[2024-01-24 13:55:41,180] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:41,182] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:41,182] [INFO] DQC Reference Directory: /var/lib/cwl/stgeb9c2c2f-f7da-4496-9020-86bad3b0cb87/dqc_reference
[2024-01-24 13:55:42,551] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:42,552] [INFO] Task started: Prodigal
[2024-01-24 13:55:42,552] [INFO] Running command: gunzip -c /var/lib/cwl/stgfb541839-1d62-4384-b4ca-804b40ca21f0/GCF_014784055.1_ASM1478405v1_genomic.fna.gz | prodigal -d GCF_014784055.1_ASM1478405v1_genomic.fna/cds.fna -a GCF_014784055.1_ASM1478405v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:55:54,578] [INFO] Task succeeded: Prodigal
[2024-01-24 13:55:54,578] [INFO] Task started: HMMsearch
[2024-01-24 13:55:54,578] [INFO] Running command: hmmsearch --tblout GCF_014784055.1_ASM1478405v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeb9c2c2f-f7da-4496-9020-86bad3b0cb87/dqc_reference/reference_markers.hmm GCF_014784055.1_ASM1478405v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:55:54,864] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:55:54,865] [INFO] Found 6/6 markers.
[2024-01-24 13:55:54,898] [INFO] Query marker FASTA was written to GCF_014784055.1_ASM1478405v1_genomic.fna/markers.fasta
[2024-01-24 13:55:54,899] [INFO] Task started: Blastn
[2024-01-24 13:55:54,899] [INFO] Running command: blastn -query GCF_014784055.1_ASM1478405v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeb9c2c2f-f7da-4496-9020-86bad3b0cb87/dqc_reference/reference_markers.fasta -out GCF_014784055.1_ASM1478405v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:55:55,639] [INFO] Task succeeded: Blastn
[2024-01-24 13:55:55,643] [INFO] Selected 9 target genomes.
[2024-01-24 13:55:55,644] [INFO] Target genome list was writen to GCF_014784055.1_ASM1478405v1_genomic.fna/target_genomes.txt
[2024-01-24 13:55:55,651] [INFO] Task started: fastANI
[2024-01-24 13:55:55,651] [INFO] Running command: fastANI --query /var/lib/cwl/stgfb541839-1d62-4384-b4ca-804b40ca21f0/GCF_014784055.1_ASM1478405v1_genomic.fna.gz --refList GCF_014784055.1_ASM1478405v1_genomic.fna/target_genomes.txt --output GCF_014784055.1_ASM1478405v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:56:04,033] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:04,033] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeb9c2c2f-f7da-4496-9020-86bad3b0cb87/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:56:04,034] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeb9c2c2f-f7da-4496-9020-86bad3b0cb87/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:56:04,045] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:56:04,045] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:56:04,046] [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 haliotis	strain=KCTC 52418	GCA_014784055.1	1888915	1888915	type	True	100.0	1266	1266	95	conclusive
Polaribacter haliotis	strain=RA4-7	GCA_002201315.1	1888915	1888915	type	True	99.9782	1246	1266	95	conclusive
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	88.0179	832	1266	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	87.8478	913	1266	95	below_threshold
Polaribacter batillariae	strain=G4M1	GCA_017498485.1	2808900	2808900	type	True	85.6502	873	1266	95	below_threshold
Polaribacter aestuariivivens	strain=DBTF-3	GCA_005885675.1	2304626	2304626	type	True	84.2742	812	1266	95	below_threshold
Polaribacter butkevichii	strain=KCTC 12100	GCA_002954605.1	218490	218490	type	True	80.8562	674	1266	95	below_threshold
Polaribacter undariae	strain=KCTC 42175	GCA_024918935.1	1574269	1574269	type	True	80.7907	644	1266	95	below_threshold
Tenacibaculum todarodis	strain=LPB0136	GCA_001889045.1	1850252	1850252	type	True	79.9085	533	1266	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:56:04,047] [INFO] DFAST Taxonomy check result was written to GCF_014784055.1_ASM1478405v1_genomic.fna/tc_result.tsv
[2024-01-24 13:56:04,048] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:56:04,048] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:56:04,048] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeb9c2c2f-f7da-4496-9020-86bad3b0cb87/dqc_reference/checkm_data
[2024-01-24 13:56:04,050] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:56:04,088] [INFO] Task started: CheckM
[2024-01-24 13:56:04,089] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014784055.1_ASM1478405v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014784055.1_ASM1478405v1_genomic.fna/checkm_input GCF_014784055.1_ASM1478405v1_genomic.fna/checkm_result
[2024-01-24 13:56:39,884] [INFO] Task succeeded: CheckM
[2024-01-24 13:56:39,886] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:56:39,907] [INFO] ===== Completeness check finished =====
[2024-01-24 13:56:39,908] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:56:39,908] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014784055.1_ASM1478405v1_genomic.fna/markers.fasta)
[2024-01-24 13:56:39,909] [INFO] Task started: Blastn
[2024-01-24 13:56:39,909] [INFO] Running command: blastn -query GCF_014784055.1_ASM1478405v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeb9c2c2f-f7da-4496-9020-86bad3b0cb87/dqc_reference/reference_markers_gtdb.fasta -out GCF_014784055.1_ASM1478405v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:40,856] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:40,860] [INFO] Selected 11 target genomes.
[2024-01-24 13:56:40,861] [INFO] Target genome list was writen to GCF_014784055.1_ASM1478405v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:56:40,876] [INFO] Task started: fastANI
[2024-01-24 13:56:40,877] [INFO] Running command: fastANI --query /var/lib/cwl/stgfb541839-1d62-4384-b4ca-804b40ca21f0/GCF_014784055.1_ASM1478405v1_genomic.fna.gz --refList GCF_014784055.1_ASM1478405v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014784055.1_ASM1478405v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:56:50,798] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:50,816] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:56:50,816] [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_014784055.1	s__Polaribacter haliotis	100.0	1266	1266	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_014352875.1	s__Polaribacter sp014352875	87.9994	833	1266	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	87.8577	915	1266	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	85.6604	872	1266	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005885675.1	s__Polaribacter aestuariivivens	84.2719	812	1266	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	81.7028	687	1266	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	81.4202	733	1266	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_007997075.1	s__Polaribacter sp007997075	81.3284	722	1266	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	81.2239	656	1266	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000687935.1	s__Polaribacter sp000687935	81.181	705	1266	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	81.1604	687	1266	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 13:56:50,818] [INFO] GTDB search result was written to GCF_014784055.1_ASM1478405v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:56:50,819] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:56:50,823] [INFO] DFAST_QC result json was written to GCF_014784055.1_ASM1478405v1_genomic.fna/dqc_result.json
[2024-01-24 13:56:50,823] [INFO] DFAST_QC completed!
[2024-01-24 13:56:50,823] [INFO] Total running time: 0h1m10s