[2023-03-16 03:47:32,870] [INFO] DFAST_QC pipeline started.
[2023-03-16 03:47:32,870] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 03:47:32,871] [INFO] DQC Reference Directory: /var/lib/cwl/stgc369f0c0-299a-473d-a689-f1b66024a7b4/dqc_reference
[2023-03-16 03:47:34,531] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 03:47:34,531] [INFO] Task started: Prodigal
[2023-03-16 03:47:34,531] [INFO] Running command: cat /var/lib/cwl/stg198ea0cc-1558-4a46-a5f3-ea1a7876d6ac/OceanDNA-b11357.fa | prodigal -d OceanDNA-b11357/cds.fna -a OceanDNA-b11357/protein.faa -g 11 -q > /dev/null
[2023-03-16 03:47:49,033] [INFO] Task succeeded: Prodigal
[2023-03-16 03:47:49,034] [INFO] Task started: HMMsearch
[2023-03-16 03:47:49,034] [INFO] Running command: hmmsearch --tblout OceanDNA-b11357/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc369f0c0-299a-473d-a689-f1b66024a7b4/dqc_reference/reference_markers.hmm OceanDNA-b11357/protein.faa > /dev/null
[2023-03-16 03:47:49,279] [INFO] Task succeeded: HMMsearch
[2023-03-16 03:47:49,280] [INFO] Found 6/6 markers.
[2023-03-16 03:47:49,299] [INFO] Query marker FASTA was written to OceanDNA-b11357/markers.fasta
[2023-03-16 03:47:49,299] [INFO] Task started: Blastn
[2023-03-16 03:47:49,299] [INFO] Running command: blastn -query OceanDNA-b11357/markers.fasta -db /var/lib/cwl/stgc369f0c0-299a-473d-a689-f1b66024a7b4/dqc_reference/reference_markers.fasta -out OceanDNA-b11357/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 03:47:49,892] [INFO] Task succeeded: Blastn
[2023-03-16 03:47:49,893] [INFO] Selected 23 target genomes.
[2023-03-16 03:47:49,893] [INFO] Target genome list was writen to OceanDNA-b11357/target_genomes.txt
[2023-03-16 03:47:49,908] [INFO] Task started: fastANI
[2023-03-16 03:47:49,908] [INFO] Running command: fastANI --query /var/lib/cwl/stg198ea0cc-1558-4a46-a5f3-ea1a7876d6ac/OceanDNA-b11357.fa --refList OceanDNA-b11357/target_genomes.txt --output OceanDNA-b11357/fastani_result.tsv --threads 1
[2023-03-16 03:48:03,734] [INFO] Task succeeded: fastANI
[2023-03-16 03:48:03,735] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc369f0c0-299a-473d-a689-f1b66024a7b4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 03:48:03,735] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc369f0c0-299a-473d-a689-f1b66024a7b4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 03:48:03,748] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 03:48:03,748] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 03:48:03,748] [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 haliclonae	strain=CCM 8681	GCA_014635865.1	2048558	2048558	type	True	77.893	278	769	95	below_threshold
Winogradskyella jejuensis	strain=DSM 25330	GCA_900129745.1	1089305	1089305	type	True	77.6945	264	769	95	below_threshold
Winogradskyella wandonensis	strain=CECT 8445	GCA_004346845.1	1442586	1442586	type	True	77.5646	258	769	95	below_threshold
Winogradskyella algicola	strain=IMCC33238	GCA_005869935.1	2575815	2575815	type	True	77.3409	190	769	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014297365.1	538189	538189	type	True	77.0646	214	769	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014284085.1	538189	538189	type	True	77.0646	214	769	95	below_threshold
Winogradskyella thalassocola	strain=DSM 15363	GCA_900099995.1	262004	262004	type	True	77.0538	170	769	95	below_threshold
Winogradskyella flava	strain=KCTC 52348	GCA_014243395.1	1884876	1884876	type	True	77.0466	162	769	95	below_threshold
Winogradskyella eckloniae	strain=EC29	GCA_013249045.1	1089306	1089306	type	True	76.8969	177	769	95	below_threshold
Winogradskyella wichelsiae	strain=Z738	GCA_013403925.1	2697007	2697007	type	True	76.8937	181	769	95	below_threshold
Winogradskyella sediminis	strain=DSM 28134	GCA_003387355.1	1382466	1382466	type	True	76.7879	171	769	95	below_threshold
Winogradskyella undariae	strain=CCUG 63832	GCA_013285155.1	1285465	1285465	type	True	76.7863	185	769	95	below_threshold
Winogradskyella litoriviva	strain=KMM6491	GCA_013249065.1	1220182	1220182	type	True	76.7854	186	769	95	below_threshold
Winogradskyella ouciana	strain=ZXX205	GCA_009709615.1	2608631	2608631	type	True	76.7473	185	769	95	below_threshold
Winogradskyella ursingii	strain=HL4150	GCA_013403975.1	2686079	2686079	type	True	76.6665	137	769	95	below_threshold
Algibacter marinivivus	strain=ZY111	GCA_003143755.1	2100723	2100723	type	True	76.6081	137	769	95	below_threshold
Hanstruepera flava	strain=NBU2984	GCA_023634025.1	2930218	2930218	type	True	76.5902	126	769	95	below_threshold
Psychroserpens mesophilus	strain=JCM 13413	GCA_000826645.1	325473	325473	type	True	76.4082	134	769	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	76.3341	106	769	95	below_threshold
Tamlana agarivorans	strain=JW-26	GCA_001642835.1	481183	481183	type	True	76.2516	94	769	95	below_threshold
Aestuariivivens marinum	strain=MT3-5-12	GCA_022662175.1	2913555	2913555	type	True	76.0635	80	769	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	75.7635	85	769	95	below_threshold
Polaribacter batillariae	strain=G4M1	GCA_017498485.1	2808900	2808900	type	True	75.728	74	769	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 03:48:03,748] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11357/tc_result.tsv
[2023-03-16 03:48:03,748] [INFO] ===== Taxonomy check completed =====
[2023-03-16 03:48:03,749] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 03:48:03,749] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc369f0c0-299a-473d-a689-f1b66024a7b4/dqc_reference/checkm_data
[2023-03-16 03:48:03,749] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 03:48:03,754] [INFO] Task started: CheckM
[2023-03-16 03:48:03,754] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11357/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11357/checkm_input OceanDNA-b11357/checkm_result
[2023-03-16 03:48:42,277] [INFO] Task succeeded: CheckM
[2023-03-16 03:48:42,277] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 60.42%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 03:48:42,280] [INFO] ===== Completeness check finished =====
[2023-03-16 03:48:42,280] [INFO] ===== Start GTDB Search =====
[2023-03-16 03:48:42,280] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11357/markers.fasta)
[2023-03-16 03:48:42,280] [INFO] Task started: Blastn
[2023-03-16 03:48:42,280] [INFO] Running command: blastn -query OceanDNA-b11357/markers.fasta -db /var/lib/cwl/stgc369f0c0-299a-473d-a689-f1b66024a7b4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11357/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 03:48:43,132] [INFO] Task succeeded: Blastn
[2023-03-16 03:48:43,133] [INFO] Selected 24 target genomes.
[2023-03-16 03:48:43,133] [INFO] Target genome list was writen to OceanDNA-b11357/target_genomes_gtdb.txt
[2023-03-16 03:48:43,177] [INFO] Task started: fastANI
[2023-03-16 03:48:43,177] [INFO] Running command: fastANI --query /var/lib/cwl/stg198ea0cc-1558-4a46-a5f3-ea1a7876d6ac/OceanDNA-b11357.fa --refList OceanDNA-b11357/target_genomes_gtdb.txt --output OceanDNA-b11357/fastani_result_gtdb.tsv --threads 1
[2023-03-16 03:48:56,574] [INFO] Task succeeded: fastANI
[2023-03-16 03:48:56,588] [INFO] Found 24 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 03:48:56,588] [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_014635865.1	s__Winogradskyella haliclonae	77.893	278	769	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	77.8648	238	769	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129745.1	s__Winogradskyella jejuensis	77.7068	263	769	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003712105.1	s__Winogradskyella sp003712105	77.603	266	769	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	77.5768	257	769	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	77.4714	247	769	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	99.88	99.82	0.99	0.99	3	-
GCA_013042245.1	s__Winogradskyella sp013042245	77.3282	217	769	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	99.97	99.97	0.95	0.95	2	-
GCA_905480385.1	s__Winogradskyella sp905480385	77.243	217	769	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	99.53	99.53	0.86	0.86	2	-
GCF_001971725.1	s__Winogradskyella sp001971725	77.1639	174	769	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003610635.1	s__Ichthyenterobacterium magnum	77.1047	135	769	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Ichthyenterobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013213975.1	s__Winogradskyella sp013213975	77.0727	152	769	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	77.0528	169	769	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	77.0466	162	769	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	76.9401	181	769	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	76.8994	175	769	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	76.805	213	769	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003387355.1	s__Winogradskyella sediminis	76.7843	169	769	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	98.63	98.63	0.93	0.93	2	-
GCF_013249065.1	s__Winogradskyella litoriviva	76.7831	185	769	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	76.7579	184	769	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	76.7496	195	769	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	76.7335	170	769	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003143755.1	s__Algibacter_B sp003143755	76.6053	135	769	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479815.1	s__Psychroserpens sp905479815	76.4917	128	769	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425305.1	s__Psychroserpens burtonensis	76.2969	129	769	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	99.48	99.48	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2023-03-16 03:48:56,588] [INFO] GTDB search result was written to OceanDNA-b11357/result_gtdb.tsv
[2023-03-16 03:48:56,588] [INFO] ===== GTDB Search completed =====
[2023-03-16 03:48:56,591] [INFO] DFAST_QC result json was written to OceanDNA-b11357/dqc_result.json
[2023-03-16 03:48:56,591] [INFO] DFAST_QC completed!
[2023-03-16 03:48:56,591] [INFO] Total running time: 0h1m24s