[2023-03-15 07:52:40,276] [INFO] DFAST_QC pipeline started.
[2023-03-15 07:52:40,276] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 07:52:40,276] [INFO] DQC Reference Directory: /var/lib/cwl/stgbb5b980a-9b98-4408-86d9-bed7199e6b0c/dqc_reference
[2023-03-15 07:52:41,515] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 07:52:41,516] [INFO] Task started: Prodigal
[2023-03-15 07:52:41,516] [INFO] Running command: cat /var/lib/cwl/stgda2358c0-85ba-4fba-992d-f49abecfaaab/OceanDNA-b7557.fa | prodigal -d OceanDNA-b7557/cds.fna -a OceanDNA-b7557/protein.faa -g 11 -q > /dev/null
[2023-03-15 07:52:53,789] [INFO] Task succeeded: Prodigal
[2023-03-15 07:52:53,789] [INFO] Task started: HMMsearch
[2023-03-15 07:52:53,789] [INFO] Running command: hmmsearch --tblout OceanDNA-b7557/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbb5b980a-9b98-4408-86d9-bed7199e6b0c/dqc_reference/reference_markers.hmm OceanDNA-b7557/protein.faa > /dev/null
[2023-03-15 07:52:54,112] [INFO] Task succeeded: HMMsearch
[2023-03-15 07:52:54,113] [INFO] Found 6/6 markers.
[2023-03-15 07:52:54,126] [INFO] Query marker FASTA was written to OceanDNA-b7557/markers.fasta
[2023-03-15 07:52:54,126] [INFO] Task started: Blastn
[2023-03-15 07:52:54,126] [INFO] Running command: blastn -query OceanDNA-b7557/markers.fasta -db /var/lib/cwl/stgbb5b980a-9b98-4408-86d9-bed7199e6b0c/dqc_reference/reference_markers.fasta -out OceanDNA-b7557/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:52:54,785] [INFO] Task succeeded: Blastn
[2023-03-15 07:52:54,786] [INFO] Selected 35 target genomes.
[2023-03-15 07:52:54,787] [INFO] Target genome list was writen to OceanDNA-b7557/target_genomes.txt
[2023-03-15 07:52:54,804] [INFO] Task started: fastANI
[2023-03-15 07:52:54,804] [INFO] Running command: fastANI --query /var/lib/cwl/stgda2358c0-85ba-4fba-992d-f49abecfaaab/OceanDNA-b7557.fa --refList OceanDNA-b7557/target_genomes.txt --output OceanDNA-b7557/fastani_result.tsv --threads 1
[2023-03-15 07:53:18,378] [INFO] Task succeeded: fastANI
[2023-03-15 07:53:18,378] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbb5b980a-9b98-4408-86d9-bed7199e6b0c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 07:53:18,378] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbb5b980a-9b98-4408-86d9-bed7199e6b0c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 07:53:18,386] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 07:53:18,387] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 07:53:18,387] [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
Cellulophaga fucicola	strain=DSM 24786	GCA_900119145.1	76595	76595	type	True	76.4887	69	562	95	below_threshold
Cellulophaga algicola	strain=DSM 14237	GCA_000186265.1	59600	59600	type	True	76.2257	56	562	95	below_threshold
Maribacter vaceletii	strain=DSM 25230	GCA_003634105.1	1206816	1206816	type	True	76.1613	70	562	95	below_threshold
Maribacter orientalis	strain=DSM 16471	GCA_900109345.1	228957	228957	type	True	76.1135	51	562	95	below_threshold
Maribacter stanieri	strain=DSM 19891	GCA_900112245.1	440514	440514	type	True	76.0249	58	562	95	below_threshold
Maribacter forsetii	strain=DSM 18668	GCA_000744105.1	444515	444515	type	True	75.988	55	562	95	below_threshold
Cellulophaga tyrosinoxydans	strain=DSM 21164	GCA_900176415.1	504486	504486	type	True	75.9776	75	562	95	below_threshold
Cellulophaga baltica	strain=DSM 24729	GCA_900102165.1	76594	76594	type	True	75.9732	62	562	95	below_threshold
Maribacter arcticus	strain=DSM 23546	GCA_900167935.1	561365	561365	type	True	75.9264	52	562	95	below_threshold
Cellulophaga omnivescoria	strain=W5C	GCA_001999725.1	1888890	1888890	type	True	75.8951	71	562	95	below_threshold
Arenibacter latericius	strain=DSM 15913	GCA_000424985.1	86104	86104	type	True	75.7883	57	562	95	below_threshold
Maribacter dokdonensis	strain=DSW-8	GCA_001447995.1	320912	320912	type	True	75.7706	64	562	95	below_threshold
Maribacter caenipelagi	strain=CECT 8455	GCA_004364175.1	1447781	1447781	type	True	75.7606	58	562	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 07:53:18,387] [INFO] DFAST Taxonomy check result was written to OceanDNA-b7557/tc_result.tsv
[2023-03-15 07:53:18,387] [INFO] ===== Taxonomy check completed =====
[2023-03-15 07:53:18,387] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 07:53:18,387] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbb5b980a-9b98-4408-86d9-bed7199e6b0c/dqc_reference/checkm_data
[2023-03-15 07:53:18,388] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 07:53:18,499] [INFO] Task started: CheckM
[2023-03-15 07:53:18,500] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b7557/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b7557/checkm_input OceanDNA-b7557/checkm_result
[2023-03-15 07:53:51,703] [INFO] Task succeeded: CheckM
[2023-03-15 07:53:51,703] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.85%
Contamintation: 1.50%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 07:53:51,705] [INFO] ===== Completeness check finished =====
[2023-03-15 07:53:51,705] [INFO] ===== Start GTDB Search =====
[2023-03-15 07:53:51,706] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b7557/markers.fasta)
[2023-03-15 07:53:51,707] [INFO] Task started: Blastn
[2023-03-15 07:53:51,707] [INFO] Running command: blastn -query OceanDNA-b7557/markers.fasta -db /var/lib/cwl/stgbb5b980a-9b98-4408-86d9-bed7199e6b0c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b7557/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:53:52,518] [INFO] Task succeeded: Blastn
[2023-03-15 07:53:52,519] [INFO] Selected 21 target genomes.
[2023-03-15 07:53:52,519] [INFO] Target genome list was writen to OceanDNA-b7557/target_genomes_gtdb.txt
[2023-03-15 07:53:52,544] [INFO] Task started: fastANI
[2023-03-15 07:53:52,545] [INFO] Running command: fastANI --query /var/lib/cwl/stgda2358c0-85ba-4fba-992d-f49abecfaaab/OceanDNA-b7557.fa --refList OceanDNA-b7557/target_genomes_gtdb.txt --output OceanDNA-b7557/fastani_result_gtdb.tsv --threads 1
[2023-03-15 07:54:05,079] [INFO] Task succeeded: fastANI
[2023-03-15 07:54:05,087] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 07:54:05,087] [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_905182295.1	s__MAG-120531 sp905182295	99.3305	372	562	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-120531	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_000173115.1	s__MAG-120531 sp000173115	91.3553	387	562	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-120531	95.0	99.02	98.72	0.73	0.67	33	-
GCA_018401115.1	s__MAG-120531 sp018401115	87.0837	507	562	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-120531	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018500065.1	s__MAG-120531 sp018500065	78.0723	185	562	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-120531	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000190595.1	s__Cellulophaga lytica	76.3127	72	562	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	99.01	98.71	0.94	0.93	6	-
GCF_000186265.1	s__Cellulophaga algicola	76.2257	56	562	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	98.35	98.34	0.88	0.87	3	-
GCF_003634105.1	s__Maribacter_B vaceletii	76.1855	69	562	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112245.1	s__Maribacter stanieri	76.0249	58	562	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	98.09	98.09	0.92	0.92	2	-
GCA_011050675.1	s__Maribacter sp011050675	76.0124	50	562	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900102165.1	s__Cellulophaga baltica	75.9732	62	562	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	97.62	97.40	0.90	0.89	7	-
GCF_001999725.1	s__Cellulophaga omnivescoria	75.8951	71	562	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000424985.1	s__Arenibacter latericius	75.7883	57	562	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004364175.1	s__Maribacter caenipelagi	75.7443	57	562	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010993855.1	s__Muricauda sp010993855	75.6695	53	562	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 07:54:05,088] [INFO] GTDB search result was written to OceanDNA-b7557/result_gtdb.tsv
[2023-03-15 07:54:05,088] [INFO] ===== GTDB Search completed =====
[2023-03-15 07:54:05,090] [INFO] DFAST_QC result json was written to OceanDNA-b7557/dqc_result.json
[2023-03-15 07:54:05,090] [INFO] DFAST_QC completed!
[2023-03-15 07:54:05,090] [INFO] Total running time: 0h1m25s