[2023-03-19 00:44:19,968] [INFO] DFAST_QC pipeline started.
[2023-03-19 00:44:19,968] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 00:44:19,968] [INFO] DQC Reference Directory: /var/lib/cwl/stgc44c4954-7ed4-4c09-967a-c2499cfb389e/dqc_reference
[2023-03-19 00:44:21,112] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 00:44:21,112] [INFO] Task started: Prodigal
[2023-03-19 00:44:21,112] [INFO] Running command: cat /var/lib/cwl/stgece8bb16-9242-4f38-bf0b-863b604db9e0/OceanDNA-b9899.fa | prodigal -d OceanDNA-b9899/cds.fna -a OceanDNA-b9899/protein.faa -g 11 -q > /dev/null
[2023-03-19 00:44:33,551] [INFO] Task succeeded: Prodigal
[2023-03-19 00:44:33,552] [INFO] Task started: HMMsearch
[2023-03-19 00:44:33,552] [INFO] Running command: hmmsearch --tblout OceanDNA-b9899/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc44c4954-7ed4-4c09-967a-c2499cfb389e/dqc_reference/reference_markers.hmm OceanDNA-b9899/protein.faa > /dev/null
[2023-03-19 00:44:33,739] [INFO] Task succeeded: HMMsearch
[2023-03-19 00:44:33,740] [INFO] Found 6/6 markers.
[2023-03-19 00:44:33,753] [INFO] Query marker FASTA was written to OceanDNA-b9899/markers.fasta
[2023-03-19 00:44:33,753] [INFO] Task started: Blastn
[2023-03-19 00:44:33,753] [INFO] Running command: blastn -query OceanDNA-b9899/markers.fasta -db /var/lib/cwl/stgc44c4954-7ed4-4c09-967a-c2499cfb389e/dqc_reference/reference_markers.fasta -out OceanDNA-b9899/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:44:34,300] [INFO] Task succeeded: Blastn
[2023-03-19 00:44:34,301] [INFO] Selected 25 target genomes.
[2023-03-19 00:44:34,302] [INFO] Target genome list was writen to OceanDNA-b9899/target_genomes.txt
[2023-03-19 00:44:34,316] [INFO] Task started: fastANI
[2023-03-19 00:44:34,316] [INFO] Running command: fastANI --query /var/lib/cwl/stgece8bb16-9242-4f38-bf0b-863b604db9e0/OceanDNA-b9899.fa --refList OceanDNA-b9899/target_genomes.txt --output OceanDNA-b9899/fastani_result.tsv --threads 1
[2023-03-19 00:44:48,614] [INFO] Task succeeded: fastANI
[2023-03-19 00:44:48,614] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc44c4954-7ed4-4c09-967a-c2499cfb389e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 00:44:48,614] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc44c4954-7ed4-4c09-967a-c2499cfb389e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 00:44:48,628] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 00:44:48,628] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 00:44:48,629] [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	79.1768	363	640	95	below_threshold
Polaribacter atrinae	strain=KACC 17473	GCA_001640115.1	1333662	1333662	type	True	79.0856	343	640	95	below_threshold
Polaribacter sejongensis	strain=KCTC 23670	GCA_002814075.1	985043	985043	type	True	78.8984	352	640	95	below_threshold
Polaribacter undariae	strain=KCTC 42175	GCA_024918935.1	1574269	1574269	type	True	78.825	356	640	95	below_threshold
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	78.6081	343	640	95	below_threshold
Polaribacter haliotis	strain=KCTC 52418	GCA_014784055.1	1888915	1888915	type	True	78.5006	317	640	95	below_threshold
Polaribacter haliotis	strain=RA4-7	GCA_002201315.1	1888915	1888915	type	True	78.4928	313	640	95	below_threshold
Polaribacter aquimarinus	strain=ZY113	GCA_003129485.1	2100726	2100726	type	True	78.3648	329	640	95	below_threshold
Polaribacter reichenbachii	strain=6Alg 8T	GCA_001975665.1	996801	996801	type	True	78.3532	299	640	95	below_threshold
Polaribacter vadi	strain=LPB0003	GCA_001761365.1	1774273	1774273	type	True	78.3389	317	640	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	78.3275	327	640	95	below_threshold
Polaribacter vadi	strain=LPB0003	GCA_001680885.1	1774273	1774273	type	True	78.2892	321	640	95	below_threshold
Polaribacter reichenbachii	strain=KCTC 23969	GCA_001680875.1	996801	996801	type	True	78.2744	310	640	95	below_threshold
Polaribacter aestuariivivens	strain=DBTF-3	GCA_005885675.1	2304626	2304626	type	True	78.259	323	640	95	below_threshold
Polaribacter filamentus	strain=ATCC 700397	GCA_002943715.1	53483	53483	type	True	78.2583	309	640	95	below_threshold
Polaribacter reichenbachii	strain=KCTC 23969	GCA_002814055.1	996801	996801	type	True	78.2106	313	640	95	below_threshold
Polaribacter reichenbachii	strain=LMG 26443	GCA_020532845.1	996801	996801	type	True	78.2046	309	640	95	below_threshold
Polaribacter glomeratus	strain=ATCC 43844	GCA_002954665.1	102	102	type	True	78.1067	309	640	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	78.1042	278	640	95	below_threshold
Polaribacter glomeratus	strain=ACAM 171	GCA_007997115.1	102	102	type	True	78.0941	312	640	95	below_threshold
Polaribacter dokdonensis	strain=DSW-5	GCA_900106865.1	326329	326329	type	True	78.0632	264	640	95	below_threshold
Polaribacter litorisediminis	strain=OITF-11	GCA_019968605.1	1908341	1908341	type	True	77.9083	284	640	95	below_threshold
Tenacibaculum aquimarinum	strain=K20-16	GCA_022478115.1	2910675	2910675	type	True	77.8876	227	640	95	below_threshold
Tenacibaculum todarodis	strain=LPB0136	GCA_001889045.1	1850252	1850252	type	True	77.595	224	640	95	below_threshold
Tenacibaculum caenipelagi	strain=CECT 8283	GCA_004363005.1	1325435	1325435	type	True	76.4608	143	640	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 00:44:48,629] [INFO] DFAST Taxonomy check result was written to OceanDNA-b9899/tc_result.tsv
[2023-03-19 00:44:48,629] [INFO] ===== Taxonomy check completed =====
[2023-03-19 00:44:48,629] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 00:44:48,630] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc44c4954-7ed4-4c09-967a-c2499cfb389e/dqc_reference/checkm_data
[2023-03-19 00:44:48,630] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 00:44:48,649] [INFO] Task started: CheckM
[2023-03-19 00:44:48,649] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b9899/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b9899/checkm_input OceanDNA-b9899/checkm_result
[2023-03-19 00:45:23,584] [INFO] Task succeeded: CheckM
[2023-03-19 00:45:23,585] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.12%
Contamintation: 3.12%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-19 00:45:23,587] [INFO] ===== Completeness check finished =====
[2023-03-19 00:45:23,587] [INFO] ===== Start GTDB Search =====
[2023-03-19 00:45:23,588] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b9899/markers.fasta)
[2023-03-19 00:45:23,589] [INFO] Task started: Blastn
[2023-03-19 00:45:23,589] [INFO] Running command: blastn -query OceanDNA-b9899/markers.fasta -db /var/lib/cwl/stgc44c4954-7ed4-4c09-967a-c2499cfb389e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b9899/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:45:24,319] [INFO] Task succeeded: Blastn
[2023-03-19 00:45:24,320] [INFO] Selected 23 target genomes.
[2023-03-19 00:45:24,320] [INFO] Target genome list was writen to OceanDNA-b9899/target_genomes_gtdb.txt
[2023-03-19 00:45:24,343] [INFO] Task started: fastANI
[2023-03-19 00:45:24,343] [INFO] Running command: fastANI --query /var/lib/cwl/stgece8bb16-9242-4f38-bf0b-863b604db9e0/OceanDNA-b9899.fa --refList OceanDNA-b9899/target_genomes_gtdb.txt --output OceanDNA-b9899/fastani_result_gtdb.tsv --threads 1
[2023-03-19 00:45:38,843] [INFO] Task succeeded: fastANI
[2023-03-19 00:45:38,855] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 00:45:38,856] [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_018608545.1	s__Polaribacter sp018608545	96.5709	561	640	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	97.39	97.39	0.93	0.93	2	conclusive
GCF_000766795.1	s__Polaribacter sp000766795	79.7474	413	640	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002163675.1	s__Polaribacter sp002163675	79.475	401	640	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	79.2349	326	640	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	79.164	364	640	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	79.0856	343	640	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019263805.1	s__Polaribacter sp011379025	79.0536	340	640	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	98.52	98.52	0.95	0.95	2	-
GCF_009796785.1	s__Polaribacter sp009796785	78.9762	375	640	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002814075.1	s__Polaribacter sejongensis	78.9232	350	640	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	97.48	97.48	0.89	0.89	2	-
GCF_002163835.1	s__Polaribacter sp002163835	78.8964	357	640	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105145.1	s__Polaribacter sp900105145	78.8214	327	640	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	78.7837	282	640	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014352875.1	s__Polaribacter sp014352875	78.6442	340	640	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014784055.1	s__Polaribacter haliotis	78.5006	317	640	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002005425.1	s__Polaribacter sp002005425	78.4371	299	640	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	96.81	96.81	0.92	0.92	2	-
GCF_003129485.1	s__Polaribacter sp003129485	78.3752	328	640	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001761365.1	s__Polaribacter vadi	78.3381	317	640	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002943715.1	s__Polaribacter filamentus	78.2584	309	640	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	78.2169	308	640	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018663625.1	s__Polaribacter sp018663625	78.1368	205	640	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	99.23	98.14	0.90	0.83	5	-
GCF_002954665.1	s__Polaribacter glomeratus	78.1067	309	640	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	99.98	99.98	1.00	1.00	2	-
GCF_007997085.1	s__Polaribacter sp007997085	77.8654	270	640	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	99.89	99.89	0.97	0.97	2	-
GCF_007827455.1	s__VISM01 sp007827455	77.4248	255	640	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__VISM01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 00:45:38,856] [INFO] GTDB search result was written to OceanDNA-b9899/result_gtdb.tsv
[2023-03-19 00:45:38,856] [INFO] ===== GTDB Search completed =====
[2023-03-19 00:45:38,859] [INFO] DFAST_QC result json was written to OceanDNA-b9899/dqc_result.json
[2023-03-19 00:45:38,859] [INFO] DFAST_QC completed!
[2023-03-19 00:45:38,859] [INFO] Total running time: 0h1m19s