[2023-03-17 23:43:20,542] [INFO] DFAST_QC pipeline started.
[2023-03-17 23:43:20,544] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 23:43:20,544] [INFO] DQC Reference Directory: /var/lib/cwl/stgc8110ef1-2f83-434e-9204-e5fef21849c3/dqc_reference
[2023-03-17 23:43:21,634] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 23:43:21,635] [INFO] Task started: Prodigal
[2023-03-17 23:43:21,635] [INFO] Running command: cat /var/lib/cwl/stgae1f5a8f-d6cd-4b1e-b82f-2381bfd6dafe/OceanDNA-b10264.fa | prodigal -d OceanDNA-b10264/cds.fna -a OceanDNA-b10264/protein.faa -g 11 -q > /dev/null
[2023-03-17 23:43:32,218] [INFO] Task succeeded: Prodigal
[2023-03-17 23:43:32,218] [INFO] Task started: HMMsearch
[2023-03-17 23:43:32,218] [INFO] Running command: hmmsearch --tblout OceanDNA-b10264/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc8110ef1-2f83-434e-9204-e5fef21849c3/dqc_reference/reference_markers.hmm OceanDNA-b10264/protein.faa > /dev/null
[2023-03-17 23:43:32,403] [INFO] Task succeeded: HMMsearch
[2023-03-17 23:43:32,404] [INFO] Found 6/6 markers.
[2023-03-17 23:43:32,418] [INFO] Query marker FASTA was written to OceanDNA-b10264/markers.fasta
[2023-03-17 23:43:32,419] [INFO] Task started: Blastn
[2023-03-17 23:43:32,419] [INFO] Running command: blastn -query OceanDNA-b10264/markers.fasta -db /var/lib/cwl/stgc8110ef1-2f83-434e-9204-e5fef21849c3/dqc_reference/reference_markers.fasta -out OceanDNA-b10264/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:43:32,997] [INFO] Task succeeded: Blastn
[2023-03-17 23:43:33,003] [INFO] Selected 24 target genomes.
[2023-03-17 23:43:33,003] [INFO] Target genome list was writen to OceanDNA-b10264/target_genomes.txt
[2023-03-17 23:43:33,028] [INFO] Task started: fastANI
[2023-03-17 23:43:33,028] [INFO] Running command: fastANI --query /var/lib/cwl/stgae1f5a8f-d6cd-4b1e-b82f-2381bfd6dafe/OceanDNA-b10264.fa --refList OceanDNA-b10264/target_genomes.txt --output OceanDNA-b10264/fastani_result.tsv --threads 1
[2023-03-17 23:43:45,625] [INFO] Task succeeded: fastANI
[2023-03-17 23:43:45,626] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc8110ef1-2f83-434e-9204-e5fef21849c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 23:43:45,626] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc8110ef1-2f83-434e-9204-e5fef21849c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 23:43:45,639] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 23:43:45,640] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 23:43:45,640] [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
Polaribacter vadi	strain=LPB0003	GCA_001761365.1	1774273	1774273	type	True	77.6588	191	552	95	below_threshold
Polaribacter vadi	strain=LPB0003	GCA_001680885.1	1774273	1774273	type	True	77.6313	194	552	95	below_threshold
Polaribacter dokdonensis	strain=DSW-5	GCA_900106865.1	326329	326329	type	True	77.6301	177	552	95	below_threshold
Polaribacter aquimarinus	strain=ZY113	GCA_003129485.1	2100726	2100726	type	True	77.5764	186	552	95	below_threshold
Polaribacter dokdonensis	strain=DSW-5	GCA_001280865.1	326329	326329	type	True	77.5657	178	552	95	below_threshold
Polaribacter dokdonensis	strain=KCTC 12392	GCA_024362345.1	326329	326329	type	True	77.5654	180	552	95	below_threshold
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	77.5584	200	552	95	below_threshold
Polaribacter aestuariivivens	strain=DBTF-3	GCA_005885675.1	2304626	2304626	type	True	77.5291	185	552	95	below_threshold
Polaribacter undariae	strain=KCTC 42175	GCA_024918935.1	1574269	1574269	type	True	77.5076	164	552	95	below_threshold
Polaribacter butkevichii	strain=KCTC 12100	GCA_002954605.1	218490	218490	type	True	77.4994	168	552	95	below_threshold
Tenacibaculum aquimarinum	strain=K20-16	GCA_022478115.1	2910675	2910675	type	True	77.4652	175	552	95	below_threshold
Polaribacter sejongensis	strain=KCTC 23670	GCA_002814075.1	985043	985043	type	True	77.4585	173	552	95	below_threshold
Polaribacter haliotis	strain=KCTC 52418	GCA_014784055.1	1888915	1888915	type	True	77.4539	187	552	95	below_threshold
Polaribacter porphyrae	strain=NBRC 108759	GCA_002954685.1	1137780	1137780	type	True	77.4393	184	552	95	below_threshold
Polaribacter porphyrae	strain=LMG 26671	GCA_020532745.1	1137780	1137780	type	True	77.4239	185	552	95	below_threshold
Polaribacter haliotis	strain=RA4-7	GCA_002201315.1	1888915	1888915	type	True	77.4194	188	552	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	77.3948	179	552	95	below_threshold
Polaribacter litorisediminis	strain=OITF-11	GCA_019968605.1	1908341	1908341	type	True	77.2652	191	552	95	below_threshold
Tenacibaculum todarodis	strain=LPB0136	GCA_001889045.1	1850252	1850252	type	True	77.2416	170	552	95	below_threshold
Polaribacter atrinae	strain=KACC 17473	GCA_001640115.1	1333662	1333662	type	True	77.2283	177	552	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	77.153	161	552	95	below_threshold
Polaribacter batillariae	strain=G4M1	GCA_017498485.1	2808900	2808900	type	True	77.1434	169	552	95	below_threshold
Tenacibaculum ovolyticum	strain=DSM 18103	GCA_000430545.1	104270	104270	type	True	76.9108	155	552	95	below_threshold
Tenacibaculum skagerrakense	strain=DSM 14836	GCA_004345825.1	186571	186571	type	True	76.7042	105	552	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 23:43:45,667] [INFO] DFAST Taxonomy check result was written to OceanDNA-b10264/tc_result.tsv
[2023-03-17 23:43:45,695] [INFO] ===== Taxonomy check completed =====
[2023-03-17 23:43:45,695] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 23:43:45,695] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc8110ef1-2f83-434e-9204-e5fef21849c3/dqc_reference/checkm_data
[2023-03-17 23:43:45,696] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 23:43:45,703] [INFO] Task started: CheckM
[2023-03-17 23:43:45,703] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b10264/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b10264/checkm_input OceanDNA-b10264/checkm_result
[2023-03-17 23:44:16,584] [INFO] Task succeeded: CheckM
[2023-03-17 23:44:16,584] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 23:44:16,601] [INFO] ===== Completeness check finished =====
[2023-03-17 23:44:16,601] [INFO] ===== Start GTDB Search =====
[2023-03-17 23:44:16,601] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b10264/markers.fasta)
[2023-03-17 23:44:16,603] [INFO] Task started: Blastn
[2023-03-17 23:44:16,603] [INFO] Running command: blastn -query OceanDNA-b10264/markers.fasta -db /var/lib/cwl/stgc8110ef1-2f83-434e-9204-e5fef21849c3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b10264/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:44:17,365] [INFO] Task succeeded: Blastn
[2023-03-17 23:44:17,366] [INFO] Selected 14 target genomes.
[2023-03-17 23:44:17,366] [INFO] Target genome list was writen to OceanDNA-b10264/target_genomes_gtdb.txt
[2023-03-17 23:44:17,377] [INFO] Task started: fastANI
[2023-03-17 23:44:17,377] [INFO] Running command: fastANI --query /var/lib/cwl/stgae1f5a8f-d6cd-4b1e-b82f-2381bfd6dafe/OceanDNA-b10264.fa --refList OceanDNA-b10264/target_genomes_gtdb.txt --output OceanDNA-b10264/fastani_result_gtdb.tsv --threads 1
[2023-03-17 23:44:25,166] [INFO] Task succeeded: fastANI
[2023-03-17 23:44:25,175] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 23:44:25,175] [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_905479435.1	s__SCGC-AAA160-P02 sp905479435	89.6068	340	552	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SCGC-AAA160-P02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015665265.1	s__SCGC-AAA160-P02 sp015665265	85.7097	420	552	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SCGC-AAA160-P02	95.0	96.43	96.43	0.88	0.88	2	-
GCA_018608485.1	s__SCGC-AAA160-P02 sp018608485	83.8649	333	552	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SCGC-AAA160-P02	95.0	99.40	99.40	0.78	0.78	2	-
GCA_000383355.1	s__SCGC-AAA160-P02 sp000383355	82.9332	421	552	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SCGC-AAA160-P02	95.0	96.64	95.28	0.86	0.84	6	-
GCF_000766795.1	s__Polaribacter sp000766795	77.8255	204	552	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007827455.1	s__VISM01 sp007827455	77.7623	194	552	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__VISM01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001761365.1	s__Polaribacter vadi	77.6754	190	552	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900106075.1	s__Polaribacter sp900106075	77.566	196	552	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	98.66	98.45	0.96	0.92	5	-
GCF_014352875.1	s__Polaribacter sp014352875	77.5584	200	552	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018861005.1	s__Polaribacter vadi_A	77.4617	195	552	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003335085.1	s__Polaribacter sp003335085	77.4509	148	552	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007997075.1	s__Polaribacter sp007997075	77.2815	174	552	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004762155.1	s__Tenacibaculum sp004762155	77.0453	160	552	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002836595.1	s__Tenacibaculum sp002836595	76.9158	145	552	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 23:44:25,176] [INFO] GTDB search result was written to OceanDNA-b10264/result_gtdb.tsv
[2023-03-17 23:44:25,176] [INFO] ===== GTDB Search completed =====
[2023-03-17 23:44:25,178] [INFO] DFAST_QC result json was written to OceanDNA-b10264/dqc_result.json
[2023-03-17 23:44:25,179] [INFO] DFAST_QC completed!
[2023-03-17 23:44:25,179] [INFO] Total running time: 0h1m5s