[2023-03-15 14:29:50,641] [INFO] DFAST_QC pipeline started.
[2023-03-15 14:29:50,641] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 14:29:50,641] [INFO] DQC Reference Directory: /var/lib/cwl/stg61009f1d-b3aa-44bc-b460-143483cdf61b/dqc_reference
[2023-03-15 14:29:51,824] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 14:29:51,824] [INFO] Task started: Prodigal
[2023-03-15 14:29:51,825] [INFO] Running command: cat /var/lib/cwl/stgc5c49480-25b7-4463-8ccf-bebc09f2f8e4/OceanDNA-b9861.fa | prodigal -d OceanDNA-b9861/cds.fna -a OceanDNA-b9861/protein.faa -g 11 -q > /dev/null
[2023-03-15 14:30:06,067] [INFO] Task succeeded: Prodigal
[2023-03-15 14:30:06,067] [INFO] Task started: HMMsearch
[2023-03-15 14:30:06,068] [INFO] Running command: hmmsearch --tblout OceanDNA-b9861/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg61009f1d-b3aa-44bc-b460-143483cdf61b/dqc_reference/reference_markers.hmm OceanDNA-b9861/protein.faa > /dev/null
[2023-03-15 14:30:06,245] [INFO] Task succeeded: HMMsearch
[2023-03-15 14:30:06,246] [INFO] Found 6/6 markers.
[2023-03-15 14:30:06,328] [INFO] Query marker FASTA was written to OceanDNA-b9861/markers.fasta
[2023-03-15 14:30:06,329] [INFO] Task started: Blastn
[2023-03-15 14:30:06,329] [INFO] Running command: blastn -query OceanDNA-b9861/markers.fasta -db /var/lib/cwl/stg61009f1d-b3aa-44bc-b460-143483cdf61b/dqc_reference/reference_markers.fasta -out OceanDNA-b9861/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 14:30:06,911] [INFO] Task succeeded: Blastn
[2023-03-15 14:30:06,920] [INFO] Selected 12 target genomes.
[2023-03-15 14:30:06,921] [INFO] Target genome list was writen to OceanDNA-b9861/target_genomes.txt
[2023-03-15 14:30:06,929] [INFO] Task started: fastANI
[2023-03-15 14:30:06,929] [INFO] Running command: fastANI --query /var/lib/cwl/stgc5c49480-25b7-4463-8ccf-bebc09f2f8e4/OceanDNA-b9861.fa --refList OceanDNA-b9861/target_genomes.txt --output OceanDNA-b9861/fastani_result.tsv --threads 1
[2023-03-15 14:30:14,556] [INFO] Task succeeded: fastANI
[2023-03-15 14:30:14,556] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg61009f1d-b3aa-44bc-b460-143483cdf61b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 14:30:14,557] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg61009f1d-b3aa-44bc-b460-143483cdf61b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 14:30:14,565] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 14:30:14,565] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 14:30:14,565] [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 pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	78.8173	330	687	95	below_threshold
Polaribacter undariae	strain=KCTC 42175	GCA_024918935.1	1574269	1574269	type	True	78.6287	274	687	95	below_threshold
Polaribacter haliotis	strain=KCTC 52418	GCA_014784055.1	1888915	1888915	type	True	78.5609	337	687	95	below_threshold
Polaribacter haliotis	strain=RA4-7	GCA_002201315.1	1888915	1888915	type	True	78.5361	334	687	95	below_threshold
Polaribacter sejongensis	strain=KCTC 23670	GCA_002814075.1	985043	985043	type	True	78.4268	287	687	95	below_threshold
Polaribacter atrinae	strain=KACC 17473	GCA_001640115.1	1333662	1333662	type	True	78.3814	293	687	95	below_threshold
Polaribacter butkevichii	strain=KCTC 12100	GCA_002954605.1	218490	218490	type	True	78.3584	305	687	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	78.2896	317	687	95	below_threshold
Polaribacter batillariae	strain=G4M1	GCA_017498485.1	2808900	2808900	type	True	78.224	318	687	95	below_threshold
Tenacibaculum aquimarinum	strain=K20-16	GCA_022478115.1	2910675	2910675	type	True	78.1578	232	687	95	below_threshold
Polaribacter vadi	strain=LPB0003	GCA_001761365.1	1774273	1774273	type	True	78.1321	312	687	95	below_threshold
Polaribacter dokdonensis	strain=DSW-5	GCA_900106865.1	326329	326329	type	True	77.6587	272	687	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 14:30:14,565] [INFO] DFAST Taxonomy check result was written to OceanDNA-b9861/tc_result.tsv
[2023-03-15 14:30:14,565] [INFO] ===== Taxonomy check completed =====
[2023-03-15 14:30:14,565] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 14:30:14,565] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg61009f1d-b3aa-44bc-b460-143483cdf61b/dqc_reference/checkm_data
[2023-03-15 14:30:14,566] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 14:30:14,588] [INFO] Task started: CheckM
[2023-03-15 14:30:14,588] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b9861/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b9861/checkm_input OceanDNA-b9861/checkm_result
[2023-03-15 14:30:55,783] [INFO] Task succeeded: CheckM
[2023-03-15 14:30:55,783] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 14:30:55,834] [INFO] ===== Completeness check finished =====
[2023-03-15 14:30:55,834] [INFO] ===== Start GTDB Search =====
[2023-03-15 14:30:55,835] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b9861/markers.fasta)
[2023-03-15 14:30:55,836] [INFO] Task started: Blastn
[2023-03-15 14:30:55,836] [INFO] Running command: blastn -query OceanDNA-b9861/markers.fasta -db /var/lib/cwl/stg61009f1d-b3aa-44bc-b460-143483cdf61b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b9861/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 14:30:56,646] [INFO] Task succeeded: Blastn
[2023-03-15 14:30:56,647] [INFO] Selected 18 target genomes.
[2023-03-15 14:30:56,647] [INFO] Target genome list was writen to OceanDNA-b9861/target_genomes_gtdb.txt
[2023-03-15 14:30:56,692] [INFO] Task started: fastANI
[2023-03-15 14:30:56,692] [INFO] Running command: fastANI --query /var/lib/cwl/stgc5c49480-25b7-4463-8ccf-bebc09f2f8e4/OceanDNA-b9861.fa --refList OceanDNA-b9861/target_genomes_gtdb.txt --output OceanDNA-b9861/fastani_result_gtdb.tsv --threads 1
[2023-03-15 14:31:07,588] [INFO] Task succeeded: fastANI
[2023-03-15 14:31:07,598] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 14:31:07,598] [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	91.2099	574	687	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	99.23	98.14	0.90	0.83	5	-
GCF_014352875.1	s__Polaribacter sp014352875	78.8173	330	687	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	78.7842	289	687	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	78.6048	310	687	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	78.5902	333	687	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016858305.2	s__Polaribacter sp016858305	78.5421	283	687	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	78.4688	353	687	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	78.4546	302	687	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	78.4448	313	687	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	78.4087	287	687	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	98.52	98.52	0.95	0.95	2	-
GCF_001640115.1	s__Polaribacter atrinae	78.3952	292	687	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	78.3886	301	687	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	78.3632	304	687	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017569185.1	s__Polaribacter sp017569185	78.2897	317	687	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	78.2167	318	687	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	78.0955	258	687	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007827455.1	s__VISM01 sp007827455	78.0582	267	687	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__VISM01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003335085.1	s__Polaribacter sp003335085	77.8484	237	687	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 14:31:07,599] [INFO] GTDB search result was written to OceanDNA-b9861/result_gtdb.tsv
[2023-03-15 14:31:07,599] [INFO] ===== GTDB Search completed =====
[2023-03-15 14:31:07,600] [INFO] DFAST_QC result json was written to OceanDNA-b9861/dqc_result.json
[2023-03-15 14:31:07,601] [INFO] DFAST_QC completed!
[2023-03-15 14:31:07,601] [INFO] Total running time: 0h1m17s