[2024-01-25 17:53:50,537] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:53:50,540] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:53:50,540] [INFO] DQC Reference Directory: /var/lib/cwl/stgc3ca0879-f788-48ac-a45d-cd2e9ec4fa88/dqc_reference
[2024-01-25 17:53:51,708] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:53:51,709] [INFO] Task started: Prodigal
[2024-01-25 17:53:51,709] [INFO] Running command: gunzip -c /var/lib/cwl/stg1a45ed4b-4225-4891-a41b-740fc670d107/GCF_002201235.1_ASM220123v1_genomic.fna.gz | prodigal -d GCF_002201235.1_ASM220123v1_genomic.fna/cds.fna -a GCF_002201235.1_ASM220123v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:53:58,326] [INFO] Task succeeded: Prodigal
[2024-01-25 17:53:58,326] [INFO] Task started: HMMsearch
[2024-01-25 17:53:58,326] [INFO] Running command: hmmsearch --tblout GCF_002201235.1_ASM220123v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc3ca0879-f788-48ac-a45d-cd2e9ec4fa88/dqc_reference/reference_markers.hmm GCF_002201235.1_ASM220123v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:53:58,544] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:53:58,545] [INFO] Found 6/6 markers.
[2024-01-25 17:53:58,569] [INFO] Query marker FASTA was written to GCF_002201235.1_ASM220123v1_genomic.fna/markers.fasta
[2024-01-25 17:53:58,569] [INFO] Task started: Blastn
[2024-01-25 17:53:58,569] [INFO] Running command: blastn -query GCF_002201235.1_ASM220123v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc3ca0879-f788-48ac-a45d-cd2e9ec4fa88/dqc_reference/reference_markers.fasta -out GCF_002201235.1_ASM220123v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:53:59,158] [INFO] Task succeeded: Blastn
[2024-01-25 17:53:59,161] [INFO] Selected 13 target genomes.
[2024-01-25 17:53:59,161] [INFO] Target genome list was writen to GCF_002201235.1_ASM220123v1_genomic.fna/target_genomes.txt
[2024-01-25 17:53:59,167] [INFO] Task started: fastANI
[2024-01-25 17:53:59,167] [INFO] Running command: fastANI --query /var/lib/cwl/stg1a45ed4b-4225-4891-a41b-740fc670d107/GCF_002201235.1_ASM220123v1_genomic.fna.gz --refList GCF_002201235.1_ASM220123v1_genomic.fna/target_genomes.txt --output GCF_002201235.1_ASM220123v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:54:07,654] [INFO] Task succeeded: fastANI
[2024-01-25 17:54:07,654] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc3ca0879-f788-48ac-a45d-cd2e9ec4fa88/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:54:07,654] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc3ca0879-f788-48ac-a45d-cd2e9ec4fa88/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:54:07,663] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:54:07,663] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:54:07,663] [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 tangerinus	strain=WS2-14	GCA_002201235.1	1920034	1920034	type	True	100.0	883	883	95	conclusive
Polaribacter haliotis	strain=KCTC 52418	GCA_014784055.1	1888915	1888915	type	True	79.4591	471	883	95	below_threshold
Polaribacter haliotis	strain=RA4-7	GCA_002201315.1	1888915	1888915	type	True	79.4133	464	883	95	below_threshold
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	79.3787	462	883	95	below_threshold
Polaribacter aestuariivivens	strain=DBTF-3	GCA_005885675.1	2304626	2304626	type	True	79.3334	502	883	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	79.2391	459	883	95	below_threshold
Polaribacter batillariae	strain=G4M1	GCA_017498485.1	2808900	2808900	type	True	79.1947	447	883	95	below_threshold
Polaribacter butkevichii	strain=KCTC 12100	GCA_002954605.1	218490	218490	type	True	78.9954	440	883	95	below_threshold
Polaribacter undariae	strain=KCTC 42175	GCA_024918935.1	1574269	1574269	type	True	78.9525	427	883	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	78.8364	394	883	95	below_threshold
Polaribacter dokdonensis	strain=KCTC 12392	GCA_024362345.1	326329	326329	type	True	78.6844	380	883	95	below_threshold
Polaribacter dokdonensis	strain=DSW-5	GCA_001280865.1	326329	326329	type	True	78.6744	384	883	95	below_threshold
Polaribacter dokdonensis	strain=DSW-5	GCA_900106865.1	326329	326329	type	True	78.6527	381	883	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:54:07,664] [INFO] DFAST Taxonomy check result was written to GCF_002201235.1_ASM220123v1_genomic.fna/tc_result.tsv
[2024-01-25 17:54:07,667] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:54:07,667] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:54:07,667] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc3ca0879-f788-48ac-a45d-cd2e9ec4fa88/dqc_reference/checkm_data
[2024-01-25 17:54:07,668] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:54:07,695] [INFO] Task started: CheckM
[2024-01-25 17:54:07,695] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002201235.1_ASM220123v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002201235.1_ASM220123v1_genomic.fna/checkm_input GCF_002201235.1_ASM220123v1_genomic.fna/checkm_result
[2024-01-25 17:54:30,598] [INFO] Task succeeded: CheckM
[2024-01-25 17:54:30,599] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:54:30,620] [INFO] ===== Completeness check finished =====
[2024-01-25 17:54:30,620] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:54:30,620] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002201235.1_ASM220123v1_genomic.fna/markers.fasta)
[2024-01-25 17:54:30,620] [INFO] Task started: Blastn
[2024-01-25 17:54:30,620] [INFO] Running command: blastn -query GCF_002201235.1_ASM220123v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc3ca0879-f788-48ac-a45d-cd2e9ec4fa88/dqc_reference/reference_markers_gtdb.fasta -out GCF_002201235.1_ASM220123v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:54:31,468] [INFO] Task succeeded: Blastn
[2024-01-25 17:54:31,471] [INFO] Selected 18 target genomes.
[2024-01-25 17:54:31,471] [INFO] Target genome list was writen to GCF_002201235.1_ASM220123v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:54:31,493] [INFO] Task started: fastANI
[2024-01-25 17:54:31,493] [INFO] Running command: fastANI --query /var/lib/cwl/stg1a45ed4b-4225-4891-a41b-740fc670d107/GCF_002201235.1_ASM220123v1_genomic.fna.gz --refList GCF_002201235.1_ASM220123v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002201235.1_ASM220123v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:54:45,547] [INFO] Task succeeded: fastANI
[2024-01-25 17:54:45,558] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:54:45,558] [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_002201235.1	s__Polaribacter tangerinus	100.0	883	883	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_002005425.1	s__Polaribacter sp002005425	79.8498	479	883	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	96.81	96.81	0.92	0.92	2	-
GCF_002831685.1	s__Polaribacter sp002831685	79.4554	470	883	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	79.4486	472	883	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014352875.1	s__Polaribacter sp014352875	79.3662	464	883	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	79.343	501	883	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	79.2642	458	883	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	79.1943	446	883	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	79.0973	455	883	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	79.0001	441	883	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	78.9776	425	883	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	98.52	98.52	0.95	0.95	2	-
GCF_001761365.1	s__Polaribacter vadi	78.9183	435	883	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009796785.1	s__Polaribacter sp009796785	78.892	446	883	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002163675.1	s__Polaribacter sp002163675	78.853	430	883	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	78.8254	395	883	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	78.8244	444	883	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001280865.1	s__Polaribacter dokdonensis	78.6902	382	883	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_007827455.1	s__VISM01 sp007827455	77.8894	316	883	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__VISM01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:54:45,560] [INFO] GTDB search result was written to GCF_002201235.1_ASM220123v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:54:45,560] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:54:45,564] [INFO] DFAST_QC result json was written to GCF_002201235.1_ASM220123v1_genomic.fna/dqc_result.json
[2024-01-25 17:54:45,565] [INFO] DFAST_QC completed!
[2024-01-25 17:54:45,565] [INFO] Total running time: 0h0m55s