[2023-03-18 07:06:22,029] [INFO] DFAST_QC pipeline started.
[2023-03-18 07:06:22,029] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 07:06:22,029] [INFO] DQC Reference Directory: /var/lib/cwl/stg7c15a416-5f08-4376-873a-e5ed29d3beb0/dqc_reference
[2023-03-18 07:06:23,118] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 07:06:23,118] [INFO] Task started: Prodigal
[2023-03-18 07:06:23,118] [INFO] Running command: cat /var/lib/cwl/stg2821ddfa-aa28-4300-b4b1-66547bebfe43/OceanDNA-b11358.fa | prodigal -d OceanDNA-b11358/cds.fna -a OceanDNA-b11358/protein.faa -g 11 -q > /dev/null
[2023-03-18 07:06:31,300] [INFO] Task succeeded: Prodigal
[2023-03-18 07:06:31,301] [INFO] Task started: HMMsearch
[2023-03-18 07:06:31,301] [INFO] Running command: hmmsearch --tblout OceanDNA-b11358/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7c15a416-5f08-4376-873a-e5ed29d3beb0/dqc_reference/reference_markers.hmm OceanDNA-b11358/protein.faa > /dev/null
[2023-03-18 07:06:31,452] [INFO] Task succeeded: HMMsearch
[2023-03-18 07:06:31,453] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg2821ddfa-aa28-4300-b4b1-66547bebfe43/OceanDNA-b11358.fa]
[2023-03-18 07:06:31,467] [INFO] Query marker FASTA was written to OceanDNA-b11358/markers.fasta
[2023-03-18 07:06:31,467] [INFO] Task started: Blastn
[2023-03-18 07:06:31,467] [INFO] Running command: blastn -query OceanDNA-b11358/markers.fasta -db /var/lib/cwl/stg7c15a416-5f08-4376-873a-e5ed29d3beb0/dqc_reference/reference_markers.fasta -out OceanDNA-b11358/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:06:32,009] [INFO] Task succeeded: Blastn
[2023-03-18 07:06:32,010] [INFO] Selected 21 target genomes.
[2023-03-18 07:06:32,010] [INFO] Target genome list was writen to OceanDNA-b11358/target_genomes.txt
[2023-03-18 07:06:32,017] [INFO] Task started: fastANI
[2023-03-18 07:06:32,017] [INFO] Running command: fastANI --query /var/lib/cwl/stg2821ddfa-aa28-4300-b4b1-66547bebfe43/OceanDNA-b11358.fa --refList OceanDNA-b11358/target_genomes.txt --output OceanDNA-b11358/fastani_result.tsv --threads 1
[2023-03-18 07:06:43,764] [INFO] Task succeeded: fastANI
[2023-03-18 07:06:43,764] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7c15a416-5f08-4376-873a-e5ed29d3beb0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 07:06:43,765] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7c15a416-5f08-4376-873a-e5ed29d3beb0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 07:06:43,776] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 07:06:43,776] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 07:06:43,776] [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 sediminis	strain=DSM 28134	GCA_003387355.1	1382466	1382466	type	True	78.086	59	319	95	below_threshold
Winogradskyella algicola	strain=IMCC33238	GCA_005869935.1	2575815	2575815	type	True	78.0699	79	319	95	below_threshold
Winogradskyella jejuensis	strain=DSM 25330	GCA_900129745.1	1089305	1089305	type	True	77.9755	128	319	95	below_threshold
Winogradskyella wandonensis	strain=CECT 8445	GCA_004346845.1	1442586	1442586	type	True	77.7092	113	319	95	below_threshold
Winogradskyella forsetii	strain=HL857	GCA_013394595.1	2686077	2686077	type	True	77.6805	63	319	95	below_threshold
Winogradskyella haliclonae	strain=CCM 8681	GCA_014635865.1	2048558	2048558	type	True	77.6268	116	319	95	below_threshold
Winogradskyella eckloniae	strain=EC29	GCA_013249045.1	1089306	1089306	type	True	77.6032	79	319	95	below_threshold
Winogradskyella litoriviva	strain=KMM6491	GCA_013249065.1	1220182	1220182	type	True	77.5956	84	319	95	below_threshold
Winogradskyella endarachnes	strain=HL2-2	GCA_009741275.1	2681965	2681965	type	True	77.4086	79	319	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014284085.1	538189	538189	type	True	77.3936	91	319	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014297365.1	538189	538189	type	True	77.3936	91	319	95	below_threshold
Winogradskyella ouciana	strain=ZXX205	GCA_009709615.1	2608631	2608631	type	True	77.3463	81	319	95	below_threshold
Winogradskyella tangerina	strain=M1309	GCA_003260205.1	2023240	2023240	type	True	77.1895	62	319	95	below_threshold
Winogradskyella vidalii	strain=HL634	GCA_013403955.1	2615024	2615024	type	True	77.1733	71	319	95	below_threshold
Winogradskyella ludwigii	strain=HL116	GCA_013403985.1	2686076	2686076	type	True	77.163	76	319	95	below_threshold
Winogradskyella wichelsiae	strain=Z738	GCA_013403925.1	2697007	2697007	type	True	77.1279	72	319	95	below_threshold
Winogradskyella flava	strain=KCTC 52348	GCA_014243395.1	1884876	1884876	type	True	77.0762	70	319	95	below_threshold
Winogradskyella marina	strain=F6397	GCA_015645385.1	2785530	2785530	type	True	77.0539	74	319	95	below_threshold
Winogradskyella psychrotolerans	strain=RS-3	GCA_000427335.1	1344585	1344585	type	True	76.9441	81	319	95	below_threshold
Psychroserpens mesophilus	strain=JCM 13413	GCA_000826645.1	325473	325473	type	True	76.7651	52	319	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 07:06:43,776] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11358/tc_result.tsv
[2023-03-18 07:06:43,776] [INFO] ===== Taxonomy check completed =====
[2023-03-18 07:06:43,776] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 07:06:43,777] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7c15a416-5f08-4376-873a-e5ed29d3beb0/dqc_reference/checkm_data
[2023-03-18 07:06:43,777] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 07:06:43,780] [INFO] Task started: CheckM
[2023-03-18 07:06:43,780] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11358/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11358/checkm_input OceanDNA-b11358/checkm_result
[2023-03-18 07:07:10,223] [INFO] Task succeeded: CheckM
[2023-03-18 07:07:10,223] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 48.73%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 07:07:10,229] [INFO] ===== Completeness check finished =====
[2023-03-18 07:07:10,229] [INFO] ===== Start GTDB Search =====
[2023-03-18 07:07:10,229] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11358/markers.fasta)
[2023-03-18 07:07:10,229] [INFO] Task started: Blastn
[2023-03-18 07:07:10,229] [INFO] Running command: blastn -query OceanDNA-b11358/markers.fasta -db /var/lib/cwl/stg7c15a416-5f08-4376-873a-e5ed29d3beb0/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11358/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:07:10,932] [INFO] Task succeeded: Blastn
[2023-03-18 07:07:10,933] [INFO] Selected 19 target genomes.
[2023-03-18 07:07:10,933] [INFO] Target genome list was writen to OceanDNA-b11358/target_genomes_gtdb.txt
[2023-03-18 07:07:11,181] [INFO] Task started: fastANI
[2023-03-18 07:07:11,181] [INFO] Running command: fastANI --query /var/lib/cwl/stg2821ddfa-aa28-4300-b4b1-66547bebfe43/OceanDNA-b11358.fa --refList OceanDNA-b11358/target_genomes_gtdb.txt --output OceanDNA-b11358/fastani_result_gtdb.tsv --threads 1
[2023-03-18 07:07:20,726] [INFO] Task succeeded: fastANI
[2023-03-18 07:07:20,736] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 07:07:20,737] [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_002163855.1	s__Winogradskyella sp002163855	78.1424	112	319	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	99.88	99.82	0.99	0.99	3	-
GCF_900129745.1	s__Winogradskyella jejuensis	77.9755	128	319	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905480385.1	s__Winogradskyella sp905480385	77.9644	94	319	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	99.53	99.53	0.86	0.86	2	-
GCA_004211785.1	s__Winogradskyella sp004211785	77.7457	113	319	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	77.6268	116	319	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	77.6253	93	319	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	77.611	79	319	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	77.6032	79	319	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	77.5956	84	319	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	77.5593	82	319	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	99.90	99.90	0.80	0.80	2	-
GCF_000828715.1	s__Winogradskyella sp000828715	77.4535	101	319	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009741275.1	s__Winogradskyella endarachnes	77.4477	78	319	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	77.4444	81	319	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	77.3936	91	319	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004366715.1	s__Meridianimaribacter flavus	77.2002	57	319	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Meridianimaribacter	95.0	97.44	97.06	0.91	0.87	3	-
GCA_013002225.1	s__Winogradskyella sp013002225	77.1899	53	319	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015645385.1	s__Winogradskyella sp015645385	77.0539	74	319	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	76.7813	84	319	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000826645.1	s__Psychroserpens mesophilus	76.7651	52	319	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 07:07:20,737] [INFO] GTDB search result was written to OceanDNA-b11358/result_gtdb.tsv
[2023-03-18 07:07:20,737] [INFO] ===== GTDB Search completed =====
[2023-03-18 07:07:20,739] [INFO] DFAST_QC result json was written to OceanDNA-b11358/dqc_result.json
[2023-03-18 07:07:20,739] [INFO] DFAST_QC completed!
[2023-03-18 07:07:20,739] [INFO] Total running time: 0h0m59s