[2024-01-24 13:10:03,795] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:10:03,797] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:10:03,797] [INFO] DQC Reference Directory: /var/lib/cwl/stg52dc7306-b78c-4770-a780-649c03a0cf60/dqc_reference
[2024-01-24 13:10:05,169] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:10:05,170] [INFO] Task started: Prodigal
[2024-01-24 13:10:05,170] [INFO] Running command: gunzip -c /var/lib/cwl/stgf3fdcb45-1f2b-4237-bd93-b5e93fe4cd4e/GCF_004167665.1_ASM416766v1_genomic.fna.gz | prodigal -d GCF_004167665.1_ASM416766v1_genomic.fna/cds.fna -a GCF_004167665.1_ASM416766v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:10:33,080] [INFO] Task succeeded: Prodigal
[2024-01-24 13:10:33,080] [INFO] Task started: HMMsearch
[2024-01-24 13:10:33,080] [INFO] Running command: hmmsearch --tblout GCF_004167665.1_ASM416766v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg52dc7306-b78c-4770-a780-649c03a0cf60/dqc_reference/reference_markers.hmm GCF_004167665.1_ASM416766v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:10:33,433] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:10:33,435] [INFO] Found 6/6 markers.
[2024-01-24 13:10:33,482] [INFO] Query marker FASTA was written to GCF_004167665.1_ASM416766v1_genomic.fna/markers.fasta
[2024-01-24 13:10:33,482] [INFO] Task started: Blastn
[2024-01-24 13:10:33,482] [INFO] Running command: blastn -query GCF_004167665.1_ASM416766v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg52dc7306-b78c-4770-a780-649c03a0cf60/dqc_reference/reference_markers.fasta -out GCF_004167665.1_ASM416766v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:34,133] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:34,138] [INFO] Selected 12 target genomes.
[2024-01-24 13:10:34,138] [INFO] Target genome list was writen to GCF_004167665.1_ASM416766v1_genomic.fna/target_genomes.txt
[2024-01-24 13:10:34,145] [INFO] Task started: fastANI
[2024-01-24 13:10:34,145] [INFO] Running command: fastANI --query /var/lib/cwl/stgf3fdcb45-1f2b-4237-bd93-b5e93fe4cd4e/GCF_004167665.1_ASM416766v1_genomic.fna.gz --refList GCF_004167665.1_ASM416766v1_genomic.fna/target_genomes.txt --output GCF_004167665.1_ASM416766v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:10:48,746] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:48,747] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg52dc7306-b78c-4770-a780-649c03a0cf60/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:10:48,747] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg52dc7306-b78c-4770-a780-649c03a0cf60/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:10:48,764] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:10:48,764] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:10:48,764] [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
Hymenobacter persicinus	strain=1-3-3-3	GCA_004167665.1	2025506	2025506	type	True	100.0	1528	1538	95	conclusive
Hymenobacter daecheongensis	strain=DSM 21074	GCA_900141805.1	496053	496053	type	True	84.4374	1061	1538	95	below_threshold
Hymenobacter aquaticus	strain=JCM 31653	GCA_004765605.1	1867101	1867101	type	True	83.8219	1114	1538	95	below_threshold
Hymenobacter chitinivorans	strain=DSM 11115	GCA_002797555.1	89969	89969	type	True	83.3144	1108	1538	95	below_threshold
Hymenobacter metallicola	strain=9PBR-1	GCA_004745645.1	2563114	2563114	type	True	82.0963	1029	1538	95	below_threshold
Hymenobacter piscis	strain=NST-14	GCA_018760735.1	2839984	2839984	type	True	81.5316	919	1538	95	below_threshold
Hymenobacter elongatus	strain=JCM 17223	GCA_004745955.1	877208	877208	type	True	81.4324	903	1538	95	below_threshold
Hymenobacter guriensis	strain=BT594	GCA_015773195.1	2793065	2793065	type	True	81.1037	881	1538	95	below_threshold
Hymenobacter rigui	strain=KCTC 12533	GCA_003944715.1	334424	334424	type	True	80.5226	880	1538	95	below_threshold
Hymenobacter armeniacus	strain=BT189	GCA_014699055.1	2771358	2771358	type	True	79.9958	820	1538	95	below_threshold
Hymenobacter telluris	strain=BT186	GCA_017313265.1	2816474	2816474	type	True	79.967	843	1538	95	below_threshold
Hymenobacter roseosalivarius	strain=DSM 11622	GCA_900176135.1	89967	89967	type	True	78.9406	638	1538	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:10:48,765] [INFO] DFAST Taxonomy check result was written to GCF_004167665.1_ASM416766v1_genomic.fna/tc_result.tsv
[2024-01-24 13:10:48,766] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:10:48,766] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:10:48,766] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg52dc7306-b78c-4770-a780-649c03a0cf60/dqc_reference/checkm_data
[2024-01-24 13:10:48,767] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:10:48,818] [INFO] Task started: CheckM
[2024-01-24 13:10:48,818] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004167665.1_ASM416766v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004167665.1_ASM416766v1_genomic.fna/checkm_input GCF_004167665.1_ASM416766v1_genomic.fna/checkm_result
[2024-01-24 13:11:59,556] [INFO] Task succeeded: CheckM
[2024-01-24 13:11:59,558] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 13:11:59,583] [INFO] ===== Completeness check finished =====
[2024-01-24 13:11:59,583] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:11:59,584] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004167665.1_ASM416766v1_genomic.fna/markers.fasta)
[2024-01-24 13:11:59,584] [INFO] Task started: Blastn
[2024-01-24 13:11:59,584] [INFO] Running command: blastn -query GCF_004167665.1_ASM416766v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg52dc7306-b78c-4770-a780-649c03a0cf60/dqc_reference/reference_markers_gtdb.fasta -out GCF_004167665.1_ASM416766v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:12:00,454] [INFO] Task succeeded: Blastn
[2024-01-24 13:12:00,458] [INFO] Selected 10 target genomes.
[2024-01-24 13:12:00,459] [INFO] Target genome list was writen to GCF_004167665.1_ASM416766v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:12:00,508] [INFO] Task started: fastANI
[2024-01-24 13:12:00,508] [INFO] Running command: fastANI --query /var/lib/cwl/stgf3fdcb45-1f2b-4237-bd93-b5e93fe4cd4e/GCF_004167665.1_ASM416766v1_genomic.fna.gz --refList GCF_004167665.1_ASM416766v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004167665.1_ASM416766v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:12:11,828] [INFO] Task succeeded: fastANI
[2024-01-24 13:12:11,837] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:12:11,837] [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_004167665.1	s__Hymenobacter persicinus	100.0	1528	1538	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900141805.1	s__Hymenobacter daecheongensis	84.4374	1061	1538	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004765605.1	s__Hymenobacter aquaticus	83.8242	1114	1538	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002797555.1	s__Hymenobacter chitinivorans	83.3092	1109	1538	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004745645.1	s__Hymenobacter sp004745645	82.0723	1032	1538	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000737515.1	s__Hymenobacter sp000737515	81.8318	960	1538	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004745955.1	s__Hymenobacter elongatus	81.4383	902	1538	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015773195.1	s__Hymenobacter sp015773195	81.0996	881	1538	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003944715.1	s__Hymenobacter rigui	80.5182	881	1538	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176135.1	s__Hymenobacter roseosalivarius	78.9418	639	1538	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:12:11,839] [INFO] GTDB search result was written to GCF_004167665.1_ASM416766v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:12:11,839] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:12:11,843] [INFO] DFAST_QC result json was written to GCF_004167665.1_ASM416766v1_genomic.fna/dqc_result.json
[2024-01-24 13:12:11,844] [INFO] DFAST_QC completed!
[2024-01-24 13:12:11,844] [INFO] Total running time: 0h2m8s