[2023-03-19 00:48:24,533] [INFO] DFAST_QC pipeline started.
[2023-03-19 00:48:24,534] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 00:48:24,534] [INFO] DQC Reference Directory: /var/lib/cwl/stg69aeb8dd-f4ce-4965-9ab1-6d9af757288e/dqc_reference
[2023-03-19 00:48:26,000] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 00:48:26,001] [INFO] Task started: Prodigal
[2023-03-19 00:48:26,001] [INFO] Running command: cat /var/lib/cwl/stgd8cc6b10-0834-49a5-b032-a1246602b66d/OceanDNA-b10067.fa | prodigal -d OceanDNA-b10067/cds.fna -a OceanDNA-b10067/protein.faa -g 11 -q > /dev/null
[2023-03-19 00:48:42,468] [INFO] Task succeeded: Prodigal
[2023-03-19 00:48:42,468] [INFO] Task started: HMMsearch
[2023-03-19 00:48:42,468] [INFO] Running command: hmmsearch --tblout OceanDNA-b10067/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg69aeb8dd-f4ce-4965-9ab1-6d9af757288e/dqc_reference/reference_markers.hmm OceanDNA-b10067/protein.faa > /dev/null
[2023-03-19 00:48:42,658] [INFO] Task succeeded: HMMsearch
[2023-03-19 00:48:42,659] [INFO] Found 6/6 markers.
[2023-03-19 00:48:42,676] [INFO] Query marker FASTA was written to OceanDNA-b10067/markers.fasta
[2023-03-19 00:48:42,677] [INFO] Task started: Blastn
[2023-03-19 00:48:42,677] [INFO] Running command: blastn -query OceanDNA-b10067/markers.fasta -db /var/lib/cwl/stg69aeb8dd-f4ce-4965-9ab1-6d9af757288e/dqc_reference/reference_markers.fasta -out OceanDNA-b10067/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:48:43,273] [INFO] Task succeeded: Blastn
[2023-03-19 00:48:43,274] [INFO] Selected 18 target genomes.
[2023-03-19 00:48:43,275] [INFO] Target genome list was writen to OceanDNA-b10067/target_genomes.txt
[2023-03-19 00:48:43,286] [INFO] Task started: fastANI
[2023-03-19 00:48:43,286] [INFO] Running command: fastANI --query /var/lib/cwl/stgd8cc6b10-0834-49a5-b032-a1246602b66d/OceanDNA-b10067.fa --refList OceanDNA-b10067/target_genomes.txt --output OceanDNA-b10067/fastani_result.tsv --threads 1
[2023-03-19 00:48:55,168] [INFO] Task succeeded: fastANI
[2023-03-19 00:48:55,168] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg69aeb8dd-f4ce-4965-9ab1-6d9af757288e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 00:48:55,169] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg69aeb8dd-f4ce-4965-9ab1-6d9af757288e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 00:48:55,180] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 00:48:55,180] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 00:48:55,180] [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 filamentus	strain=ATCC 700397	GCA_002943715.1	53483	53483	type	True	80.7741	596	898	95	below_threshold
Polaribacter glomeratus	strain=ACAM 171	GCA_007997115.1	102	102	type	True	80.7551	620	898	95	below_threshold
Polaribacter glomeratus	strain=ATCC 43844	GCA_002954665.1	102	102	type	True	80.7072	619	898	95	below_threshold
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	80.5409	560	898	95	below_threshold
Polaribacter vadi	strain=LPB0003	GCA_001680885.1	1774273	1774273	type	True	80.4841	585	898	95	below_threshold
Polaribacter vadi	strain=LPB0003	GCA_001761365.1	1774273	1774273	type	True	80.4458	585	898	95	below_threshold
Polaribacter butkevichii	strain=KCTC 12100	GCA_002954605.1	218490	218490	type	True	80.3751	530	898	95	below_threshold
Polaribacter atrinae	strain=KACC 17473	GCA_001640115.1	1333662	1333662	type	True	80.1887	508	898	95	below_threshold
Polaribacter haliotis	strain=KCTC 52418	GCA_014784055.1	1888915	1888915	type	True	80.1857	525	898	95	below_threshold
Polaribacter haliotis	strain=RA4-7	GCA_002201315.1	1888915	1888915	type	True	80.1541	536	898	95	below_threshold
Polaribacter undariae	strain=KCTC 42175	GCA_024918935.1	1574269	1574269	type	True	80.1458	524	898	95	below_threshold
Polaribacter sejongensis	strain=KCTC 23670	GCA_002814075.1	985043	985043	type	True	80.0334	521	898	95	below_threshold
Polaribacter litorisediminis	strain=OITF-11	GCA_019968605.1	1908341	1908341	type	True	79.8354	556	898	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	79.5503	503	898	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	79.5121	465	898	95	below_threshold
Polaribacter porphyrae	strain=LMG 26671	GCA_020532745.1	1137780	1137780	type	True	79.3743	516	898	95	below_threshold
Tenacibaculum aquimarinum	strain=K20-16	GCA_022478115.1	2910675	2910675	type	True	79.0724	405	898	95	below_threshold
Tenacibaculum todarodis	strain=LPB0136	GCA_001889045.1	1850252	1850252	type	True	78.9111	389	898	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 00:48:55,180] [INFO] DFAST Taxonomy check result was written to OceanDNA-b10067/tc_result.tsv
[2023-03-19 00:48:55,181] [INFO] ===== Taxonomy check completed =====
[2023-03-19 00:48:55,181] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 00:48:55,181] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg69aeb8dd-f4ce-4965-9ab1-6d9af757288e/dqc_reference/checkm_data
[2023-03-19 00:48:55,182] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 00:48:55,194] [INFO] Task started: CheckM
[2023-03-19 00:48:55,194] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b10067/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b10067/checkm_input OceanDNA-b10067/checkm_result
[2023-03-19 00:49:38,261] [INFO] Task succeeded: CheckM
[2023-03-19 00:49:38,261] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 00:49:38,420] [INFO] ===== Completeness check finished =====
[2023-03-19 00:49:38,421] [INFO] ===== Start GTDB Search =====
[2023-03-19 00:49:38,421] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b10067/markers.fasta)
[2023-03-19 00:49:38,422] [INFO] Task started: Blastn
[2023-03-19 00:49:38,422] [INFO] Running command: blastn -query OceanDNA-b10067/markers.fasta -db /var/lib/cwl/stg69aeb8dd-f4ce-4965-9ab1-6d9af757288e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b10067/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:49:39,268] [INFO] Task succeeded: Blastn
[2023-03-19 00:49:39,270] [INFO] Selected 14 target genomes.
[2023-03-19 00:49:39,270] [INFO] Target genome list was writen to OceanDNA-b10067/target_genomes_gtdb.txt
[2023-03-19 00:49:39,284] [INFO] Task started: fastANI
[2023-03-19 00:49:39,284] [INFO] Running command: fastANI --query /var/lib/cwl/stgd8cc6b10-0834-49a5-b032-a1246602b66d/OceanDNA-b10067.fa --refList OceanDNA-b10067/target_genomes_gtdb.txt --output OceanDNA-b10067/fastani_result_gtdb.tsv --threads 1
[2023-03-19 00:49:50,419] [INFO] Task succeeded: fastANI
[2023-03-19 00:49:50,427] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 00:49:50,428] [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_900106075.1	s__Polaribacter sp900106075	98.7873	862	898	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	98.66	98.45	0.96	0.92	5	conclusive
GCA_000981625.1	s__Polaribacter sp000981625	83.7972	550	898	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	81.2631	613	898	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	81.0978	606	898	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	80.7044	619	898	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	99.98	99.98	1.00	1.00	2	-
GCA_905480405.1	s__Polaribacter sp905480405	80.6979	570	898	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	80.4793	530	898	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	80.4458	585	898	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002954605.1	s__Polaribacter butkevichii	80.3742	530	898	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	80.1936	523	898	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001640115.1	s__Polaribacter atrinae	80.173	509	898	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	80.0372	516	898	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	80.0254	531	898	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	98.52	98.52	0.95	0.95	2	-
GCF_007997075.1	s__Polaribacter sp007997075	79.9591	518	898	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 00:49:50,430] [INFO] GTDB search result was written to OceanDNA-b10067/result_gtdb.tsv
[2023-03-19 00:49:50,431] [INFO] ===== GTDB Search completed =====
[2023-03-19 00:49:50,433] [INFO] DFAST_QC result json was written to OceanDNA-b10067/dqc_result.json
[2023-03-19 00:49:50,434] [INFO] DFAST_QC completed!
[2023-03-19 00:49:50,434] [INFO] Total running time: 0h1m26s