[2023-03-16 09:43:37,228] [INFO] DFAST_QC pipeline started.
[2023-03-16 09:43:37,229] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 09:43:37,229] [INFO] DQC Reference Directory: /var/lib/cwl/stgdf48396d-b99e-4302-8f4f-dc6123261a2f/dqc_reference
[2023-03-16 09:43:39,239] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 09:43:39,239] [INFO] Task started: Prodigal
[2023-03-16 09:43:39,239] [INFO] Running command: cat /var/lib/cwl/stga6c0befd-08da-40c3-8f7f-c51c4008c7f9/OceanDNA-b6660.fa | prodigal -d OceanDNA-b6660/cds.fna -a OceanDNA-b6660/protein.faa -g 11 -q > /dev/null
[2023-03-16 09:43:59,385] [INFO] Task succeeded: Prodigal
[2023-03-16 09:43:59,385] [INFO] Task started: HMMsearch
[2023-03-16 09:43:59,385] [INFO] Running command: hmmsearch --tblout OceanDNA-b6660/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdf48396d-b99e-4302-8f4f-dc6123261a2f/dqc_reference/reference_markers.hmm OceanDNA-b6660/protein.faa > /dev/null
[2023-03-16 09:43:59,596] [INFO] Task succeeded: HMMsearch
[2023-03-16 09:43:59,597] [INFO] Found 6/6 markers.
[2023-03-16 09:43:59,614] [INFO] Query marker FASTA was written to OceanDNA-b6660/markers.fasta
[2023-03-16 09:43:59,615] [INFO] Task started: Blastn
[2023-03-16 09:43:59,615] [INFO] Running command: blastn -query OceanDNA-b6660/markers.fasta -db /var/lib/cwl/stgdf48396d-b99e-4302-8f4f-dc6123261a2f/dqc_reference/reference_markers.fasta -out OceanDNA-b6660/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:44:00,212] [INFO] Task succeeded: Blastn
[2023-03-16 09:44:00,213] [INFO] Selected 31 target genomes.
[2023-03-16 09:44:00,213] [INFO] Target genome list was writen to OceanDNA-b6660/target_genomes.txt
[2023-03-16 09:44:00,618] [INFO] Task started: fastANI
[2023-03-16 09:44:00,618] [INFO] Running command: fastANI --query /var/lib/cwl/stga6c0befd-08da-40c3-8f7f-c51c4008c7f9/OceanDNA-b6660.fa --refList OceanDNA-b6660/target_genomes.txt --output OceanDNA-b6660/fastani_result.tsv --threads 1
[2023-03-16 09:44:17,789] [INFO] Task succeeded: fastANI
[2023-03-16 09:44:17,790] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdf48396d-b99e-4302-8f4f-dc6123261a2f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 09:44:17,790] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdf48396d-b99e-4302-8f4f-dc6123261a2f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 09:44:17,798] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 09:44:17,798] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 09:44:17,799] [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
Planktosalinus lacus	strain=CGMCC 1.12924	GCA_014640155.1	1526573	1526573	type	True	81.147	409	903	95	below_threshold
Aequorivita vladivostokensis	strain=KMM 3516	GCA_000952855.1	171194	171194	type	True	76.7716	64	903	95	below_threshold
Cochleicola gelatinilyticus	strain=LPB0005	GCA_001637325.1	1763537	1763537	type	True	76.5435	62	903	95	below_threshold
Constantimarinum furrinae	strain=ALE3EI	GCA_014295415.1	2562285	2562285	type	True	76.529	65	903	95	below_threshold
Aequorivita lipolytica	strain=Y10-2	GCA_007997135.1	153267	153267	type	True	76.2772	73	903	95	below_threshold
Aequorivita sublithincola	strain=DSM 14238	GCA_000265385.1	101385	101385	type	True	76.2071	66	903	95	below_threshold
Ulvibacter antarcticus	strain=DSM 23424	GCA_003688405.1	442714	442714	type	True	76.1707	54	903	95	below_threshold
Marixanthomonas spongiae	strain=HN-E44	GCA_003095375.1	2174845	2174845	type	True	76.0485	61	903	95	below_threshold
Halomarinibacterium sedimenti	strain=CAU 1614	GCA_019312585.1	2857106	2857106	type	True	75.9454	68	903	95	below_threshold
Salegentibacter mishustinae	strain=KCTC 12263	GCA_001431365.1	270918	270918	type	True	75.9453	65	903	95	below_threshold
Salegentibacter mishustinae	strain=DSM 23404	GCA_002900095.1	270918	270918	type	True	75.924	66	903	95	below_threshold
Salegentibacter mishustinae	strain=KCTC 12263	GCA_014651335.1	270918	270918	type	True	75.9095	65	903	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 09:44:17,799] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6660/tc_result.tsv
[2023-03-16 09:44:17,799] [INFO] ===== Taxonomy check completed =====
[2023-03-16 09:44:17,799] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 09:44:17,799] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdf48396d-b99e-4302-8f4f-dc6123261a2f/dqc_reference/checkm_data
[2023-03-16 09:44:17,800] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 09:44:17,804] [INFO] Task started: CheckM
[2023-03-16 09:44:17,804] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6660/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6660/checkm_input OceanDNA-b6660/checkm_result
[2023-03-16 09:45:10,916] [INFO] Task succeeded: CheckM
[2023-03-16 09:45:10,916] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 92.99%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 09:45:10,933] [INFO] ===== Completeness check finished =====
[2023-03-16 09:45:10,933] [INFO] ===== Start GTDB Search =====
[2023-03-16 09:45:10,933] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6660/markers.fasta)
[2023-03-16 09:45:10,934] [INFO] Task started: Blastn
[2023-03-16 09:45:10,934] [INFO] Running command: blastn -query OceanDNA-b6660/markers.fasta -db /var/lib/cwl/stgdf48396d-b99e-4302-8f4f-dc6123261a2f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6660/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:45:11,772] [INFO] Task succeeded: Blastn
[2023-03-16 09:45:11,791] [INFO] Selected 27 target genomes.
[2023-03-16 09:45:11,791] [INFO] Target genome list was writen to OceanDNA-b6660/target_genomes_gtdb.txt
[2023-03-16 09:45:11,819] [INFO] Task started: fastANI
[2023-03-16 09:45:11,820] [INFO] Running command: fastANI --query /var/lib/cwl/stga6c0befd-08da-40c3-8f7f-c51c4008c7f9/OceanDNA-b6660.fa --refList OceanDNA-b6660/target_genomes_gtdb.txt --output OceanDNA-b6660/fastani_result_gtdb.tsv --threads 1
[2023-03-16 09:45:26,307] [INFO] Task succeeded: fastANI
[2023-03-16 09:45:26,316] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 09:45:26,316] [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_014640155.1	s__Planktosalinus lacus	81.1798	407	903	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Planktosalinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018402385.1	s__Planktosalinus sp018402385	80.33	377	903	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Planktosalinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002842575.1	s__Planktosalinus sp002842575	77.9002	194	903	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Planktosalinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000952855.1	s__Aequorivita vladivostokensis	76.7716	64	903	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	98.24	98.00	0.93	0.90	7	-
GCA_002364215.1	s__Aequorivita sp002364215	76.6358	74	903	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	99.66	98.55	0.97	0.89	12	-
GCF_014295415.1	s__Altibacter sp014295415	76.5385	66	903	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Altibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007997155.1	s__Aequorivita antarctica	76.4722	70	903	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	99.98	99.98	0.99	0.99	2	-
GCA_002694465.1	s__IN17 sp002694465	76.4166	65	903	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__IN17	95.0	99.93	99.93	0.95	0.95	2	-
GCF_007997135.1	s__Aequorivita lipolytica	76.2523	74	903	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002715485.1	s__Aequorivita sp002715485	76.0523	81	903	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	99.49	99.49	0.87	0.87	2	-
GCF_003095375.1	s__Marixanthomonas sp003095375	76.0485	61	903	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011762485.1	s__Yeosuana marina	76.024	52	903	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Yeosuana	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002426755.1	s__Aquaticitalea sp002426755	75.9247	53	903	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquaticitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002900095.1	s__Salegentibacter mishustinae	75.924	66	903	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	99.99	99.99	1.00	1.00	4	-
GCA_002708845.1	s__Leeuwenhoekiella sp002708845	75.6056	53	903	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	99.96	99.95	0.93	0.90	5	-
--------------------------------------------------------------------------------
[2023-03-16 09:45:26,320] [INFO] GTDB search result was written to OceanDNA-b6660/result_gtdb.tsv
[2023-03-16 09:45:26,328] [INFO] ===== GTDB Search completed =====
[2023-03-16 09:45:26,336] [INFO] DFAST_QC result json was written to OceanDNA-b6660/dqc_result.json
[2023-03-16 09:45:26,336] [INFO] DFAST_QC completed!
[2023-03-16 09:45:26,336] [INFO] Total running time: 0h1m49s