[2023-03-17 10:19:15,246] [INFO] DFAST_QC pipeline started.
[2023-03-17 10:19:15,247] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 10:19:15,247] [INFO] DQC Reference Directory: /var/lib/cwl/stg2d3371d9-354d-47e4-be96-92c56a908989/dqc_reference
[2023-03-17 10:19:16,988] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 10:19:16,989] [INFO] Task started: Prodigal
[2023-03-17 10:19:16,989] [INFO] Running command: cat /var/lib/cwl/stga82f2a24-d621-45d5-a9bc-5c195f0fa986/OceanDNA-b13050.fa | prodigal -d OceanDNA-b13050/cds.fna -a OceanDNA-b13050/protein.faa -g 11 -q > /dev/null
[2023-03-17 10:19:38,126] [INFO] Task succeeded: Prodigal
[2023-03-17 10:19:38,126] [INFO] Task started: HMMsearch
[2023-03-17 10:19:38,126] [INFO] Running command: hmmsearch --tblout OceanDNA-b13050/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2d3371d9-354d-47e4-be96-92c56a908989/dqc_reference/reference_markers.hmm OceanDNA-b13050/protein.faa > /dev/null
[2023-03-17 10:19:38,310] [INFO] Task succeeded: HMMsearch
[2023-03-17 10:19:38,310] [INFO] Found 6/6 markers.
[2023-03-17 10:19:38,334] [INFO] Query marker FASTA was written to OceanDNA-b13050/markers.fasta
[2023-03-17 10:19:38,336] [INFO] Task started: Blastn
[2023-03-17 10:19:38,336] [INFO] Running command: blastn -query OceanDNA-b13050/markers.fasta -db /var/lib/cwl/stg2d3371d9-354d-47e4-be96-92c56a908989/dqc_reference/reference_markers.fasta -out OceanDNA-b13050/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:19:38,855] [INFO] Task succeeded: Blastn
[2023-03-17 10:19:38,857] [INFO] Selected 21 target genomes.
[2023-03-17 10:19:38,858] [INFO] Target genome list was writen to OceanDNA-b13050/target_genomes.txt
[2023-03-17 10:19:38,868] [INFO] Task started: fastANI
[2023-03-17 10:19:38,869] [INFO] Running command: fastANI --query /var/lib/cwl/stga82f2a24-d621-45d5-a9bc-5c195f0fa986/OceanDNA-b13050.fa --refList OceanDNA-b13050/target_genomes.txt --output OceanDNA-b13050/fastani_result.tsv --threads 1
[2023-03-17 10:19:52,172] [INFO] Task succeeded: fastANI
[2023-03-17 10:19:52,173] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2d3371d9-354d-47e4-be96-92c56a908989/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 10:19:52,173] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2d3371d9-354d-47e4-be96-92c56a908989/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 10:19:52,176] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 10:19:52,176] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 10:19:52,176] [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
Balneola vulgaris	strain=DSM 17893	GCA_000375465.1	287535	287535	type	True	76.4445	75	1100	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 10:19:52,177] [INFO] DFAST Taxonomy check result was written to OceanDNA-b13050/tc_result.tsv
[2023-03-17 10:19:52,178] [INFO] ===== Taxonomy check completed =====
[2023-03-17 10:19:52,178] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 10:19:52,179] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2d3371d9-354d-47e4-be96-92c56a908989/dqc_reference/checkm_data
[2023-03-17 10:19:52,179] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 10:19:52,198] [INFO] Task started: CheckM
[2023-03-17 10:19:52,198] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b13050/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b13050/checkm_input OceanDNA-b13050/checkm_result
[2023-03-17 10:20:45,955] [INFO] Task succeeded: CheckM
[2023-03-17 10:20:45,955] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 45.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 10:20:46,005] [INFO] ===== Completeness check finished =====
[2023-03-17 10:20:46,005] [INFO] ===== Start GTDB Search =====
[2023-03-17 10:20:46,005] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b13050/markers.fasta)
[2023-03-17 10:20:46,006] [INFO] Task started: Blastn
[2023-03-17 10:20:46,006] [INFO] Running command: blastn -query OceanDNA-b13050/markers.fasta -db /var/lib/cwl/stg2d3371d9-354d-47e4-be96-92c56a908989/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b13050/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:20:46,714] [INFO] Task succeeded: Blastn
[2023-03-17 10:20:46,721] [INFO] Selected 16 target genomes.
[2023-03-17 10:20:46,721] [INFO] Target genome list was writen to OceanDNA-b13050/target_genomes_gtdb.txt
[2023-03-17 10:20:46,823] [INFO] Task started: fastANI
[2023-03-17 10:20:46,823] [INFO] Running command: fastANI --query /var/lib/cwl/stga82f2a24-d621-45d5-a9bc-5c195f0fa986/OceanDNA-b13050.fa --refList OceanDNA-b13050/target_genomes_gtdb.txt --output OceanDNA-b13050/fastani_result_gtdb.tsv --threads 1
[2023-03-17 10:20:54,354] [INFO] Task succeeded: fastANI
[2023-03-17 10:20:54,360] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 10:20:54,360] [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_017640665.1	s__RHLJ01 sp017640665	77.743	281	1100	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__RHLJ01	95.0	100.00	100.00	1.00	1.00	3	-
GCA_017795005.1	s__RHLJ01 sp017795005	77.3197	250	1100	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__RHLJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001650905.1	s__Balneola sp001650905	76.9167	104	1100	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Balneola	95.0	96.92	96.92	0.89	0.89	2	-
GCA_002694685.1	s__Gracilimonas sp002694685	76.8693	73	1100	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Gracilimonas	95.0	99.97	99.87	0.99	0.97	9	-
GCA_017640785.1	s__Balneola sp017640785	76.7771	113	1100	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Balneola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003712055.1	s__RHLJ01 sp003712055	76.4806	140	1100	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__RHLJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017643645.1	s__Balneola sp017643645	76.4732	107	1100	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Balneola	95.0	99.99	99.98	1.00	0.99	5	-
GCA_002364085.1	s__Balneola sp002364085	76.4338	96	1100	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Balneola	95.0	99.57	98.41	0.97	0.85	26	-
GCA_017640605.1	s__HXMU1420-13 sp017640605	76.2295	92	1100	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__HXMU1420-13	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 10:20:54,362] [INFO] GTDB search result was written to OceanDNA-b13050/result_gtdb.tsv
[2023-03-17 10:20:54,364] [INFO] ===== GTDB Search completed =====
[2023-03-17 10:20:54,367] [INFO] DFAST_QC result json was written to OceanDNA-b13050/dqc_result.json
[2023-03-17 10:20:54,367] [INFO] DFAST_QC completed!
[2023-03-17 10:20:54,367] [INFO] Total running time: 0h1m39s