[2023-06-19 12:10:16,168] [INFO] DFAST_QC pipeline started.
[2023-06-19 12:10:16,170] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 12:10:16,171] [INFO] DQC Reference Directory: /var/lib/cwl/stg08bffdb7-0bf3-434b-96f3-dcec16382b73/dqc_reference
[2023-06-19 12:10:18,963] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 12:10:18,964] [INFO] Task started: Prodigal
[2023-06-19 12:10:18,964] [INFO] Running command: gunzip -c /var/lib/cwl/stg98fbce8c-48de-44be-9ba0-2cbe6e1a566d/GCA_018664625.1_ASM1866462v1_genomic.fna.gz | prodigal -d GCA_018664625.1_ASM1866462v1_genomic.fna/cds.fna -a GCA_018664625.1_ASM1866462v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 12:10:23,242] [INFO] Task succeeded: Prodigal
[2023-06-19 12:10:23,243] [INFO] Task started: HMMsearch
[2023-06-19 12:10:23,243] [INFO] Running command: hmmsearch --tblout GCA_018664625.1_ASM1866462v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg08bffdb7-0bf3-434b-96f3-dcec16382b73/dqc_reference/reference_markers.hmm GCA_018664625.1_ASM1866462v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 12:10:23,452] [INFO] Task succeeded: HMMsearch
[2023-06-19 12:10:23,454] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg98fbce8c-48de-44be-9ba0-2cbe6e1a566d/GCA_018664625.1_ASM1866462v1_genomic.fna.gz]
[2023-06-19 12:10:23,477] [INFO] Query marker FASTA was written to GCA_018664625.1_ASM1866462v1_genomic.fna/markers.fasta
[2023-06-19 12:10:23,477] [INFO] Task started: Blastn
[2023-06-19 12:10:23,478] [INFO] Running command: blastn -query GCA_018664625.1_ASM1866462v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg08bffdb7-0bf3-434b-96f3-dcec16382b73/dqc_reference/reference_markers.fasta -out GCA_018664625.1_ASM1866462v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 12:10:24,113] [INFO] Task succeeded: Blastn
[2023-06-19 12:10:24,117] [INFO] Selected 24 target genomes.
[2023-06-19 12:10:24,117] [INFO] Target genome list was writen to GCA_018664625.1_ASM1866462v1_genomic.fna/target_genomes.txt
[2023-06-19 12:10:24,121] [INFO] Task started: fastANI
[2023-06-19 12:10:24,121] [INFO] Running command: fastANI --query /var/lib/cwl/stg98fbce8c-48de-44be-9ba0-2cbe6e1a566d/GCA_018664625.1_ASM1866462v1_genomic.fna.gz --refList GCA_018664625.1_ASM1866462v1_genomic.fna/target_genomes.txt --output GCA_018664625.1_ASM1866462v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 12:10:36,603] [INFO] Task succeeded: fastANI
[2023-06-19 12:10:36,604] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg08bffdb7-0bf3-434b-96f3-dcec16382b73/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 12:10:36,604] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg08bffdb7-0bf3-434b-96f3-dcec16382b73/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 12:10:36,624] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 12:10:36,624] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 12:10:36,624] [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	79.577	174	282	95	below_threshold
Polaribacter undariae	strain=KCTC 42175	GCA_024918935.1	1574269	1574269	type	True	79.4639	175	282	95	below_threshold
Polaribacter butkevichii	strain=KCTC 12100	GCA_002954605.1	218490	218490	type	True	79.3449	183	282	95	below_threshold
Polaribacter atrinae	strain=KACC 17473	GCA_001640115.1	1333662	1333662	type	True	79.2738	184	282	95	below_threshold
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	79.113	177	282	95	below_threshold
Polaribacter reichenbachii	strain=KCTC 23969	GCA_002814055.1	996801	996801	type	True	78.8377	154	282	95	below_threshold
Polaribacter reichenbachii	strain=LMG 26443	GCA_020532845.1	996801	996801	type	True	78.7826	152	282	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	78.7288	159	282	95	below_threshold
Polaribacter reichenbachii	strain=KCTC 23969	GCA_001680875.1	996801	996801	type	True	78.725	155	282	95	below_threshold
Polaribacter filamentus	strain=ATCC 700397	GCA_002943715.1	53483	53483	type	True	78.5998	159	282	95	below_threshold
Polaribacter aquimarinus	strain=ZY113	GCA_003129485.1	2100726	2100726	type	True	78.5848	177	282	95	below_threshold
Polaribacter vadi	strain=LPB0003	GCA_001761365.1	1774273	1774273	type	True	78.5703	158	282	95	below_threshold
Polaribacter vadi	strain=LPB0003	GCA_001680885.1	1774273	1774273	type	True	78.5313	160	282	95	below_threshold
Polaribacter glomeratus	strain=ACAM 171	GCA_007997115.1	102	102	type	True	78.3653	160	282	95	below_threshold
Polaribacter batillariae	strain=G4M1	GCA_017498485.1	2808900	2808900	type	True	78.3518	150	282	95	below_threshold
Polaribacter glomeratus	strain=ATCC 43844	GCA_002954665.1	102	102	type	True	78.3445	162	282	95	below_threshold
Polaribacter dokdonensis	strain=DSW-5	GCA_900106865.1	326329	326329	type	True	78.341	142	282	95	below_threshold
Polaribacter dokdonensis	strain=DSW-5	GCA_001280865.1	326329	326329	type	True	78.3382	142	282	95	below_threshold
Polaribacter dokdonensis	strain=KCTC 12392	GCA_024362345.1	326329	326329	type	True	78.3324	141	282	95	below_threshold
Polaribacter litorisediminis	strain=OITF-11	GCA_019968605.1	1908341	1908341	type	True	78.2767	158	282	95	below_threshold
Polaribacter tangerinus	strain=WS2-14	GCA_002201235.1	1920034	1920034	type	True	78.2471	111	282	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	78.156	160	282	95	below_threshold
Tenacibaculum todarodis	strain=LPB0136	GCA_001889045.1	1850252	1850252	type	True	78.0517	124	282	95	below_threshold
Tenacibaculum haliotis	strain=KCTC 52419	GCA_025215075.1	1888914	1888914	type	True	77.3028	88	282	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 12:10:36,627] [INFO] DFAST Taxonomy check result was written to GCA_018664625.1_ASM1866462v1_genomic.fna/tc_result.tsv
[2023-06-19 12:10:36,627] [INFO] ===== Taxonomy check completed =====
[2023-06-19 12:10:36,628] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 12:10:36,628] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg08bffdb7-0bf3-434b-96f3-dcec16382b73/dqc_reference/checkm_data
[2023-06-19 12:10:36,629] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 12:10:36,646] [INFO] Task started: CheckM
[2023-06-19 12:10:36,646] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018664625.1_ASM1866462v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018664625.1_ASM1866462v1_genomic.fna/checkm_input GCA_018664625.1_ASM1866462v1_genomic.fna/checkm_result
[2023-06-19 12:10:56,752] [INFO] Task succeeded: CheckM
[2023-06-19 12:10:56,754] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 64.58%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 12:10:56,773] [INFO] ===== Completeness check finished =====
[2023-06-19 12:10:56,774] [INFO] ===== Start GTDB Search =====
[2023-06-19 12:10:56,774] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018664625.1_ASM1866462v1_genomic.fna/markers.fasta)
[2023-06-19 12:10:56,774] [INFO] Task started: Blastn
[2023-06-19 12:10:56,775] [INFO] Running command: blastn -query GCA_018664625.1_ASM1866462v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg08bffdb7-0bf3-434b-96f3-dcec16382b73/dqc_reference/reference_markers_gtdb.fasta -out GCA_018664625.1_ASM1866462v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 12:10:57,612] [INFO] Task succeeded: Blastn
[2023-06-19 12:10:57,621] [INFO] Selected 19 target genomes.
[2023-06-19 12:10:57,621] [INFO] Target genome list was writen to GCA_018664625.1_ASM1866462v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 12:10:57,630] [INFO] Task started: fastANI
[2023-06-19 12:10:57,630] [INFO] Running command: fastANI --query /var/lib/cwl/stg98fbce8c-48de-44be-9ba0-2cbe6e1a566d/GCA_018664625.1_ASM1866462v1_genomic.fna.gz --refList GCA_018664625.1_ASM1866462v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018664625.1_ASM1866462v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 12:11:07,864] [INFO] Task succeeded: fastANI
[2023-06-19 12:11:07,892] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 12:11:07,893] [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_018608545.1	s__Polaribacter sp018608545	97.4637	264	282	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	97.39	97.39	0.93	0.93	2	conclusive
GCF_000766795.1	s__Polaribacter sp000766795	79.8394	212	282	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	79.6624	178	282	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	98.52	98.52	0.95	0.95	2	-
GCF_002163675.1	s__Polaribacter sp002163675	79.6473	200	282	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002814075.1	s__Polaribacter sejongensis	79.577	174	282	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	97.48	97.48	0.89	0.89	2	-
GCF_002163835.1	s__Polaribacter sp002163835	79.3775	175	282	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	79.3449	183	282	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106075.1	s__Polaribacter sp900106075	79.306	180	282	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	98.66	98.45	0.96	0.92	5	-
GCF_001640115.1	s__Polaribacter atrinae	79.2738	184	282	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905181765.1	s__Polaribacter sp905181765	79.1163	133	282	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	96.49	96.49	0.69	0.69	2	-
GCF_014352875.1	s__Polaribacter sp014352875	79.113	177	282	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	78.8368	177	282	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	78.7974	159	282	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	78.7639	167	282	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	78.7294	156	282	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009832745.1	s__Polaribacter sp009832745	78.7288	159	282	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	78.5618	178	282	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007997085.1	s__Polaribacter sp007997085	78.349	140	282	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	99.89	99.89	0.97	0.97	2	-
GCF_000430545.1	s__Tenacibaculum ovolyticum	77.1999	95	282	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	97.63	97.63	0.88	0.88	2	-
--------------------------------------------------------------------------------
[2023-06-19 12:11:07,895] [INFO] GTDB search result was written to GCA_018664625.1_ASM1866462v1_genomic.fna/result_gtdb.tsv
[2023-06-19 12:11:07,895] [INFO] ===== GTDB Search completed =====
[2023-06-19 12:11:07,903] [INFO] DFAST_QC result json was written to GCA_018664625.1_ASM1866462v1_genomic.fna/dqc_result.json
[2023-06-19 12:11:07,903] [INFO] DFAST_QC completed!
[2023-06-19 12:11:07,903] [INFO] Total running time: 0h0m52s