[2023-03-15 11:20:29,265] [INFO] DFAST_QC pipeline started.
[2023-03-15 11:20:29,266] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 11:20:29,266] [INFO] DQC Reference Directory: /var/lib/cwl/stgbe0ee403-7108-479a-beb0-45d67896a467/dqc_reference
[2023-03-15 11:20:30,411] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 11:20:30,411] [INFO] Task started: Prodigal
[2023-03-15 11:20:30,411] [INFO] Running command: cat /var/lib/cwl/stga4f52c78-f36e-4f1e-a66b-6933cca290a3/OceanDNA-b10040.fa | prodigal -d OceanDNA-b10040/cds.fna -a OceanDNA-b10040/protein.faa -g 11 -q > /dev/null
[2023-03-15 11:20:41,821] [INFO] Task succeeded: Prodigal
[2023-03-15 11:20:41,822] [INFO] Task started: HMMsearch
[2023-03-15 11:20:41,822] [INFO] Running command: hmmsearch --tblout OceanDNA-b10040/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbe0ee403-7108-479a-beb0-45d67896a467/dqc_reference/reference_markers.hmm OceanDNA-b10040/protein.faa > /dev/null
[2023-03-15 11:20:42,030] [INFO] Task succeeded: HMMsearch
[2023-03-15 11:20:42,030] [WARNING] Found 5/6 markers. [/var/lib/cwl/stga4f52c78-f36e-4f1e-a66b-6933cca290a3/OceanDNA-b10040.fa]
[2023-03-15 11:20:42,052] [INFO] Query marker FASTA was written to OceanDNA-b10040/markers.fasta
[2023-03-15 11:20:42,053] [INFO] Task started: Blastn
[2023-03-15 11:20:42,053] [INFO] Running command: blastn -query OceanDNA-b10040/markers.fasta -db /var/lib/cwl/stgbe0ee403-7108-479a-beb0-45d67896a467/dqc_reference/reference_markers.fasta -out OceanDNA-b10040/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:20:42,645] [INFO] Task succeeded: Blastn
[2023-03-15 11:20:42,650] [INFO] Selected 12 target genomes.
[2023-03-15 11:20:42,650] [INFO] Target genome list was writen to OceanDNA-b10040/target_genomes.txt
[2023-03-15 11:20:42,659] [INFO] Task started: fastANI
[2023-03-15 11:20:42,659] [INFO] Running command: fastANI --query /var/lib/cwl/stga4f52c78-f36e-4f1e-a66b-6933cca290a3/OceanDNA-b10040.fa --refList OceanDNA-b10040/target_genomes.txt --output OceanDNA-b10040/fastani_result.tsv --threads 1
[2023-03-15 11:20:50,741] [INFO] Task succeeded: fastANI
[2023-03-15 11:20:50,741] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbe0ee403-7108-479a-beb0-45d67896a467/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 11:20:50,741] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbe0ee403-7108-479a-beb0-45d67896a467/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 11:20:50,749] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 11:20:50,750] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 11:20:50,750] [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	80.7299	424	579	95	below_threshold
Polaribacter atrinae	strain=KACC 17473	GCA_001640115.1	1333662	1333662	type	True	80.6129	401	579	95	below_threshold
Polaribacter undariae	strain=KCTC 42175	GCA_024918935.1	1574269	1574269	type	True	80.4468	410	579	95	below_threshold
Polaribacter sejongensis	strain=KCTC 23670	GCA_002814075.1	985043	985043	type	True	80.3312	411	579	95	below_threshold
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	79.8324	405	579	95	below_threshold
Polaribacter haliotis	strain=KCTC 52418	GCA_014784055.1	1888915	1888915	type	True	79.5155	367	579	95	below_threshold
Polaribacter haliotis	strain=RA4-7	GCA_002201315.1	1888915	1888915	type	True	79.479	366	579	95	below_threshold
Polaribacter glomeratus	strain=ATCC 43844	GCA_002954665.1	102	102	type	True	79.4004	330	579	95	below_threshold
Polaribacter vadi	strain=LPB0003	GCA_001761365.1	1774273	1774273	type	True	79.3084	367	579	95	below_threshold
Polaribacter vadi	strain=LPB0003	GCA_001680885.1	1774273	1774273	type	True	79.3032	365	579	95	below_threshold
Polaribacter glomeratus	strain=ACAM 171	GCA_007997115.1	102	102	type	True	79.2999	340	579	95	below_threshold
Polaribacter litorisediminis	strain=OITF-11	GCA_019968605.1	1908341	1908341	type	True	78.5612	333	579	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 11:20:50,751] [INFO] DFAST Taxonomy check result was written to OceanDNA-b10040/tc_result.tsv
[2023-03-15 11:20:50,752] [INFO] ===== Taxonomy check completed =====
[2023-03-15 11:20:50,752] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 11:20:50,752] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbe0ee403-7108-479a-beb0-45d67896a467/dqc_reference/checkm_data
[2023-03-15 11:20:50,753] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 11:20:50,757] [INFO] Task started: CheckM
[2023-03-15 11:20:50,758] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b10040/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b10040/checkm_input OceanDNA-b10040/checkm_result
[2023-03-15 11:21:22,488] [INFO] Task succeeded: CheckM
[2023-03-15 11:21:22,489] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 64.58%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 11:21:22,531] [INFO] ===== Completeness check finished =====
[2023-03-15 11:21:22,531] [INFO] ===== Start GTDB Search =====
[2023-03-15 11:21:22,531] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b10040/markers.fasta)
[2023-03-15 11:21:22,533] [INFO] Task started: Blastn
[2023-03-15 11:21:22,533] [INFO] Running command: blastn -query OceanDNA-b10040/markers.fasta -db /var/lib/cwl/stgbe0ee403-7108-479a-beb0-45d67896a467/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b10040/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:21:23,289] [INFO] Task succeeded: Blastn
[2023-03-15 11:21:23,290] [INFO] Selected 13 target genomes.
[2023-03-15 11:21:23,290] [INFO] Target genome list was writen to OceanDNA-b10040/target_genomes_gtdb.txt
[2023-03-15 11:21:23,300] [INFO] Task started: fastANI
[2023-03-15 11:21:23,300] [INFO] Running command: fastANI --query /var/lib/cwl/stga4f52c78-f36e-4f1e-a66b-6933cca290a3/OceanDNA-b10040.fa --refList OceanDNA-b10040/target_genomes_gtdb.txt --output OceanDNA-b10040/fastani_result_gtdb.tsv --threads 1
[2023-03-15 11:21:32,120] [INFO] Task succeeded: fastANI
[2023-03-15 11:21:32,128] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 11:21:32,128] [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	81.6414	450	579	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	81.6293	436	579	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	80.7184	436	579	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	80.7152	425	579	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	80.658	424	579	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	80.4853	404	579	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	98.52	98.52	0.95	0.95	2	-
GCF_002814075.1	s__Polaribacter sejongensis	80.339	410	579	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	80.2297	388	579	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	79.6984	328	579	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	79.5362	366	579	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002954665.1	s__Polaribacter glomeratus	79.4076	330	579	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	78.7089	325	579	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	78.1433	281	579	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__VISM01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 11:21:32,130] [INFO] GTDB search result was written to OceanDNA-b10040/result_gtdb.tsv
[2023-03-15 11:21:32,131] [INFO] ===== GTDB Search completed =====
[2023-03-15 11:21:32,133] [INFO] DFAST_QC result json was written to OceanDNA-b10040/dqc_result.json
[2023-03-15 11:21:32,133] [INFO] DFAST_QC completed!
[2023-03-15 11:21:32,133] [INFO] Total running time: 0h1m3s