[2023-03-18 01:13:56,406] [INFO] DFAST_QC pipeline started.
[2023-03-18 01:13:56,406] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 01:13:56,406] [INFO] DQC Reference Directory: /var/lib/cwl/stgd2fc5695-a72a-44f2-834b-9168e1f4ec9e/dqc_reference
[2023-03-18 01:13:57,502] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 01:13:57,503] [INFO] Task started: Prodigal
[2023-03-18 01:13:57,503] [INFO] Running command: cat /var/lib/cwl/stgb8d9c553-3401-429e-ba38-4f099ccff7bf/OceanDNA-b10029.fa | prodigal -d OceanDNA-b10029/cds.fna -a OceanDNA-b10029/protein.faa -g 11 -q > /dev/null
[2023-03-18 01:14:15,016] [INFO] Task succeeded: Prodigal
[2023-03-18 01:14:15,017] [INFO] Task started: HMMsearch
[2023-03-18 01:14:15,017] [INFO] Running command: hmmsearch --tblout OceanDNA-b10029/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd2fc5695-a72a-44f2-834b-9168e1f4ec9e/dqc_reference/reference_markers.hmm OceanDNA-b10029/protein.faa > /dev/null
[2023-03-18 01:14:15,220] [INFO] Task succeeded: HMMsearch
[2023-03-18 01:14:15,220] [INFO] Found 6/6 markers.
[2023-03-18 01:14:15,238] [INFO] Query marker FASTA was written to OceanDNA-b10029/markers.fasta
[2023-03-18 01:14:15,239] [INFO] Task started: Blastn
[2023-03-18 01:14:15,239] [INFO] Running command: blastn -query OceanDNA-b10029/markers.fasta -db /var/lib/cwl/stgd2fc5695-a72a-44f2-834b-9168e1f4ec9e/dqc_reference/reference_markers.fasta -out OceanDNA-b10029/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:14:15,894] [INFO] Task succeeded: Blastn
[2023-03-18 01:14:15,895] [INFO] Selected 19 target genomes.
[2023-03-18 01:14:15,895] [INFO] Target genome list was writen to OceanDNA-b10029/target_genomes.txt
[2023-03-18 01:14:15,909] [INFO] Task started: fastANI
[2023-03-18 01:14:15,909] [INFO] Running command: fastANI --query /var/lib/cwl/stgb8d9c553-3401-429e-ba38-4f099ccff7bf/OceanDNA-b10029.fa --refList OceanDNA-b10029/target_genomes.txt --output OceanDNA-b10029/fastani_result.tsv --threads 1
[2023-03-18 01:14:28,977] [INFO] Task succeeded: fastANI
[2023-03-18 01:14:28,977] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd2fc5695-a72a-44f2-834b-9168e1f4ec9e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 01:14:28,977] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd2fc5695-a72a-44f2-834b-9168e1f4ec9e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 01:14:28,988] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 01:14:28,989] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 01:14:28,989] [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 glomeratus	strain=ACAM 171	GCA_007997115.1	102	102	type	True	84.0216	726	968	95	below_threshold
Polaribacter glomeratus	strain=ATCC 43844	GCA_002954665.1	102	102	type	True	84.0054	729	968	95	below_threshold
Polaribacter filamentus	strain=ATCC 700397	GCA_002943715.1	53483	53483	type	True	83.9722	653	968	95	below_threshold
Polaribacter vadi	strain=LPB0003	GCA_001680885.1	1774273	1774273	type	True	81.3872	631	968	95	below_threshold
Polaribacter vadi	strain=LPB0003	GCA_001761365.1	1774273	1774273	type	True	81.36	635	968	95	below_threshold
Polaribacter butkevichii	strain=KCTC 12100	GCA_002954605.1	218490	218490	type	True	81.2082	594	968	95	below_threshold
Polaribacter undariae	strain=KCTC 42175	GCA_024918935.1	1574269	1574269	type	True	81.2036	593	968	95	below_threshold
Polaribacter atrinae	strain=KACC 17473	GCA_001640115.1	1333662	1333662	type	True	81.1803	577	968	95	below_threshold
Polaribacter reichenbachii	strain=KCTC 23969	GCA_002814055.1	996801	996801	type	True	81.0789	629	968	95	below_threshold
Polaribacter reichenbachii	strain=KCTC 23969	GCA_001680875.1	996801	996801	type	True	81.0617	630	968	95	below_threshold
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	80.9769	558	968	95	below_threshold
Polaribacter haliotis	strain=KCTC 52418	GCA_014784055.1	1888915	1888915	type	True	80.5851	540	968	95	below_threshold
Polaribacter haliotis	strain=RA4-7	GCA_002201315.1	1888915	1888915	type	True	80.5753	540	968	95	below_threshold
Polaribacter aestuariivivens	strain=DBTF-3	GCA_005885675.1	2304626	2304626	type	True	80.1629	514	968	95	below_threshold
Polaribacter litorisediminis	strain=OITF-11	GCA_019968605.1	1908341	1908341	type	True	80.0724	582	968	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	80.0593	501	968	95	below_threshold
Polaribacter dokdonensis	strain=KCTC 12392	GCA_024362345.1	326329	326329	type	True	79.8017	483	968	95	below_threshold
Polaribacter batillariae	strain=G4M1	GCA_017498485.1	2808900	2808900	type	True	79.7007	503	968	95	below_threshold
Tenacibaculum todarodis	strain=LPB0136	GCA_001889045.1	1850252	1850252	type	True	79.5225	410	968	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 01:14:28,989] [INFO] DFAST Taxonomy check result was written to OceanDNA-b10029/tc_result.tsv
[2023-03-18 01:14:28,989] [INFO] ===== Taxonomy check completed =====
[2023-03-18 01:14:28,989] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 01:14:28,989] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd2fc5695-a72a-44f2-834b-9168e1f4ec9e/dqc_reference/checkm_data
[2023-03-18 01:14:28,990] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 01:14:28,994] [INFO] Task started: CheckM
[2023-03-18 01:14:28,994] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b10029/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b10029/checkm_input OceanDNA-b10029/checkm_result
[2023-03-18 01:15:14,320] [INFO] Task succeeded: CheckM
[2023-03-18 01:15:14,320] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 01:15:14,322] [INFO] ===== Completeness check finished =====
[2023-03-18 01:15:14,323] [INFO] ===== Start GTDB Search =====
[2023-03-18 01:15:14,323] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b10029/markers.fasta)
[2023-03-18 01:15:14,323] [INFO] Task started: Blastn
[2023-03-18 01:15:14,323] [INFO] Running command: blastn -query OceanDNA-b10029/markers.fasta -db /var/lib/cwl/stgd2fc5695-a72a-44f2-834b-9168e1f4ec9e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b10029/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:15:15,225] [INFO] Task succeeded: Blastn
[2023-03-18 01:15:15,225] [INFO] Selected 15 target genomes.
[2023-03-18 01:15:15,226] [INFO] Target genome list was writen to OceanDNA-b10029/target_genomes_gtdb.txt
[2023-03-18 01:15:15,246] [INFO] Task started: fastANI
[2023-03-18 01:15:15,246] [INFO] Running command: fastANI --query /var/lib/cwl/stgb8d9c553-3401-429e-ba38-4f099ccff7bf/OceanDNA-b10029.fa --refList OceanDNA-b10029/target_genomes_gtdb.txt --output OceanDNA-b10029/fastani_result_gtdb.tsv --threads 1
[2023-03-18 01:15:26,497] [INFO] Task succeeded: fastANI
[2023-03-18 01:15:26,506] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 01:15:26,506] [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_900105145.1	s__Polaribacter sp900105145	86.3031	740	968	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002954665.1	s__Polaribacter glomeratus	83.9922	730	968	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	99.98	99.98	1.00	1.00	2	-
GCF_002943715.1	s__Polaribacter filamentus	83.9902	651	968	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	81.5389	612	968	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	81.3604	635	968	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	81.3592	591	968	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	81.2217	615	968	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	81.216	594	968	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	81.2099	613	968	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	81.1725	590	968	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	81.1529	544	968	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	81.1409	624	968	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	80.9461	560	968	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	80.5847	540	968	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	79.9041	524	968	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	96.81	96.81	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2023-03-18 01:15:26,506] [INFO] GTDB search result was written to OceanDNA-b10029/result_gtdb.tsv
[2023-03-18 01:15:26,506] [INFO] ===== GTDB Search completed =====
[2023-03-18 01:15:26,508] [INFO] DFAST_QC result json was written to OceanDNA-b10029/dqc_result.json
[2023-03-18 01:15:26,508] [INFO] DFAST_QC completed!
[2023-03-18 01:15:26,508] [INFO] Total running time: 0h1m30s