[2023-03-16 13:03:54,679] [INFO] DFAST_QC pipeline started.
[2023-03-16 13:03:54,679] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 13:03:54,679] [INFO] DQC Reference Directory: /var/lib/cwl/stg1789d076-4e49-42cd-872c-47b6082cd216/dqc_reference
[2023-03-16 13:03:55,979] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 13:03:55,979] [INFO] Task started: Prodigal
[2023-03-16 13:03:55,980] [INFO] Running command: cat /var/lib/cwl/stg87b83cd6-ad75-496b-a104-e4b27242aef7/OceanDNA-b6836.fa | prodigal -d OceanDNA-b6836/cds.fna -a OceanDNA-b6836/protein.faa -g 11 -q > /dev/null
[2023-03-16 13:04:10,886] [INFO] Task succeeded: Prodigal
[2023-03-16 13:04:10,886] [INFO] Task started: HMMsearch
[2023-03-16 13:04:10,886] [INFO] Running command: hmmsearch --tblout OceanDNA-b6836/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1789d076-4e49-42cd-872c-47b6082cd216/dqc_reference/reference_markers.hmm OceanDNA-b6836/protein.faa > /dev/null
[2023-03-16 13:04:11,073] [INFO] Task succeeded: HMMsearch
[2023-03-16 13:04:11,074] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg87b83cd6-ad75-496b-a104-e4b27242aef7/OceanDNA-b6836.fa]
[2023-03-16 13:04:11,093] [INFO] Query marker FASTA was written to OceanDNA-b6836/markers.fasta
[2023-03-16 13:04:11,093] [INFO] Task started: Blastn
[2023-03-16 13:04:11,093] [INFO] Running command: blastn -query OceanDNA-b6836/markers.fasta -db /var/lib/cwl/stg1789d076-4e49-42cd-872c-47b6082cd216/dqc_reference/reference_markers.fasta -out OceanDNA-b6836/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 13:04:11,660] [INFO] Task succeeded: Blastn
[2023-03-16 13:04:11,661] [INFO] Selected 20 target genomes.
[2023-03-16 13:04:11,661] [INFO] Target genome list was writen to OceanDNA-b6836/target_genomes.txt
[2023-03-16 13:04:11,675] [INFO] Task started: fastANI
[2023-03-16 13:04:11,675] [INFO] Running command: fastANI --query /var/lib/cwl/stg87b83cd6-ad75-496b-a104-e4b27242aef7/OceanDNA-b6836.fa --refList OceanDNA-b6836/target_genomes.txt --output OceanDNA-b6836/fastani_result.tsv --threads 1
[2023-03-16 13:04:24,947] [INFO] Task succeeded: fastANI
[2023-03-16 13:04:24,948] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1789d076-4e49-42cd-872c-47b6082cd216/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 13:04:24,948] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1789d076-4e49-42cd-872c-47b6082cd216/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 13:04:24,959] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 13:04:24,959] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 13:04:24,959] [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
Flavobacterium macacae	strain=YIM 102600	GCA_003865365.1	2488993	2488993	type	True	85.614	451	594	95	below_threshold
Flavobacterium gossypii	strain=DSM 100397	GCA_014138495.1	1646119	1646119	type	True	79.428	279	594	95	below_threshold
Flavobacterium endophyticum	strain=DSM 29537	GCA_003634455.1	1540163	1540163	type	True	79.2807	274	594	95	below_threshold
Flavobacterium lindanitolerans	strain=IP-10	GCA_002846575.1	428988	428988	type	True	78.5189	245	594	95	below_threshold
Flavobacterium lindanitolerans	strain=DSM 21886	GCA_003663835.1	428988	428988	type	True	78.4931	241	594	95	below_threshold
Flavobacterium ichthyis	strain=NST-5	GCA_009915155.1	2698827	2698827	type	True	78.4241	222	594	95	below_threshold
Flavobacterium microcysteis	strain=MaA-Y11	GCA_006385255.1	2596891	2596891	type	True	78.3211	262	594	95	below_threshold
Flavobacterium saccharophilum	strain=DSM 1811	GCA_900142735.1	29534	29534	type	True	77.689	150	594	95	below_threshold
Flavobacterium flabelliforme	strain=P4023	GCA_017948675.1	2816119	2816119	type	True	77.496	144	594	95	below_threshold
Flavobacterium resistens	strain=DSM 19382	GCA_009674815.1	443612	443612	type	True	77.462	165	594	95	below_threshold
Flavobacterium endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	77.4494	143	594	95	below_threshold
Flavobacterium antarcticum	strain=DSM 19726	GCA_000419685.1	271155	271155	type	True	77.4463	166	594	95	below_threshold
Flavobacterium faecale	strain=WV33	GCA_003076455.1	1355330	1355330	type	True	77.4065	105	594	95	below_threshold
Flavobacterium psychroterrae	strain=CCM 8827	GCA_018380615.1	2133767	2133767	type	True	77.3416	171	594	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	77.3099	153	594	95	below_threshold
Flavobacterium tyrosinilyticum	strain=KCTC 42726	GCA_023656565.1	1658740	1658740	type	True	77.2596	166	594	95	below_threshold
Flavobacterium hydrocarbonoxydans	strain=GA093	GCA_009789235.1	2683249	2683249	type	True	77.2208	166	594	95	below_threshold
Flavobacterium taihuense	strain=NAS39	GCA_019351435.1	2857508	2857508	type	True	76.8693	118	594	95	below_threshold
Flavobacterium lutivivi	strain=CGMCC 1.15347	GCA_014642275.1	1677894	1677894	type	True	76.652	100	594	95	below_threshold
Flavobacterium sediminilitoris	strain=YSM-43	GCA_023008245.1	2024526	2024526	type	True	76.1941	101	594	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 13:04:24,959] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6836/tc_result.tsv
[2023-03-16 13:04:24,959] [INFO] ===== Taxonomy check completed =====
[2023-03-16 13:04:24,959] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 13:04:24,960] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1789d076-4e49-42cd-872c-47b6082cd216/dqc_reference/checkm_data
[2023-03-16 13:04:24,960] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 13:04:24,965] [INFO] Task started: CheckM
[2023-03-16 13:04:24,965] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6836/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6836/checkm_input OceanDNA-b6836/checkm_result
[2023-03-16 13:05:17,553] [INFO] Task succeeded: CheckM
[2023-03-16 13:05:17,554] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 45.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 13:05:17,557] [INFO] ===== Completeness check finished =====
[2023-03-16 13:05:17,557] [INFO] ===== Start GTDB Search =====
[2023-03-16 13:05:17,557] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6836/markers.fasta)
[2023-03-16 13:05:17,557] [INFO] Task started: Blastn
[2023-03-16 13:05:17,557] [INFO] Running command: blastn -query OceanDNA-b6836/markers.fasta -db /var/lib/cwl/stg1789d076-4e49-42cd-872c-47b6082cd216/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6836/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 13:05:18,435] [INFO] Task succeeded: Blastn
[2023-03-16 13:05:18,449] [INFO] Selected 18 target genomes.
[2023-03-16 13:05:18,449] [INFO] Target genome list was writen to OceanDNA-b6836/target_genomes_gtdb.txt
[2023-03-16 13:05:18,658] [INFO] Task started: fastANI
[2023-03-16 13:05:18,658] [INFO] Running command: fastANI --query /var/lib/cwl/stg87b83cd6-ad75-496b-a104-e4b27242aef7/OceanDNA-b6836.fa --refList OceanDNA-b6836/target_genomes_gtdb.txt --output OceanDNA-b6836/fastani_result_gtdb.tsv --threads 1
[2023-03-16 13:05:38,339] [INFO] Task succeeded: fastANI
[2023-03-16 13:05:38,349] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 13:05:38,349] [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_003865365.1	s__Flavobacterium macacae	85.614	451	594	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634455.1	s__Flavobacterium endophyticum	79.2807	274	594	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.19	97.19	0.95	0.95	2	-
GCF_000422705.1	s__Flavobacterium soli	78.8407	220	594	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002846575.1	s__Flavobacterium lindanitolerans	78.5028	246	594	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.86	97.14	0.91	0.85	11	-
GCF_009915155.1	s__Flavobacterium sp009915155	78.4068	223	594	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006385255.1	s__Flavobacterium microcysteis	78.3211	262	594	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142735.1	s__Flavobacterium saccharophilum	77.711	149	594	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000708595.2	s__Flavobacterium sp000708595	77.5339	166	594	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.30	98.27	0.95	0.93	3	-
GCF_003314435.2	s__Flavobacterium petrolei	77.45	154	594	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.35	97.35	0.87	0.87	2	-
GCF_000419685.1	s__Flavobacterium antarcticum	77.4463	166	594	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001464475.1	s__Flavobacterium sp001464475	77.4318	153	594	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002754195.1	s__Flavobacterium sp002754195	77.3976	172	594	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003076455.1	s__Flavobacterium faecale	77.3767	107	594	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014281985.1	s__Flavobacterium sp014281985	77.3758	145	594	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.07	98.07	0.91	0.91	2	-
GCA_009693635.1	s__Flavobacterium sp009693635	77.289	119	594	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004339525.1	s__Flavobacterium sp004339525	77.258	174	594	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_007097365.1	s__Flavobacterium franklandianum	77.2081	146	594	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.99	98.99	0.94	0.94	2	-
GCF_014642275.1	s__Flavobacterium lutivivi	76.652	100	594	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 13:05:38,350] [INFO] GTDB search result was written to OceanDNA-b6836/result_gtdb.tsv
[2023-03-16 13:05:38,350] [INFO] ===== GTDB Search completed =====
[2023-03-16 13:05:38,352] [INFO] DFAST_QC result json was written to OceanDNA-b6836/dqc_result.json
[2023-03-16 13:05:38,352] [INFO] DFAST_QC completed!
[2023-03-16 13:05:38,352] [INFO] Total running time: 0h1m44s