[2024-01-24 10:47:06,546] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:06,551] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:06,551] [INFO] DQC Reference Directory: /var/lib/cwl/stge0fc9776-150e-410f-80d6-afb396f4a043/dqc_reference
[2024-01-24 10:47:12,100] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:12,102] [INFO] Task started: Prodigal
[2024-01-24 10:47:12,102] [INFO] Running command: gunzip -c /var/lib/cwl/stge694410d-a542-4cf7-9969-2686111230b4/GCF_017569185.1_ASM1756918v1_genomic.fna.gz | prodigal -d GCF_017569185.1_ASM1756918v1_genomic.fna/cds.fna -a GCF_017569185.1_ASM1756918v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:24,445] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:24,445] [INFO] Task started: HMMsearch
[2024-01-24 10:47:24,445] [INFO] Running command: hmmsearch --tblout GCF_017569185.1_ASM1756918v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge0fc9776-150e-410f-80d6-afb396f4a043/dqc_reference/reference_markers.hmm GCF_017569185.1_ASM1756918v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:24,703] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:24,705] [INFO] Found 6/6 markers.
[2024-01-24 10:47:24,754] [INFO] Query marker FASTA was written to GCF_017569185.1_ASM1756918v1_genomic.fna/markers.fasta
[2024-01-24 10:47:24,755] [INFO] Task started: Blastn
[2024-01-24 10:47:24,755] [INFO] Running command: blastn -query GCF_017569185.1_ASM1756918v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge0fc9776-150e-410f-80d6-afb396f4a043/dqc_reference/reference_markers.fasta -out GCF_017569185.1_ASM1756918v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:25,396] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:25,399] [INFO] Selected 8 target genomes.
[2024-01-24 10:47:25,399] [INFO] Target genome list was writen to GCF_017569185.1_ASM1756918v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:25,402] [INFO] Task started: fastANI
[2024-01-24 10:47:25,403] [INFO] Running command: fastANI --query /var/lib/cwl/stge694410d-a542-4cf7-9969-2686111230b4/GCF_017569185.1_ASM1756918v1_genomic.fna.gz --refList GCF_017569185.1_ASM1756918v1_genomic.fna/target_genomes.txt --output GCF_017569185.1_ASM1756918v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:33,451] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:33,451] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge0fc9776-150e-410f-80d6-afb396f4a043/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:33,452] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge0fc9776-150e-410f-80d6-afb396f4a043/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:33,459] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:47:33,459] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:47:33,459] [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 cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	100.0	1373	1381	95	conclusive
Polaribacter haliotis	strain=KCTC 52418	GCA_014784055.1	1888915	1888915	type	True	88.0775	874	1381	95	below_threshold
Polaribacter haliotis	strain=RA4-7	GCA_002201315.1	1888915	1888915	type	True	87.9304	880	1381	95	below_threshold
Polaribacter batillariae	strain=G4M1	GCA_017498485.1	2808900	2808900	type	True	86.0836	896	1381	95	below_threshold
Polaribacter aestuariivivens	strain=DBTF-3	GCA_005885675.1	2304626	2304626	type	True	83.9231	773	1381	95	below_threshold
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	83.7918	771	1381	95	below_threshold
Polaribacter undariae	strain=KCTC 42175	GCA_024918935.1	1574269	1574269	type	True	80.2757	606	1381	95	below_threshold
Polaribacter dokdonensis	strain=KCTC 12392	GCA_024362345.1	326329	326329	type	True	79.662	540	1381	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:33,461] [INFO] DFAST Taxonomy check result was written to GCF_017569185.1_ASM1756918v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:33,462] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:33,462] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:33,462] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge0fc9776-150e-410f-80d6-afb396f4a043/dqc_reference/checkm_data
[2024-01-24 10:47:33,463] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:33,501] [INFO] Task started: CheckM
[2024-01-24 10:47:33,501] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017569185.1_ASM1756918v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017569185.1_ASM1756918v1_genomic.fna/checkm_input GCF_017569185.1_ASM1756918v1_genomic.fna/checkm_result
[2024-01-24 10:48:12,609] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:12,610] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:12,625] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:12,625] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:12,626] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017569185.1_ASM1756918v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:12,626] [INFO] Task started: Blastn
[2024-01-24 10:48:12,626] [INFO] Running command: blastn -query GCF_017569185.1_ASM1756918v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge0fc9776-150e-410f-80d6-afb396f4a043/dqc_reference/reference_markers_gtdb.fasta -out GCF_017569185.1_ASM1756918v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:13,525] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:13,528] [INFO] Selected 8 target genomes.
[2024-01-24 10:48:13,528] [INFO] Target genome list was writen to GCF_017569185.1_ASM1756918v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:13,541] [INFO] Task started: fastANI
[2024-01-24 10:48:13,541] [INFO] Running command: fastANI --query /var/lib/cwl/stge694410d-a542-4cf7-9969-2686111230b4/GCF_017569185.1_ASM1756918v1_genomic.fna.gz --refList GCF_017569185.1_ASM1756918v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017569185.1_ASM1756918v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:21,704] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:21,711] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:48:21,712] [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_017569185.1	s__Polaribacter sp017569185	100.0	1374	1381	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_014784055.1	s__Polaribacter haliotis	88.0512	875	1381	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_017498485.1	s__Polaribacter sp017498485	86.1029	896	1381	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	83.948	772	1381	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	83.8187	771	1381	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	80.8555	676	1381	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002954605.1	s__Polaribacter butkevichii	80.3179	629	1381	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	80.2621	657	1381	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 10:48:21,713] [INFO] GTDB search result was written to GCF_017569185.1_ASM1756918v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:21,714] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:21,717] [INFO] DFAST_QC result json was written to GCF_017569185.1_ASM1756918v1_genomic.fna/dqc_result.json
[2024-01-24 10:48:21,717] [INFO] DFAST_QC completed!
[2024-01-24 10:48:21,717] [INFO] Total running time: 0h1m15s