[2023-03-15 04:14:00,611] [INFO] DFAST_QC pipeline started.
[2023-03-15 04:14:00,611] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 04:14:00,611] [INFO] DQC Reference Directory: /var/lib/cwl/stg909fdfa0-107c-46c3-b94c-2309aa06450d/dqc_reference
[2023-03-15 04:14:01,705] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 04:14:01,706] [INFO] Task started: Prodigal
[2023-03-15 04:14:01,706] [INFO] Running command: cat /var/lib/cwl/stg5e4d83f9-272a-480c-895a-396906f6f246/OceanDNA-b11424.fa | prodigal -d OceanDNA-b11424/cds.fna -a OceanDNA-b11424/protein.faa -g 11 -q > /dev/null
[2023-03-15 04:14:17,393] [INFO] Task succeeded: Prodigal
[2023-03-15 04:14:17,393] [INFO] Task started: HMMsearch
[2023-03-15 04:14:17,393] [INFO] Running command: hmmsearch --tblout OceanDNA-b11424/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg909fdfa0-107c-46c3-b94c-2309aa06450d/dqc_reference/reference_markers.hmm OceanDNA-b11424/protein.faa > /dev/null
[2023-03-15 04:14:17,580] [INFO] Task succeeded: HMMsearch
[2023-03-15 04:14:17,581] [INFO] Found 6/6 markers.
[2023-03-15 04:14:17,624] [INFO] Query marker FASTA was written to OceanDNA-b11424/markers.fasta
[2023-03-15 04:14:17,625] [INFO] Task started: Blastn
[2023-03-15 04:14:17,625] [INFO] Running command: blastn -query OceanDNA-b11424/markers.fasta -db /var/lib/cwl/stg909fdfa0-107c-46c3-b94c-2309aa06450d/dqc_reference/reference_markers.fasta -out OceanDNA-b11424/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 04:14:18,243] [INFO] Task succeeded: Blastn
[2023-03-15 04:14:18,249] [INFO] Selected 18 target genomes.
[2023-03-15 04:14:18,249] [INFO] Target genome list was writen to OceanDNA-b11424/target_genomes.txt
[2023-03-15 04:14:18,260] [INFO] Task started: fastANI
[2023-03-15 04:14:18,260] [INFO] Running command: fastANI --query /var/lib/cwl/stg5e4d83f9-272a-480c-895a-396906f6f246/OceanDNA-b11424.fa --refList OceanDNA-b11424/target_genomes.txt --output OceanDNA-b11424/fastani_result.tsv --threads 1
[2023-03-15 04:14:29,909] [INFO] Task succeeded: fastANI
[2023-03-15 04:14:29,910] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg909fdfa0-107c-46c3-b94c-2309aa06450d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 04:14:29,910] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg909fdfa0-107c-46c3-b94c-2309aa06450d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 04:14:29,920] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 04:14:29,920] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 04:14:29,921] [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	79.6191	357	778	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014297365.1	538189	538189	type	True	78.729	352	778	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014284085.1	538189	538189	type	True	78.7168	353	778	95	below_threshold
Winogradskyella litoriviva	strain=KMM6491	GCA_013249065.1	1220182	1220182	type	True	78.414	306	778	95	below_threshold
Winogradskyella marina	strain=F6397	GCA_015645385.1	2785530	2785530	type	True	78.3406	297	778	95	below_threshold
Winogradskyella vidalii	strain=HL634	GCA_013403955.1	2615024	2615024	type	True	78.331	294	778	95	below_threshold
Winogradskyella psychrotolerans	strain=RS-3	GCA_000427335.1	1344585	1344585	type	True	78.3195	286	778	95	below_threshold
Winogradskyella sediminis	strain=DSM 28134	GCA_003387355.1	1382466	1382466	type	True	78.3039	277	778	95	below_threshold
Winogradskyella undariae	strain=CCUG 63832	GCA_013285155.1	1285465	1285465	type	True	78.2988	311	778	95	below_threshold
Winogradskyella costae	strain=Z3138	GCA_013403865.1	2697008	2697008	type	True	78.2565	274	778	95	below_threshold
Winogradskyella flava	strain=KCTC 52348	GCA_014243395.1	1884876	1884876	type	True	78.2517	256	778	95	below_threshold
Mesoflavibacter zeaxanthinifaciens	strain=DSM 18436	GCA_000422365.1	393060	393060	type	True	78.2327	203	778	95	below_threshold
Winogradskyella eckloniae	strain=EC29	GCA_013249045.1	1089306	1089306	type	True	78.2261	276	778	95	below_threshold
Mesoflavibacter zeaxanthinifaciens subsp. sabulilitoris	strain=CECT 8597	GCA_014191595.1	1520893	393060	type	True	78.2039	193	778	95	below_threshold
Mesoflavibacter zeaxanthinifaciens subsp. sabulilitoris	strain=KCTC 42117	GCA_003008435.1	1520893	393060	type	True	78.1469	194	778	95	below_threshold
Winogradskyella forsetii	strain=HL857	GCA_013394595.1	2686077	2686077	type	True	78.0475	272	778	95	below_threshold
Winogradskyella schleiferi	strain=Z215	GCA_013394655.1	2686078	2686078	type	True	77.9978	275	778	95	below_threshold
Lacinutrix himadriensis	strain=E4-9a	GCA_001418105.1	641549	641549	type	True	77.0363	172	778	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 04:14:29,921] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11424/tc_result.tsv
[2023-03-15 04:14:29,921] [INFO] ===== Taxonomy check completed =====
[2023-03-15 04:14:29,921] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 04:14:29,922] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg909fdfa0-107c-46c3-b94c-2309aa06450d/dqc_reference/checkm_data
[2023-03-15 04:14:29,922] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 04:14:29,927] [INFO] Task started: CheckM
[2023-03-15 04:14:29,927] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11424/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11424/checkm_input OceanDNA-b11424/checkm_result
[2023-03-15 04:15:12,186] [INFO] Task succeeded: CheckM
[2023-03-15 04:15:12,187] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 04:15:12,189] [INFO] ===== Completeness check finished =====
[2023-03-15 04:15:12,190] [INFO] ===== Start GTDB Search =====
[2023-03-15 04:15:12,190] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11424/markers.fasta)
[2023-03-15 04:15:12,191] [INFO] Task started: Blastn
[2023-03-15 04:15:12,191] [INFO] Running command: blastn -query OceanDNA-b11424/markers.fasta -db /var/lib/cwl/stg909fdfa0-107c-46c3-b94c-2309aa06450d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11424/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 04:15:13,075] [INFO] Task succeeded: Blastn
[2023-03-15 04:15:13,076] [INFO] Selected 16 target genomes.
[2023-03-15 04:15:13,076] [INFO] Target genome list was writen to OceanDNA-b11424/target_genomes_gtdb.txt
[2023-03-15 04:15:13,097] [INFO] Task started: fastANI
[2023-03-15 04:15:13,098] [INFO] Running command: fastANI --query /var/lib/cwl/stg5e4d83f9-272a-480c-895a-396906f6f246/OceanDNA-b11424.fa --refList OceanDNA-b11424/target_genomes_gtdb.txt --output OceanDNA-b11424/fastani_result_gtdb.tsv --threads 1
[2023-03-15 04:15:22,966] [INFO] Task succeeded: fastANI
[2023-03-15 04:15:22,975] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 04:15:22,975] [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_002706045.1	s__Winogradskyella sp002706045	98.8492	592	778	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_002682935.1	s__Winogradskyella sp002682935	80.3055	369	778	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	80.0094	346	778	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	99.90	99.90	0.80	0.80	2	-
GCF_001971725.1	s__Winogradskyella sp001971725	78.9162	310	778	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	78.7168	353	778	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	78.7055	307	778	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	78.7018	305	778	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	78.4271	305	778	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	78.3039	277	778	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	98.63	98.63	0.93	0.93	2	-
GCF_003386165.1	s__Winogradskyella eximia	78.2931	328	778	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	78.2517	256	778	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	78.2135	277	778	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004366715.1	s__Meridianimaribacter flavus	78.1018	231	778	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Meridianimaribacter	95.0	97.44	97.06	0.91	0.87	3	-
GCA_013213835.1	s__Winogradskyella sp013213835	77.8333	235	778	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016864015.1	s__Oceanihabitans sp016864015	76.8928	172	778	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018067265.1	s__Oceanihabitans sp018067265	76.7977	138	778	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 04:15:22,976] [INFO] GTDB search result was written to OceanDNA-b11424/result_gtdb.tsv
[2023-03-15 04:15:22,976] [INFO] ===== GTDB Search completed =====
[2023-03-15 04:15:22,977] [INFO] DFAST_QC result json was written to OceanDNA-b11424/dqc_result.json
[2023-03-15 04:15:22,978] [INFO] DFAST_QC completed!
[2023-03-15 04:15:22,978] [INFO] Total running time: 0h1m22s