[2023-03-15 11:20:29,256] [INFO] DFAST_QC pipeline started.
[2023-03-15 11:20:29,257] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 11:20:29,257] [INFO] DQC Reference Directory: /var/lib/cwl/stgaa9400b6-ed1b-45d8-8e96-d7696a506a85/dqc_reference
[2023-03-15 11:20:30,419] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 11:20:30,420] [INFO] Task started: Prodigal
[2023-03-15 11:20:30,420] [INFO] Running command: cat /var/lib/cwl/stg51093681-c185-4ac0-95c0-c87a8d7f51c6/OceanDNA-b10034.fa | prodigal -d OceanDNA-b10034/cds.fna -a OceanDNA-b10034/protein.faa -g 11 -q > /dev/null
[2023-03-15 11:20:44,222] [INFO] Task succeeded: Prodigal
[2023-03-15 11:20:44,222] [INFO] Task started: HMMsearch
[2023-03-15 11:20:44,222] [INFO] Running command: hmmsearch --tblout OceanDNA-b10034/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaa9400b6-ed1b-45d8-8e96-d7696a506a85/dqc_reference/reference_markers.hmm OceanDNA-b10034/protein.faa > /dev/null
[2023-03-15 11:20:44,398] [INFO] Task succeeded: HMMsearch
[2023-03-15 11:20:44,399] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg51093681-c185-4ac0-95c0-c87a8d7f51c6/OceanDNA-b10034.fa]
[2023-03-15 11:20:44,421] [INFO] Query marker FASTA was written to OceanDNA-b10034/markers.fasta
[2023-03-15 11:20:44,421] [INFO] Task started: Blastn
[2023-03-15 11:20:44,421] [INFO] Running command: blastn -query OceanDNA-b10034/markers.fasta -db /var/lib/cwl/stgaa9400b6-ed1b-45d8-8e96-d7696a506a85/dqc_reference/reference_markers.fasta -out OceanDNA-b10034/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:20:44,995] [INFO] Task succeeded: Blastn
[2023-03-15 11:20:45,001] [INFO] Selected 17 target genomes.
[2023-03-15 11:20:45,001] [INFO] Target genome list was writen to OceanDNA-b10034/target_genomes.txt
[2023-03-15 11:20:45,010] [INFO] Task started: fastANI
[2023-03-15 11:20:45,010] [INFO] Running command: fastANI --query /var/lib/cwl/stg51093681-c185-4ac0-95c0-c87a8d7f51c6/OceanDNA-b10034.fa --refList OceanDNA-b10034/target_genomes.txt --output OceanDNA-b10034/fastani_result.tsv --threads 1
[2023-03-15 11:20:55,891] [INFO] Task succeeded: fastANI
[2023-03-15 11:20:55,891] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaa9400b6-ed1b-45d8-8e96-d7696a506a85/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 11:20:55,891] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaa9400b6-ed1b-45d8-8e96-d7696a506a85/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 11:20:55,904] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 11:20:55,904] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 11:20:55,904] [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 butkevichii	strain=KCTC 12100	GCA_002954605.1	218490	218490	type	True	81.6961	474	722	95	below_threshold
Polaribacter atrinae	strain=KACC 17473	GCA_001640115.1	1333662	1333662	type	True	81.3082	472	722	95	below_threshold
Polaribacter sejongensis	strain=KCTC 23670	GCA_002814075.1	985043	985043	type	True	81.3021	464	722	95	below_threshold
Polaribacter undariae	strain=KCTC 42175	GCA_024918935.1	1574269	1574269	type	True	81.2447	462	722	95	below_threshold
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	80.2689	447	722	95	below_threshold
Polaribacter haliotis	strain=RA4-7	GCA_002201315.1	1888915	1888915	type	True	79.6607	425	722	95	below_threshold
Polaribacter haliotis	strain=KCTC 52418	GCA_014784055.1	1888915	1888915	type	True	79.6553	429	722	95	below_threshold
Polaribacter vadi	strain=LPB0003	GCA_001680885.1	1774273	1774273	type	True	79.4853	410	722	95	below_threshold
Polaribacter vadi	strain=LPB0003	GCA_001761365.1	1774273	1774273	type	True	79.466	416	722	95	below_threshold
Polaribacter filamentus	strain=ATCC 700397	GCA_002943715.1	53483	53483	type	True	79.3212	393	722	95	below_threshold
Polaribacter aestuariivivens	strain=DBTF-3	GCA_005885675.1	2304626	2304626	type	True	79.3063	394	722	95	below_threshold
Polaribacter glomeratus	strain=ATCC 43844	GCA_002954665.1	102	102	type	True	79.2527	405	722	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	79.2201	383	722	95	below_threshold
Polaribacter glomeratus	strain=ACAM 171	GCA_007997115.1	102	102	type	True	79.1842	410	722	95	below_threshold
Polaribacter litorisediminis	strain=OITF-11	GCA_019968605.1	1908341	1908341	type	True	78.8894	359	722	95	below_threshold
Polaribacter dokdonensis	strain=KCTC 12392	GCA_024362345.1	326329	326329	type	True	78.8815	350	722	95	below_threshold
Polaribacter batillariae	strain=G4M1	GCA_017498485.1	2808900	2808900	type	True	78.8364	371	722	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 11:20:55,907] [INFO] DFAST Taxonomy check result was written to OceanDNA-b10034/tc_result.tsv
[2023-03-15 11:20:55,910] [INFO] ===== Taxonomy check completed =====
[2023-03-15 11:20:55,910] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 11:20:55,910] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaa9400b6-ed1b-45d8-8e96-d7696a506a85/dqc_reference/checkm_data
[2023-03-15 11:20:55,911] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 11:20:55,920] [INFO] Task started: CheckM
[2023-03-15 11:20:55,920] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b10034/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b10034/checkm_input OceanDNA-b10034/checkm_result
[2023-03-15 11:21:34,062] [INFO] Task succeeded: CheckM
[2023-03-15 11:21:34,062] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 63.89%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 11:21:34,130] [INFO] ===== Completeness check finished =====
[2023-03-15 11:21:34,130] [INFO] ===== Start GTDB Search =====
[2023-03-15 11:21:34,130] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b10034/markers.fasta)
[2023-03-15 11:21:34,131] [INFO] Task started: Blastn
[2023-03-15 11:21:34,131] [INFO] Running command: blastn -query OceanDNA-b10034/markers.fasta -db /var/lib/cwl/stgaa9400b6-ed1b-45d8-8e96-d7696a506a85/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b10034/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:21:34,900] [INFO] Task succeeded: Blastn
[2023-03-15 11:21:34,903] [INFO] Selected 13 target genomes.
[2023-03-15 11:21:34,904] [INFO] Target genome list was writen to OceanDNA-b10034/target_genomes_gtdb.txt
[2023-03-15 11:21:34,913] [INFO] Task started: fastANI
[2023-03-15 11:21:34,913] [INFO] Running command: fastANI --query /var/lib/cwl/stg51093681-c185-4ac0-95c0-c87a8d7f51c6/OceanDNA-b10034.fa --refList OceanDNA-b10034/target_genomes_gtdb.txt --output OceanDNA-b10034/fastani_result_gtdb.tsv --threads 1
[2023-03-15 11:21:43,365] [INFO] Task succeeded: fastANI
[2023-03-15 11:21:43,373] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 11:21:43,373] [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_002163675.1	s__Polaribacter sp002163675	85.632	548	722	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000766795.1	s__Polaribacter sp000766795	82.975	510	722	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009796785.1	s__Polaribacter sp009796785	81.7644	491	722	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002954605.1	s__Polaribacter butkevichii	81.6812	475	722	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001640115.1	s__Polaribacter atrinae	81.3082	472	722	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016858305.2	s__Polaribacter sp016858305	81.2576	474	722	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002163835.1	s__Polaribacter sp002163835	81.1403	446	722	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905480405.1	s__Polaribacter sp905480405	80.2436	404	722	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002831685.1	s__Polaribacter sp002831685	80.1629	405	722	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000981625.1	s__Polaribacter sp000981625	79.8191	360	722	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002005425.1	s__Polaribacter sp002005425	79.5736	396	722	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	96.81	96.81	0.92	0.92	2	-
GCF_001761365.1	s__Polaribacter vadi	79.466	416	722	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000152945.2	s__Polaribacter sp000152945	78.6361	339	722	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 11:21:43,375] [INFO] GTDB search result was written to OceanDNA-b10034/result_gtdb.tsv
[2023-03-15 11:21:43,377] [INFO] ===== GTDB Search completed =====
[2023-03-15 11:21:43,381] [INFO] DFAST_QC result json was written to OceanDNA-b10034/dqc_result.json
[2023-03-15 11:21:43,381] [INFO] DFAST_QC completed!
[2023-03-15 11:21:43,381] [INFO] Total running time: 0h1m14s