[2023-03-18 23:32:58,532] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:32:58,532] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:32:58,532] [INFO] DQC Reference Directory: /var/lib/cwl/stg2188aabf-41f1-48df-bdb8-f50b13c8efff/dqc_reference
[2023-03-18 23:32:59,911] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:32:59,912] [INFO] Task started: Prodigal
[2023-03-18 23:32:59,912] [INFO] Running command: cat /var/lib/cwl/stge5836abc-732f-4066-a25e-4ec06abea956/OceanDNA-b10367.fa | prodigal -d OceanDNA-b10367/cds.fna -a OceanDNA-b10367/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:33:22,186] [INFO] Task succeeded: Prodigal
[2023-03-18 23:33:22,187] [INFO] Task started: HMMsearch
[2023-03-18 23:33:22,187] [INFO] Running command: hmmsearch --tblout OceanDNA-b10367/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2188aabf-41f1-48df-bdb8-f50b13c8efff/dqc_reference/reference_markers.hmm OceanDNA-b10367/protein.faa > /dev/null
[2023-03-18 23:33:22,391] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:33:22,392] [WARNING] Found 5/6 markers. [/var/lib/cwl/stge5836abc-732f-4066-a25e-4ec06abea956/OceanDNA-b10367.fa]
[2023-03-18 23:33:22,412] [INFO] Query marker FASTA was written to OceanDNA-b10367/markers.fasta
[2023-03-18 23:33:22,413] [INFO] Task started: Blastn
[2023-03-18 23:33:22,413] [INFO] Running command: blastn -query OceanDNA-b10367/markers.fasta -db /var/lib/cwl/stg2188aabf-41f1-48df-bdb8-f50b13c8efff/dqc_reference/reference_markers.fasta -out OceanDNA-b10367/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:33:22,987] [INFO] Task succeeded: Blastn
[2023-03-18 23:33:22,988] [INFO] Selected 21 target genomes.
[2023-03-18 23:33:22,988] [INFO] Target genome list was writen to OceanDNA-b10367/target_genomes.txt
[2023-03-18 23:33:23,000] [INFO] Task started: fastANI
[2023-03-18 23:33:23,000] [INFO] Running command: fastANI --query /var/lib/cwl/stge5836abc-732f-4066-a25e-4ec06abea956/OceanDNA-b10367.fa --refList OceanDNA-b10367/target_genomes.txt --output OceanDNA-b10367/fastani_result.tsv --threads 1
[2023-03-18 23:33:38,081] [INFO] Task succeeded: fastANI
[2023-03-18 23:33:38,081] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2188aabf-41f1-48df-bdb8-f50b13c8efff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:33:38,081] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2188aabf-41f1-48df-bdb8-f50b13c8efff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:33:38,092] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 23:33:38,092] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 23:33:38,092] [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
Arenibacter algicola	strain=TG409	GCA_000733925.1	616991	616991	type	True	77.2747	179	967	95	below_threshold
Arenibacter echinorum	strain=DSM 23522	GCA_003259375.1	440515	440515	type	True	77.2255	166	967	95	below_threshold
Arenibacter palladensis	strain=DSM 17539	GCA_900129275.1	237373	237373	type	True	77.1558	174	967	95	below_threshold
Arenibacter catalasegens	strain=P308H10	GCA_002909235.1	2056779	2056779	type	True	76.9877	168	967	95	below_threshold
Arenibacter hampyeongensis	strain=JCM 17788	GCA_002909255.1	1028743	1028743	type	True	76.9718	150	967	95	below_threshold
Arenibacter arenosicollis	strain=BSSL-BM3	GCA_014397245.1	2762274	2762274	type	True	76.8297	185	967	95	below_threshold
Arenibacter aquaticus	strain=GUO	GCA_003957295.1	2489054	2489054	type	True	76.8056	152	967	95	below_threshold
Cellulophaga baltica	strain=DSM 24729	GCA_900102165.1	76594	76594	type	True	76.7243	132	967	95	below_threshold
Arenibacter latericius	strain=DSM 15913	GCA_000424985.1	86104	86104	type	True	76.6595	117	967	95	below_threshold
Arenibacter certesii	strain=KCTC 12113	GCA_014651295.1	228955	228955	type	True	76.611	125	967	95	below_threshold
Arenibacter certesii	strain=DSM 19833	GCA_000429545.1	228955	228955	type	True	76.5936	126	967	95	below_threshold
Maribacter algarum	strain=RZ26	GCA_005885635.1	2578118	2578118	type	True	76.4422	92	967	95	below_threshold
Zobellia laminariae	strain=KMM 3676	GCA_009725995.1	248906	248906	type	True	76.3622	94	967	95	below_threshold
Zobellia amurskyensis	strain=KMM 3526	GCA_009725985.1	248905	248905	type	True	76.3266	98	967	95	below_threshold
Maribacter polysiphoniae	strain=DSM 23514	GCA_003148665.1	429344	429344	type	True	76.2998	121	967	95	below_threshold
Muricauda beolgyonensis	strain=KCTC 23501	GCA_003992615.1	864064	864064	type	True	76.2987	92	967	95	below_threshold
Maribacter polysiphoniae	strain=KCTC 22021	GCA_014673435.1	429344	429344	type	True	76.2707	123	967	95	below_threshold
Cellulophaga omnivescoria	strain=W5C	GCA_001999725.1	1888890	1888890	type	True	76.1719	106	967	95	below_threshold
Muricauda nanhaiensis	strain=SM1704	GCA_003382275.1	2292706	2292706	type	True	76.1035	82	967	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 23:33:38,093] [INFO] DFAST Taxonomy check result was written to OceanDNA-b10367/tc_result.tsv
[2023-03-18 23:33:38,093] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:33:38,093] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:33:38,093] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2188aabf-41f1-48df-bdb8-f50b13c8efff/dqc_reference/checkm_data
[2023-03-18 23:33:38,094] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:33:38,099] [INFO] Task started: CheckM
[2023-03-18 23:33:38,099] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b10367/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b10367/checkm_input OceanDNA-b10367/checkm_result
[2023-03-18 23:34:34,324] [INFO] Task succeeded: CheckM
[2023-03-18 23:34:34,325] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 23:34:34,339] [INFO] ===== Completeness check finished =====
[2023-03-18 23:34:34,339] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:34:34,339] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b10367/markers.fasta)
[2023-03-18 23:34:34,340] [INFO] Task started: Blastn
[2023-03-18 23:34:34,340] [INFO] Running command: blastn -query OceanDNA-b10367/markers.fasta -db /var/lib/cwl/stg2188aabf-41f1-48df-bdb8-f50b13c8efff/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b10367/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:34:35,149] [INFO] Task succeeded: Blastn
[2023-03-18 23:34:35,150] [INFO] Selected 20 target genomes.
[2023-03-18 23:34:35,150] [INFO] Target genome list was writen to OceanDNA-b10367/target_genomes_gtdb.txt
[2023-03-18 23:34:35,171] [INFO] Task started: fastANI
[2023-03-18 23:34:35,171] [INFO] Running command: fastANI --query /var/lib/cwl/stge5836abc-732f-4066-a25e-4ec06abea956/OceanDNA-b10367.fa --refList OceanDNA-b10367/target_genomes_gtdb.txt --output OceanDNA-b10367/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:34:51,387] [INFO] Task succeeded: fastANI
[2023-03-18 23:34:51,398] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 23:34:51,399] [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_001430825.1	s__Sediminicola sp001430825	83.3653	730	967	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Sediminicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000733925.1	s__Arenibacter algicola	77.2747	179	967	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	98.04	97.34	0.85	0.81	5	-
GCF_003259375.1	s__Arenibacter echinorum	77.2426	165	967	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129275.1	s__Arenibacter palladensis	77.1719	173	967	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	97.38	97.38	0.84	0.84	2	-
GCF_003201775.1	s__Arenibacter sp003201775	77.0504	167	967	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860365.1	s__Arenibacter algicola_B	77.0254	171	967	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002909235.1	s__Arenibacter catalasegens	76.9877	168	967	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002909255.1	s__Arenibacter hampyeongensis	76.9718	150	967	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900141935.1	s__Arenibacter nanhaiticus	76.8635	138	967	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014397245.1	s__Arenibacter arenosicollis	76.8297	185	967	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003957295.1	s__Arenibacter aquaticus	76.8056	152	967	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102165.1	s__Cellulophaga baltica	76.7243	132	967	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	97.62	97.40	0.90	0.89	7	-
GCF_000424985.1	s__Arenibacter latericius	76.6595	117	967	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014596745.1	s__Maribacter_A sp014596745	76.5404	122	967	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005885635.1	s__RZ26 sp005885635	76.4422	92	967	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__RZ26	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003232155.1	s__RZ26 sp003232155	76.3712	57	967	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__RZ26	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009725995.1	s__Zobellia laminariae	76.3622	94	967	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zobellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009725985.1	s__Zobellia amurskyensis	76.3266	98	967	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zobellia	95.0	98.14	98.14	0.91	0.91	2	-
GCF_003992615.1	s__Muricauda beolgyonensis	76.2987	92	967	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003148665.1	s__Maribacter_A polysiphoniae	76.2858	122	967	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_A	95.0	99.27	98.55	0.95	0.91	3	-
--------------------------------------------------------------------------------
[2023-03-18 23:34:51,401] [INFO] GTDB search result was written to OceanDNA-b10367/result_gtdb.tsv
[2023-03-18 23:34:51,402] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:34:51,405] [INFO] DFAST_QC result json was written to OceanDNA-b10367/dqc_result.json
[2023-03-18 23:34:51,405] [INFO] DFAST_QC completed!
[2023-03-18 23:34:51,405] [INFO] Total running time: 0h1m53s