[2023-03-17 00:45:47,174] [INFO] DFAST_QC pipeline started.
[2023-03-17 00:45:47,174] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 00:45:47,174] [INFO] DQC Reference Directory: /var/lib/cwl/stg11771320-627d-4713-9662-95482aee69c9/dqc_reference
[2023-03-17 00:45:48,351] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 00:45:48,352] [INFO] Task started: Prodigal
[2023-03-17 00:45:48,353] [INFO] Running command: cat /var/lib/cwl/stga753cc0a-5c00-44ed-929b-b7803639ab3e/OceanDNA-b6844.fa | prodigal -d OceanDNA-b6844/cds.fna -a OceanDNA-b6844/protein.faa -g 11 -q > /dev/null
[2023-03-17 00:46:10,911] [INFO] Task succeeded: Prodigal
[2023-03-17 00:46:10,912] [INFO] Task started: HMMsearch
[2023-03-17 00:46:10,912] [INFO] Running command: hmmsearch --tblout OceanDNA-b6844/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg11771320-627d-4713-9662-95482aee69c9/dqc_reference/reference_markers.hmm OceanDNA-b6844/protein.faa > /dev/null
[2023-03-17 00:46:11,113] [INFO] Task succeeded: HMMsearch
[2023-03-17 00:46:11,113] [INFO] Found 6/6 markers.
[2023-03-17 00:46:11,133] [INFO] Query marker FASTA was written to OceanDNA-b6844/markers.fasta
[2023-03-17 00:46:11,134] [INFO] Task started: Blastn
[2023-03-17 00:46:11,134] [INFO] Running command: blastn -query OceanDNA-b6844/markers.fasta -db /var/lib/cwl/stg11771320-627d-4713-9662-95482aee69c9/dqc_reference/reference_markers.fasta -out OceanDNA-b6844/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:46:11,717] [INFO] Task succeeded: Blastn
[2023-03-17 00:46:11,718] [INFO] Selected 15 target genomes.
[2023-03-17 00:46:11,718] [INFO] Target genome list was writen to OceanDNA-b6844/target_genomes.txt
[2023-03-17 00:46:11,744] [INFO] Task started: fastANI
[2023-03-17 00:46:11,744] [INFO] Running command: fastANI --query /var/lib/cwl/stga753cc0a-5c00-44ed-929b-b7803639ab3e/OceanDNA-b6844.fa --refList OceanDNA-b6844/target_genomes.txt --output OceanDNA-b6844/fastani_result.tsv --threads 1
[2023-03-17 00:46:21,949] [INFO] Task succeeded: fastANI
[2023-03-17 00:46:21,949] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg11771320-627d-4713-9662-95482aee69c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 00:46:21,949] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg11771320-627d-4713-9662-95482aee69c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 00:46:21,957] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2023-03-17 00:46:21,957] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-17 00:46:21,958] [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 coralii	strain=D11R37	GCA_019891545.1	2838017	2838017	type	True	95.4807	914	1071	95	conclusive
Flavobacterium salilacus subsp. salilacus	strain=SaA2.12	GCA_004634195.1	2545633	2898423	type	True	78.8792	410	1071	95	below_threshold
Flavobacterium salilacus subsp. altitudinum	strain=LaA7.5	GCA_010078225.1	2691899	2898423	type	True	78.3723	430	1071	95	below_threshold
Flavobacterium akiainvivens	strain=IK-1	GCA_001278115.1	1202724	1202724	type	True	78.3161	309	1071	95	below_threshold
Flavobacterium akiainvivens	strain=DSM 25510	GCA_900115875.1	1202724	1202724	type	True	78.2698	308	1071	95	below_threshold
Flavobacterium subsaxonicum	strain=DSM 21790	GCA_000422725.1	426226	426226	type	True	77.9086	302	1071	95	below_threshold
Flavobacterium zepuense	strain=ZT4R6	GCA_007097145.1	2593302	2593302	type	True	77.9057	344	1071	95	below_threshold
Flavobacterium alkalisoli	strain=XS-5	GCA_008000935.1	2602769	2602769	type	True	77.8498	282	1071	95	below_threshold
Flavobacterium suaedae	strain=CGMCC 1.15461	GCA_014642915.1	1767027	1767027	type	True	77.7965	335	1071	95	below_threshold
Flavobacterium litorale	strain=WSW3-B6	GCA_019613795.1	2856519	2856519	type	True	77.7648	265	1071	95	below_threshold
Flavobacterium cyanobacteriorum	strain=TH021	GCA_002251835.1	2022802	2022802	type	True	77.6967	262	1071	95	below_threshold
Flavobacterium album	strain=HYN0059	GCA_003096035.1	2175091	2175091	type	True	77.575	271	1071	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 00:46:21,958] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6844/tc_result.tsv
[2023-03-17 00:46:21,958] [INFO] ===== Taxonomy check completed =====
[2023-03-17 00:46:21,958] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 00:46:21,958] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg11771320-627d-4713-9662-95482aee69c9/dqc_reference/checkm_data
[2023-03-17 00:46:21,959] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 00:46:21,964] [INFO] Task started: CheckM
[2023-03-17 00:46:21,964] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6844/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6844/checkm_input OceanDNA-b6844/checkm_result
[2023-03-17 00:47:17,635] [INFO] Task succeeded: CheckM
[2023-03-17 00:47:17,636] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 00:47:17,638] [INFO] ===== Completeness check finished =====
[2023-03-17 00:47:17,638] [INFO] ===== Start GTDB Search =====
[2023-03-17 00:47:17,638] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6844/markers.fasta)
[2023-03-17 00:47:17,639] [INFO] Task started: Blastn
[2023-03-17 00:47:17,639] [INFO] Running command: blastn -query OceanDNA-b6844/markers.fasta -db /var/lib/cwl/stg11771320-627d-4713-9662-95482aee69c9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6844/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:47:18,441] [INFO] Task succeeded: Blastn
[2023-03-17 00:47:18,441] [INFO] Selected 14 target genomes.
[2023-03-17 00:47:18,441] [INFO] Target genome list was writen to OceanDNA-b6844/target_genomes_gtdb.txt
[2023-03-17 00:47:18,639] [INFO] Task started: fastANI
[2023-03-17 00:47:18,639] [INFO] Running command: fastANI --query /var/lib/cwl/stga753cc0a-5c00-44ed-929b-b7803639ab3e/OceanDNA-b6844.fa --refList OceanDNA-b6844/target_genomes_gtdb.txt --output OceanDNA-b6844/fastani_result_gtdb.tsv --threads 1
[2023-03-17 00:47:28,064] [INFO] Task succeeded: fastANI
[2023-03-17 00:47:28,073] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 00:47:28,073] [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_002714575.1	s__Flavobacterium sp002714575	99.9829	1068	1071	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004634195.1	s__Flavobacterium sp004634195	78.8802	410	1071	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.56	97.13	0.95	0.91	3	-
GCF_009848495.1	s__Flavobacterium sp009848495	78.8378	408	1071	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001278115.1	s__Flavobacterium akiainvivens	78.3099	310	1071	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_012270005.1	s__Flavobacterium sp012270005	78.0793	222	1071	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009826935.1	s__Flavobacterium sp009826935	77.9785	260	1071	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007097145.1	s__Flavobacterium sp007097145	77.9154	343	1071	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422725.1	s__Flavobacterium subsaxonicum	77.8978	303	1071	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_008000935.1	s__Flavobacterium alkalisoli	77.8498	282	1071	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004151245.1	s__Flavobacterium beibuense_A	77.7508	278	1071	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003344925.1	s__Flavobacterium arcticum	77.7101	331	1071	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002251835.1	s__Flavobacterium cyanobacteriorum	77.6828	264	1071	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003403075.1	s__Flavobacterium sp003403075	77.6695	309	1071	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003096035.1	s__Flavobacterium album	77.575	271	1071	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 00:47:28,073] [INFO] GTDB search result was written to OceanDNA-b6844/result_gtdb.tsv
[2023-03-17 00:47:28,073] [INFO] ===== GTDB Search completed =====
[2023-03-17 00:47:28,075] [INFO] DFAST_QC result json was written to OceanDNA-b6844/dqc_result.json
[2023-03-17 00:47:28,075] [INFO] DFAST_QC completed!
[2023-03-17 00:47:28,075] [INFO] Total running time: 0h1m41s