[2024-01-24 13:01:26,694] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:26,696] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:26,697] [INFO] DQC Reference Directory: /var/lib/cwl/stg6b3c6366-f766-4a08-945f-3e817c82227e/dqc_reference
[2024-01-24 13:01:28,045] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:28,046] [INFO] Task started: Prodigal
[2024-01-24 13:01:28,047] [INFO] Running command: gunzip -c /var/lib/cwl/stgaedca00e-5bf5-4960-84c5-cb723d50d67f/GCF_002954645.1_ASM295464v1_genomic.fna.gz | prodigal -d GCF_002954645.1_ASM295464v1_genomic.fna/cds.fna -a GCF_002954645.1_ASM295464v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:40,506] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:40,506] [INFO] Task started: HMMsearch
[2024-01-24 13:01:40,506] [INFO] Running command: hmmsearch --tblout GCF_002954645.1_ASM295464v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6b3c6366-f766-4a08-945f-3e817c82227e/dqc_reference/reference_markers.hmm GCF_002954645.1_ASM295464v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:40,795] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:40,797] [INFO] Found 6/6 markers.
[2024-01-24 13:01:40,824] [INFO] Query marker FASTA was written to GCF_002954645.1_ASM295464v1_genomic.fna/markers.fasta
[2024-01-24 13:01:40,824] [INFO] Task started: Blastn
[2024-01-24 13:01:40,825] [INFO] Running command: blastn -query GCF_002954645.1_ASM295464v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6b3c6366-f766-4a08-945f-3e817c82227e/dqc_reference/reference_markers.fasta -out GCF_002954645.1_ASM295464v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:41,540] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:41,544] [INFO] Selected 19 target genomes.
[2024-01-24 13:01:41,544] [INFO] Target genome list was writen to GCF_002954645.1_ASM295464v1_genomic.fna/target_genomes.txt
[2024-01-24 13:01:41,552] [INFO] Task started: fastANI
[2024-01-24 13:01:41,552] [INFO] Running command: fastANI --query /var/lib/cwl/stgaedca00e-5bf5-4960-84c5-cb723d50d67f/GCF_002954645.1_ASM295464v1_genomic.fna.gz --refList GCF_002954645.1_ASM295464v1_genomic.fna/target_genomes.txt --output GCF_002954645.1_ASM295464v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:01:55,155] [INFO] Task succeeded: fastANI
[2024-01-24 13:01:55,155] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6b3c6366-f766-4a08-945f-3e817c82227e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:01:55,155] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6b3c6366-f766-4a08-945f-3e817c82227e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:01:55,171] [INFO] Found 19 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:01:55,171] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:01:55,171] [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 gangjinensis	strain=KCTC 22729	GCA_002954645.1	574710	574710	type	True	99.999	970	980	95	conclusive
Polaribacter gangjinensis	strain=JCM 16152	GCA_020532765.1	574710	574710	type	True	99.9814	956	980	95	conclusive
Polaribacter vadi	strain=LPB0003	GCA_001761365.1	1774273	1774273	type	True	78.845	510	980	95	below_threshold
Polaribacter vadi	strain=LPB0003	GCA_001680885.1	1774273	1774273	type	True	78.8107	509	980	95	below_threshold
Polaribacter porphyrae	strain=LMG 26671	GCA_020532745.1	1137780	1137780	type	True	78.6439	440	980	95	below_threshold
Polaribacter aquimarinus	strain=ZY113	GCA_003129485.1	2100726	2100726	type	True	78.6365	415	980	95	below_threshold
Polaribacter porphyrae	strain=NBRC 108759	GCA_002954685.1	1137780	1137780	type	True	78.6	446	980	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	78.5984	456	980	95	below_threshold
Polaribacter haliotis	strain=RA4-7	GCA_002201315.1	1888915	1888915	type	True	78.5607	440	980	95	below_threshold
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	78.539	464	980	95	below_threshold
Polaribacter filamentus	strain=ATCC 700397	GCA_002943715.1	53483	53483	type	True	78.5244	437	980	95	below_threshold
Polaribacter aestuariivivens	strain=DBTF-3	GCA_005885675.1	2304626	2304626	type	True	78.4629	453	980	95	below_threshold
Polaribacter dokdonensis	strain=KCTC 12392	GCA_024362345.1	326329	326329	type	True	78.4302	411	980	95	below_threshold
Polaribacter glomeratus	strain=ATCC 43844	GCA_002954665.1	102	102	type	True	78.3487	483	980	95	below_threshold
Polaribacter glomeratus	strain=ACAM 171	GCA_007997115.1	102	102	type	True	78.3475	475	980	95	below_threshold
Polaribacter reichenbachii	strain=KCTC 23969	GCA_002814055.1	996801	996801	type	True	78.3399	462	980	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	78.3251	427	980	95	below_threshold
Polaribacter batillariae	strain=G4M1	GCA_017498485.1	2808900	2808900	type	True	78.1427	431	980	95	below_threshold
Polaribacter litorisediminis	strain=OITF-11	GCA_019968605.1	1908341	1908341	type	True	78.0952	450	980	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:01:55,173] [INFO] DFAST Taxonomy check result was written to GCF_002954645.1_ASM295464v1_genomic.fna/tc_result.tsv
[2024-01-24 13:01:55,174] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:01:55,174] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:01:55,174] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6b3c6366-f766-4a08-945f-3e817c82227e/dqc_reference/checkm_data
[2024-01-24 13:01:55,176] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:01:55,206] [INFO] Task started: CheckM
[2024-01-24 13:01:55,206] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002954645.1_ASM295464v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002954645.1_ASM295464v1_genomic.fna/checkm_input GCF_002954645.1_ASM295464v1_genomic.fna/checkm_result
[2024-01-24 13:02:33,474] [INFO] Task succeeded: CheckM
[2024-01-24 13:02:33,476] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:02:33,500] [INFO] ===== Completeness check finished =====
[2024-01-24 13:02:33,501] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:02:33,501] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002954645.1_ASM295464v1_genomic.fna/markers.fasta)
[2024-01-24 13:02:33,502] [INFO] Task started: Blastn
[2024-01-24 13:02:33,502] [INFO] Running command: blastn -query GCF_002954645.1_ASM295464v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6b3c6366-f766-4a08-945f-3e817c82227e/dqc_reference/reference_markers_gtdb.fasta -out GCF_002954645.1_ASM295464v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:34,394] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:34,398] [INFO] Selected 14 target genomes.
[2024-01-24 13:02:34,399] [INFO] Target genome list was writen to GCF_002954645.1_ASM295464v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:02:34,427] [INFO] Task started: fastANI
[2024-01-24 13:02:34,427] [INFO] Running command: fastANI --query /var/lib/cwl/stgaedca00e-5bf5-4960-84c5-cb723d50d67f/GCF_002954645.1_ASM295464v1_genomic.fna.gz --refList GCF_002954645.1_ASM295464v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002954645.1_ASM295464v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:02:43,864] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:43,876] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:02:43,877] [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_002954645.1	s__Polaribacter gangjinensis	99.999	970	980	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_015767435.1	s__Polaribacter sp015767435	85.0852	742	980	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001873065.1	s__Polaribacter sp001873065	83.0727	646	980	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	99.94	99.89	0.95	0.94	8	-
GCA_002340765.1	s__Polaribacter sp002340765	82.5532	479	980	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	99.32	98.94	0.76	0.72	3	-
GCF_001761365.1	s__Polaribacter vadi	78.8343	511	980	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	78.7894	509	980	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003129485.1	s__Polaribacter sp003129485	78.6196	416	980	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	78.6169	443	980	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002954685.1	s__Polaribacter porphyrae	78.607	445	980	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105145.1	s__Polaribacter sp900105145	78.5448	466	980	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	78.5426	463	980	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	78.4745	451	980	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003335085.1	s__Polaribacter sp003335085	78.0621	338	980	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	77.992	351	980	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 13:02:43,880] [INFO] GTDB search result was written to GCF_002954645.1_ASM295464v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:02:43,880] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:02:43,884] [INFO] DFAST_QC result json was written to GCF_002954645.1_ASM295464v1_genomic.fna/dqc_result.json
[2024-01-24 13:02:43,884] [INFO] DFAST_QC completed!
[2024-01-24 13:02:43,884] [INFO] Total running time: 0h1m17s