[2024-01-24 14:05:00,694] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:00,696] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:00,696] [INFO] DQC Reference Directory: /var/lib/cwl/stg5d81c434-688a-4524-beeb-943a567477e9/dqc_reference
[2024-01-24 14:05:01,883] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:01,884] [INFO] Task started: Prodigal
[2024-01-24 14:05:01,884] [INFO] Running command: gunzip -c /var/lib/cwl/stgb8892865-abee-46aa-bc28-99e2a58c0579/GCF_005885675.1_ASM588567v1_genomic.fna.gz | prodigal -d GCF_005885675.1_ASM588567v1_genomic.fna/cds.fna -a GCF_005885675.1_ASM588567v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:05:11,024] [INFO] Task succeeded: Prodigal
[2024-01-24 14:05:11,024] [INFO] Task started: HMMsearch
[2024-01-24 14:05:11,025] [INFO] Running command: hmmsearch --tblout GCF_005885675.1_ASM588567v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5d81c434-688a-4524-beeb-943a567477e9/dqc_reference/reference_markers.hmm GCF_005885675.1_ASM588567v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:05:11,226] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:05:11,227] [INFO] Found 6/6 markers.
[2024-01-24 14:05:11,254] [INFO] Query marker FASTA was written to GCF_005885675.1_ASM588567v1_genomic.fna/markers.fasta
[2024-01-24 14:05:11,255] [INFO] Task started: Blastn
[2024-01-24 14:05:11,255] [INFO] Running command: blastn -query GCF_005885675.1_ASM588567v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5d81c434-688a-4524-beeb-943a567477e9/dqc_reference/reference_markers.fasta -out GCF_005885675.1_ASM588567v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:11,879] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:11,882] [INFO] Selected 10 target genomes.
[2024-01-24 14:05:11,883] [INFO] Target genome list was writen to GCF_005885675.1_ASM588567v1_genomic.fna/target_genomes.txt
[2024-01-24 14:05:11,911] [INFO] Task started: fastANI
[2024-01-24 14:05:11,911] [INFO] Running command: fastANI --query /var/lib/cwl/stgb8892865-abee-46aa-bc28-99e2a58c0579/GCF_005885675.1_ASM588567v1_genomic.fna.gz --refList GCF_005885675.1_ASM588567v1_genomic.fna/target_genomes.txt --output GCF_005885675.1_ASM588567v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:05:19,365] [INFO] Task succeeded: fastANI
[2024-01-24 14:05:19,365] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5d81c434-688a-4524-beeb-943a567477e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:05:19,366] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5d81c434-688a-4524-beeb-943a567477e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:05:19,375] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:05:19,376] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:05:19,376] [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 aestuariivivens	strain=DBTF-3	GCA_005885675.1	2304626	2304626	type	True	100.0	1053	1053	95	conclusive
Polaribacter haliotis	strain=KCTC 52418	GCA_014784055.1	1888915	1888915	type	True	84.3378	818	1053	95	below_threshold
Polaribacter batillariae	strain=G4M1	GCA_017498485.1	2808900	2808900	type	True	84.3074	763	1053	95	below_threshold
Polaribacter haliotis	strain=RA4-7	GCA_002201315.1	1888915	1888915	type	True	84.2293	819	1053	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	83.968	765	1053	95	below_threshold
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	83.0545	748	1053	95	below_threshold
Polaribacter vadi	strain=LPB0003	GCA_001680885.1	1774273	1774273	type	True	81.1005	659	1053	95	below_threshold
Polaribacter vadi	strain=LPB0003	GCA_001761365.1	1774273	1774273	type	True	81.0813	672	1053	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	80.1484	628	1053	95	below_threshold
Polaribacter dokdonensis	strain=KCTC 12392	GCA_024362345.1	326329	326329	type	True	80.0617	573	1053	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:05:19,377] [INFO] DFAST Taxonomy check result was written to GCF_005885675.1_ASM588567v1_genomic.fna/tc_result.tsv
[2024-01-24 14:05:19,378] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:05:19,378] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:05:19,378] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5d81c434-688a-4524-beeb-943a567477e9/dqc_reference/checkm_data
[2024-01-24 14:05:19,380] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:05:19,412] [INFO] Task started: CheckM
[2024-01-24 14:05:19,412] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005885675.1_ASM588567v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005885675.1_ASM588567v1_genomic.fna/checkm_input GCF_005885675.1_ASM588567v1_genomic.fna/checkm_result
[2024-01-24 14:05:51,714] [INFO] Task succeeded: CheckM
[2024-01-24 14:05:51,715] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:05:51,747] [INFO] ===== Completeness check finished =====
[2024-01-24 14:05:51,747] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:05:51,748] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005885675.1_ASM588567v1_genomic.fna/markers.fasta)
[2024-01-24 14:05:51,748] [INFO] Task started: Blastn
[2024-01-24 14:05:51,748] [INFO] Running command: blastn -query GCF_005885675.1_ASM588567v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5d81c434-688a-4524-beeb-943a567477e9/dqc_reference/reference_markers_gtdb.fasta -out GCF_005885675.1_ASM588567v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:52,691] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:52,695] [INFO] Selected 7 target genomes.
[2024-01-24 14:05:52,695] [INFO] Target genome list was writen to GCF_005885675.1_ASM588567v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:05:52,719] [INFO] Task started: fastANI
[2024-01-24 14:05:52,719] [INFO] Running command: fastANI --query /var/lib/cwl/stgb8892865-abee-46aa-bc28-99e2a58c0579/GCF_005885675.1_ASM588567v1_genomic.fna.gz --refList GCF_005885675.1_ASM588567v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005885675.1_ASM588567v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:05:58,762] [INFO] Task succeeded: fastANI
[2024-01-24 14:05:58,769] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:05:58,769] [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_005885675.1	s__Polaribacter aestuariivivens	100.0	1053	1053	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014784055.1	s__Polaribacter haliotis	84.3378	818	1053	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_017498485.1	s__Polaribacter sp017498485	84.3114	764	1053	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	83.9556	766	1053	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	83.0747	747	1053	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	81.0746	672	1053	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000687935.1	s__Polaribacter sp000687935	80.7655	692	1053	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:05:58,771] [INFO] GTDB search result was written to GCF_005885675.1_ASM588567v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:05:58,771] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:05:58,774] [INFO] DFAST_QC result json was written to GCF_005885675.1_ASM588567v1_genomic.fna/dqc_result.json
[2024-01-24 14:05:58,775] [INFO] DFAST_QC completed!
[2024-01-24 14:05:58,775] [INFO] Total running time: 0h0m58s