[2023-03-18 07:06:22,063] [INFO] DFAST_QC pipeline started.
[2023-03-18 07:06:22,063] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 07:06:22,063] [INFO] DQC Reference Directory: /var/lib/cwl/stgf348e1ea-1650-4096-aa2f-0124a61d41e7/dqc_reference
[2023-03-18 07:06:23,217] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 07:06:23,217] [INFO] Task started: Prodigal
[2023-03-18 07:06:23,218] [INFO] Running command: cat /var/lib/cwl/stgfcee1bbc-18d9-4cf7-8b70-f2055b43ffdd/OceanDNA-b10073.fa | prodigal -d OceanDNA-b10073/cds.fna -a OceanDNA-b10073/protein.faa -g 11 -q > /dev/null
[2023-03-18 07:06:44,109] [INFO] Task succeeded: Prodigal
[2023-03-18 07:06:44,110] [INFO] Task started: HMMsearch
[2023-03-18 07:06:44,110] [INFO] Running command: hmmsearch --tblout OceanDNA-b10073/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf348e1ea-1650-4096-aa2f-0124a61d41e7/dqc_reference/reference_markers.hmm OceanDNA-b10073/protein.faa > /dev/null
[2023-03-18 07:06:44,329] [INFO] Task succeeded: HMMsearch
[2023-03-18 07:06:44,329] [INFO] Found 6/6 markers.
[2023-03-18 07:06:44,351] [INFO] Query marker FASTA was written to OceanDNA-b10073/markers.fasta
[2023-03-18 07:06:44,351] [INFO] Task started: Blastn
[2023-03-18 07:06:44,351] [INFO] Running command: blastn -query OceanDNA-b10073/markers.fasta -db /var/lib/cwl/stgf348e1ea-1650-4096-aa2f-0124a61d41e7/dqc_reference/reference_markers.fasta -out OceanDNA-b10073/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:06:44,953] [INFO] Task succeeded: Blastn
[2023-03-18 07:06:44,954] [INFO] Selected 15 target genomes.
[2023-03-18 07:06:44,954] [INFO] Target genome list was writen to OceanDNA-b10073/target_genomes.txt
[2023-03-18 07:06:44,956] [INFO] Task started: fastANI
[2023-03-18 07:06:44,956] [INFO] Running command: fastANI --query /var/lib/cwl/stgfcee1bbc-18d9-4cf7-8b70-f2055b43ffdd/OceanDNA-b10073.fa --refList OceanDNA-b10073/target_genomes.txt --output OceanDNA-b10073/fastani_result.tsv --threads 1
[2023-03-18 07:06:56,555] [INFO] Task succeeded: fastANI
[2023-03-18 07:06:56,555] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf348e1ea-1650-4096-aa2f-0124a61d41e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 07:06:56,555] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf348e1ea-1650-4096-aa2f-0124a61d41e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 07:06:56,564] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2023-03-18 07:06:56,564] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-18 07:06:56,565] [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_001680885.1	1774273	1774273	type	True	97.3398	1024	1144	95	conclusive
Polaribacter vadi	strain=LPB0003	GCA_001761365.1	1774273	1774273	type	True	97.2929	1034	1144	95	conclusive
Polaribacter reichenbachii	strain=KCTC 23969	GCA_001680875.1	996801	996801	type	True	81.9923	722	1144	95	below_threshold
Polaribacter reichenbachii	strain=LMG 26443	GCA_020532845.1	996801	996801	type	True	81.9495	732	1144	95	below_threshold
Polaribacter reichenbachii	strain=KCTC 23969	GCA_002814055.1	996801	996801	type	True	81.9058	755	1144	95	below_threshold
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	81.8162	668	1144	95	below_threshold
Polaribacter haliotis	strain=KCTC 52418	GCA_014784055.1	1888915	1888915	type	True	81.4362	679	1144	95	below_threshold
Polaribacter haliotis	strain=RA4-7	GCA_002201315.1	1888915	1888915	type	True	81.3852	680	1144	95	below_threshold
Polaribacter litorisediminis	strain=OITF-11	GCA_019968605.1	1908341	1908341	type	True	81.0092	673	1144	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	80.9953	610	1144	95	below_threshold
Polaribacter glomeratus	strain=ACAM 171	GCA_007997115.1	102	102	type	True	80.9872	658	1144	95	below_threshold
Polaribacter dokdonensis	strain=KCTC 12392	GCA_024362345.1	326329	326329	type	True	80.9672	635	1144	95	below_threshold
Polaribacter glomeratus	strain=ATCC 43844	GCA_002954665.1	102	102	type	True	80.9521	658	1144	95	below_threshold
Polaribacter undariae	strain=KCTC 42175	GCA_024918935.1	1574269	1574269	type	True	80.4065	628	1144	95	below_threshold
Polaribacter batillariae	strain=G4M1	GCA_017498485.1	2808900	2808900	type	True	80.3809	600	1144	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 07:06:56,565] [INFO] DFAST Taxonomy check result was written to OceanDNA-b10073/tc_result.tsv
[2023-03-18 07:06:56,565] [INFO] ===== Taxonomy check completed =====
[2023-03-18 07:06:56,565] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 07:06:56,565] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf348e1ea-1650-4096-aa2f-0124a61d41e7/dqc_reference/checkm_data
[2023-03-18 07:06:56,566] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 07:06:56,570] [INFO] Task started: CheckM
[2023-03-18 07:06:56,571] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b10073/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b10073/checkm_input OceanDNA-b10073/checkm_result
[2023-03-18 07:07:48,918] [INFO] Task succeeded: CheckM
[2023-03-18 07:07:48,918] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.12%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 07:07:48,921] [INFO] ===== Completeness check finished =====
[2023-03-18 07:07:48,921] [INFO] ===== Start GTDB Search =====
[2023-03-18 07:07:48,921] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b10073/markers.fasta)
[2023-03-18 07:07:48,921] [INFO] Task started: Blastn
[2023-03-18 07:07:48,921] [INFO] Running command: blastn -query OceanDNA-b10073/markers.fasta -db /var/lib/cwl/stgf348e1ea-1650-4096-aa2f-0124a61d41e7/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b10073/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:07:49,796] [INFO] Task succeeded: Blastn
[2023-03-18 07:07:49,797] [INFO] Selected 15 target genomes.
[2023-03-18 07:07:49,797] [INFO] Target genome list was writen to OceanDNA-b10073/target_genomes_gtdb.txt
[2023-03-18 07:07:49,804] [INFO] Task started: fastANI
[2023-03-18 07:07:49,804] [INFO] Running command: fastANI --query /var/lib/cwl/stgfcee1bbc-18d9-4cf7-8b70-f2055b43ffdd/OceanDNA-b10073.fa --refList OceanDNA-b10073/target_genomes_gtdb.txt --output OceanDNA-b10073/fastani_result_gtdb.tsv --threads 1
[2023-03-18 07:08:02,345] [INFO] Task succeeded: fastANI
[2023-03-18 07:08:02,354] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 07:08:02,354] [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_001761365.1	s__Polaribacter vadi	97.2929	1034	1144	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_000687935.1	s__Polaribacter sp000687935	88.7627	911	1144	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	82.0805	727	1144	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001975665.1	s__Polaribacter reichenbachii	81.8771	745	1144	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	99.98	99.97	1.00	1.00	3	-
GCF_014352875.1	s__Polaribacter sp014352875	81.7923	671	1144	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	81.5239	721	1144	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	81.4233	681	1144	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000766795.1	s__Polaribacter sp000766795	81.0475	634	1144	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007997085.1	s__Polaribacter sp007997085	80.9975	703	1144	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	99.89	99.89	0.97	0.97	2	-
GCA_905480405.1	s__Polaribacter sp905480405	80.7609	582	1144	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	80.6745	605	1144	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	80.5726	588	1144	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	80.3785	661	1144	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	80.3782	612	1144	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017498485.1	s__Polaribacter sp017498485	80.3756	601	1144	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 07:08:02,354] [INFO] GTDB search result was written to OceanDNA-b10073/result_gtdb.tsv
[2023-03-18 07:08:02,354] [INFO] ===== GTDB Search completed =====
[2023-03-18 07:08:02,356] [INFO] DFAST_QC result json was written to OceanDNA-b10073/dqc_result.json
[2023-03-18 07:08:02,356] [INFO] DFAST_QC completed!
[2023-03-18 07:08:02,356] [INFO] Total running time: 0h1m40s