola	77.0746	242	878	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013403955.1	s__Winogradskyella vidalii	77.0267	213	878	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014635865.1	s__Winogradskyella haliclonae	76.8914	178	878	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004211785.1	s__Winogradskyella sp004211785	76.8468	146	878	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	76.5051	141	878	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	99.97	99.97	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2023-03-18 00:23:27,787] [INFO] GTDB search result was written to OceanDNA-b11401/result_gtdb.tsv
[2023-03-18 00:23:27,787] [INFO] ===== GTDB Search completed =====
[2023-03-18 00:23:27,789] [INFO] DFAST_QC result json was written to OceanDNA-b11401/dqc_result.json
[2023-03-18 00:23:27,789] [INFO] DFAST_QC completed!
[2023-03-18 00:23:27,789] [INFO] Total running time: 0h1m32s