[2023-03-18 23:48:46,608] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:48:46,608] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:48:46,608] [INFO] DQC Reference Directory: /var/lib/cwl/stgd86931fa-94e2-4483-afae-33ad5488dcf5/dqc_reference
[2023-03-18 23:48:47,795] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:48:47,796] [INFO] Task started: Prodigal
[2023-03-18 23:48:47,796] [INFO] Running command: cat /var/lib/cwl/stgbac95804-ed4e-4a01-98fd-062b0f542331/OceanDNA-b9840.fa | prodigal -d OceanDNA-b9840/cds.fna -a OceanDNA-b9840/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:49:01,013] [INFO] Task succeeded: Prodigal
[2023-03-18 23:49:01,013] [INFO] Task started: HMMsearch
[2023-03-18 23:49:01,013] [INFO] Running command: hmmsearch --tblout OceanDNA-b9840/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd86931fa-94e2-4483-afae-33ad5488dcf5/dqc_reference/reference_markers.hmm OceanDNA-b9840/protein.faa > /dev/null
[2023-03-18 23:49:01,208] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:49:01,209] [INFO] Found 6/6 markers.
[2023-03-18 23:49:01,221] [INFO] Query marker FASTA was written to OceanDNA-b9840/markers.fasta
[2023-03-18 23:49:01,222] [INFO] Task started: Blastn
[2023-03-18 23:49:01,222] [INFO] Running command: blastn -query OceanDNA-b9840/markers.fasta -db /var/lib/cwl/stgd86931fa-94e2-4483-afae-33ad5488dcf5/dqc_reference/reference_markers.fasta -out OceanDNA-b9840/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:49:01,803] [INFO] Task succeeded: Blastn
[2023-03-18 23:49:01,804] [INFO] Selected 11 target genomes.
[2023-03-18 23:49:01,804] [INFO] Target genome list was writen to OceanDNA-b9840/target_genomes.txt
[2023-03-18 23:49:01,810] [INFO] Task started: fastANI
[2023-03-18 23:49:01,810] [INFO] Running command: fastANI --query /var/lib/cwl/stgbac95804-ed4e-4a01-98fd-062b0f542331/OceanDNA-b9840.fa --refList OceanDNA-b9840/target_genomes.txt --output OceanDNA-b9840/fastani_result.tsv --threads 1
[2023-03-18 23:49:08,929] [INFO] Task succeeded: fastANI
[2023-03-18 23:49:08,930] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd86931fa-94e2-4483-afae-33ad5488dcf5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:49:08,930] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd86931fa-94e2-4483-afae-33ad5488dcf5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:49:08,938] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 23:49:08,938] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 23:49:08,938] [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 pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	78.7726	366	649	95	below_threshold
Polaribacter sejongensis	strain=KCTC 23670	GCA_002814075.1	985043	985043	type	True	78.5269	305	649	95	below_threshold
Polaribacter undariae	strain=KCTC 42175	GCA_024918935.1	1574269	1574269	type	True	78.4651	310	649	95	below_threshold
Polaribacter butkevichii	strain=KCTC 12100	GCA_002954605.1	218490	218490	type	True	78.4288	321	649	95	below_threshold
Polaribacter haliotis	strain=RA4-7	GCA_002201315.1	1888915	1888915	type	True	78.427	351	649	95	below_threshold
Polaribacter atrinae	strain=KACC 17473	GCA_001640115.1	1333662	1333662	type	True	78.4069	308	649	95	below_threshold
Polaribacter haliotis	strain=KCTC 52418	GCA_014784055.1	1888915	1888915	type	True	78.343	360	649	95	below_threshold
Polaribacter vadi	strain=LPB0003	GCA_001761365.1	1774273	1774273	type	True	78.2329	325	649	95	below_threshold
Polaribacter batillariae	strain=G4M1	GCA_017498485.1	2808900	2808900	type	True	78.2273	328	649	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	78.2126	355	649	95	below_threshold
Tenacibaculum todarodis	strain=LPB0136	GCA_001889045.1	1850252	1850252	type	True	77.8079	263	649	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 23:49:08,938] [INFO] DFAST Taxonomy check result was written to OceanDNA-b9840/tc_result.tsv
[2023-03-18 23:49:08,938] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:49:08,939] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:49:08,939] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd86931fa-94e2-4483-afae-33ad5488dcf5/dqc_reference/checkm_data
[2023-03-18 23:49:08,939] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:49:08,943] [INFO] Task started: CheckM
[2023-03-18 23:49:08,943] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b9840/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b9840/checkm_input OceanDNA-b9840/checkm_result
[2023-03-18 23:49:45,318] [INFO] Task succeeded: CheckM
[2023-03-18 23:49:45,318] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 64.58%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 23:49:45,457] [INFO] ===== Completeness check finished =====
[2023-03-18 23:49:45,457] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:49:45,458] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b9840/markers.fasta)
[2023-03-18 23:49:45,459] [INFO] Task started: Blastn
[2023-03-18 23:49:45,459] [INFO] Running command: blastn -query OceanDNA-b9840/markers.fasta -db /var/lib/cwl/stgd86931fa-94e2-4483-afae-33ad5488dcf5/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b9840/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:49:46,247] [INFO] Task succeeded: Blastn
[2023-03-18 23:49:46,258] [INFO] Selected 19 target genomes.
[2023-03-18 23:49:46,258] [INFO] Target genome list was writen to OceanDNA-b9840/target_genomes_gtdb.txt
[2023-03-18 23:49:46,272] [INFO] Task started: fastANI
[2023-03-18 23:49:46,272] [INFO] Running command: fastANI --query /var/lib/cwl/stgbac95804-ed4e-4a01-98fd-062b0f542331/OceanDNA-b9840.fa --refList OceanDNA-b9840/target_genomes_gtdb.txt --output OceanDNA-b9840/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:49:57,492] [INFO] Task succeeded: fastANI
[2023-03-18 23:49:57,504] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 23:49:57,504] [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_018663625.1	s__Polaribacter sp018663625	88.3602	546	649	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	99.23	98.14	0.90	0.83	5	-
GCF_002163835.1	s__Polaribacter sp002163835	78.8115	360	649	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	78.7498	368	649	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	78.627	326	649	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002831685.1	s__Polaribacter sp002831685	78.5573	334	649	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	78.5472	335	649	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007997075.1	s__Polaribacter sp007997075	78.5409	329	649	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	78.5006	307	649	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	97.48	97.48	0.89	0.89	2	-
GCA_019263805.1	s__Polaribacter sp011379025	78.473	306	649	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	98.52	98.52	0.95	0.95	2	-
GCF_002954605.1	s__Polaribacter butkevichii	78.4285	321	649	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	78.4066	308	649	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	78.333	361	649	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_017569185.1	s__Polaribacter sp017569185	78.2271	353	649	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	78.2169	327	649	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	78.203	277	649	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	78.1753	340	649	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106075.1	s__Polaribacter sp900106075	77.9479	319	649	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	98.66	98.45	0.96	0.92	5	-
GCA_905480405.1	s__Polaribacter sp905480405	77.8457	310	649	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006383075.2	s__Kordia sp006383075	76.4027	63	649	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Kordia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 23:49:57,507] [INFO] GTDB search result was written to OceanDNA-b9840/result_gtdb.tsv
[2023-03-18 23:49:57,507] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:49:57,509] [INFO] DFAST_QC result json was written to OceanDNA-b9840/dqc_result.json
[2023-03-18 23:49:57,509] [INFO] DFAST_QC completed!
[2023-03-18 23:49:57,509] [INFO] Total running time: 0h1m11s