[2024-01-24 13:21:47,179] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:21:47,181] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:21:47,182] [INFO] DQC Reference Directory: /var/lib/cwl/stg3d789e4b-28fd-4f05-9182-e6a35cb7d4ef/dqc_reference
[2024-01-24 13:21:48,555] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:21:48,555] [INFO] Task started: Prodigal
[2024-01-24 13:21:48,556] [INFO] Running command: gunzip -c /var/lib/cwl/stgd773c05d-2902-452d-9765-7d933dbaf819/GCF_002814075.1_ASM281407v1_genomic.fna.gz | prodigal -d GCF_002814075.1_ASM281407v1_genomic.fna/cds.fna -a GCF_002814075.1_ASM281407v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:01,102] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:01,102] [INFO] Task started: HMMsearch
[2024-01-24 13:22:01,102] [INFO] Running command: hmmsearch --tblout GCF_002814075.1_ASM281407v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3d789e4b-28fd-4f05-9182-e6a35cb7d4ef/dqc_reference/reference_markers.hmm GCF_002814075.1_ASM281407v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:01,398] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:01,399] [INFO] Found 6/6 markers.
[2024-01-24 13:22:01,440] [INFO] Query marker FASTA was written to GCF_002814075.1_ASM281407v1_genomic.fna/markers.fasta
[2024-01-24 13:22:01,440] [INFO] Task started: Blastn
[2024-01-24 13:22:01,440] [INFO] Running command: blastn -query GCF_002814075.1_ASM281407v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3d789e4b-28fd-4f05-9182-e6a35cb7d4ef/dqc_reference/reference_markers.fasta -out GCF_002814075.1_ASM281407v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:02,117] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:02,120] [INFO] Selected 9 target genomes.
[2024-01-24 13:22:02,120] [INFO] Target genome list was writen to GCF_002814075.1_ASM281407v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:02,125] [INFO] Task started: fastANI
[2024-01-24 13:22:02,126] [INFO] Running command: fastANI --query /var/lib/cwl/stgd773c05d-2902-452d-9765-7d933dbaf819/GCF_002814075.1_ASM281407v1_genomic.fna.gz --refList GCF_002814075.1_ASM281407v1_genomic.fna/target_genomes.txt --output GCF_002814075.1_ASM281407v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:11,285] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:11,286] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3d789e4b-28fd-4f05-9182-e6a35cb7d4ef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:11,286] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3d789e4b-28fd-4f05-9182-e6a35cb7d4ef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:11,296] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:22:11,296] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:22:11,296] [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 sejongensis	strain=KCTC 23670	GCA_002814075.1	985043	985043	type	True	99.9806	1475	1508	95	inconclusive
Polaribacter undariae	strain=KCTC 42175	GCA_024918935.1	1574269	1574269	type	True	97.6471	1392	1508	95	inconclusive
Polaribacter atrinae	strain=KACC 17473	GCA_001640115.1	1333662	1333662	type	True	88.6335	1018	1508	95	below_threshold
Polaribacter butkevichii	strain=KCTC 12100	GCA_002954605.1	218490	218490	type	True	84.7533	929	1508	95	below_threshold
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	81.2592	689	1508	95	below_threshold
Polaribacter haliotis	strain=RA4-7	GCA_002201315.1	1888915	1888915	type	True	80.5974	667	1508	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	80.1859	610	1508	95	below_threshold
Tenacibaculum todarodis	strain=LPB0136	GCA_001889045.1	1850252	1850252	type	True	79.8194	528	1508	95	below_threshold
Polaribacter batillariae	strain=G4M1	GCA_017498485.1	2808900	2808900	type	True	79.5212	614	1508	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:11,299] [INFO] DFAST Taxonomy check result was written to GCF_002814075.1_ASM281407v1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:11,300] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:11,300] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:11,300] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3d789e4b-28fd-4f05-9182-e6a35cb7d4ef/dqc_reference/checkm_data
[2024-01-24 13:22:11,302] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:11,348] [INFO] Task started: CheckM
[2024-01-24 13:22:11,349] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002814075.1_ASM281407v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002814075.1_ASM281407v1_genomic.fna/checkm_input GCF_002814075.1_ASM281407v1_genomic.fna/checkm_result
[2024-01-24 13:22:53,211] [INFO] Task succeeded: CheckM
[2024-01-24 13:22:53,212] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:22:53,232] [INFO] ===== Completeness check finished =====
[2024-01-24 13:22:53,233] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:22:53,233] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002814075.1_ASM281407v1_genomic.fna/markers.fasta)
[2024-01-24 13:22:53,233] [INFO] Task started: Blastn
[2024-01-24 13:22:53,234] [INFO] Running command: blastn -query GCF_002814075.1_ASM281407v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3d789e4b-28fd-4f05-9182-e6a35cb7d4ef/dqc_reference/reference_markers_gtdb.fasta -out GCF_002814075.1_ASM281407v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:54,235] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:54,238] [INFO] Selected 6 target genomes.
[2024-01-24 13:22:54,238] [INFO] Target genome list was writen to GCF_002814075.1_ASM281407v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:22:54,245] [INFO] Task started: fastANI
[2024-01-24 13:22:54,246] [INFO] Running command: fastANI --query /var/lib/cwl/stgd773c05d-2902-452d-9765-7d933dbaf819/GCF_002814075.1_ASM281407v1_genomic.fna.gz --refList GCF_002814075.1_ASM281407v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002814075.1_ASM281407v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:23:01,405] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:01,411] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:23:01,411] [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_002814075.1	s__Polaribacter sejongensis	99.9806	1475	1508	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	97.48	97.48	0.89	0.89	2	conclusive
GCA_019263805.1	s__Polaribacter sp011379025	91.2794	1107	1508	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	88.6417	1016	1508	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	87.4571	1028	1508	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	85.1598	936	1508	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	84.7406	931	1508	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 13:23:01,413] [INFO] GTDB search result was written to GCF_002814075.1_ASM281407v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:23:01,413] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:23:01,416] [INFO] DFAST_QC result json was written to GCF_002814075.1_ASM281407v1_genomic.fna/dqc_result.json
[2024-01-24 13:23:01,416] [INFO] DFAST_QC completed!
[2024-01-24 13:23:01,416] [INFO] Total running time: 0h1m14s