[2024-01-24 14:14:05,871] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:05,873] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:05,873] [INFO] DQC Reference Directory: /var/lib/cwl/stg0c398332-3e84-4360-9ede-f39d2982c390/dqc_reference
[2024-01-24 14:14:07,317] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:07,318] [INFO] Task started: Prodigal
[2024-01-24 14:14:07,318] [INFO] Running command: gunzip -c /var/lib/cwl/stg448b5243-5ed1-4bdb-932a-685b9b174730/GCF_001654455.1_ASM165445v1_genomic.fna.gz | prodigal -d GCF_001654455.1_ASM165445v1_genomic.fna/cds.fna -a GCF_001654455.1_ASM165445v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:14:32,918] [INFO] Task succeeded: Prodigal
[2024-01-24 14:14:32,919] [INFO] Task started: HMMsearch
[2024-01-24 14:14:32,919] [INFO] Running command: hmmsearch --tblout GCF_001654455.1_ASM165445v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0c398332-3e84-4360-9ede-f39d2982c390/dqc_reference/reference_markers.hmm GCF_001654455.1_ASM165445v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:14:33,224] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:14:33,225] [INFO] Found 6/6 markers.
[2024-01-24 14:14:33,277] [INFO] Query marker FASTA was written to GCF_001654455.1_ASM165445v1_genomic.fna/markers.fasta
[2024-01-24 14:14:33,277] [INFO] Task started: Blastn
[2024-01-24 14:14:33,277] [INFO] Running command: blastn -query GCF_001654455.1_ASM165445v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0c398332-3e84-4360-9ede-f39d2982c390/dqc_reference/reference_markers.fasta -out GCF_001654455.1_ASM165445v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:33,865] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:33,867] [INFO] Selected 14 target genomes.
[2024-01-24 14:14:33,867] [INFO] Target genome list was writen to GCF_001654455.1_ASM165445v1_genomic.fna/target_genomes.txt
[2024-01-24 14:14:33,888] [INFO] Task started: fastANI
[2024-01-24 14:14:33,888] [INFO] Running command: fastANI --query /var/lib/cwl/stg448b5243-5ed1-4bdb-932a-685b9b174730/GCF_001654455.1_ASM165445v1_genomic.fna.gz --refList GCF_001654455.1_ASM165445v1_genomic.fna/target_genomes.txt --output GCF_001654455.1_ASM165445v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:14:47,827] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:47,828] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0c398332-3e84-4360-9ede-f39d2982c390/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:14:47,829] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0c398332-3e84-4360-9ede-f39d2982c390/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:14:47,843] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:14:47,844] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:14:47,844] [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
Niabella ginsenosidivorans	strain=BS26	GCA_001654455.1	1176587	1176587	type	True	100.0	1874	1875	95	conclusive
Niabella beijingensis	strain=3A5MI-3	GCA_020034665.1	2872700	2872700	type	True	78.2235	516	1875	95	below_threshold
Niabella soli	strain=JS13-8; DSM 19437	GCA_000243115.3	446683	446683	type	True	78.2009	540	1875	95	below_threshold
Niabella drilacis	strain=DSM 25811	GCA_900101395.1	1285928	1285928	type	True	77.9613	475	1875	95	below_threshold
Niabella aurantiaca	strain=DSM 17617	GCA_000374125.1	379900	379900	type	True	77.9457	503	1875	95	below_threshold
Niabella pedocola	strain=JCM 31011	GCA_021044425.1	1752077	1752077	type	True	77.8355	484	1875	95	below_threshold
Flavihumibacter stibioxidans	strain=YS-17	GCA_014332695.1	1834163	1834163	type	True	76.8862	63	1875	95	below_threshold
Flavihumibacter cheonanensis	strain=WS16	GCA_022352215.1	1442385	1442385	type	True	75.9106	55	1875	95	below_threshold
Pseudobacter ginsenosidimutans	strain=Gsoil 221	GCA_007970185.1	661488	661488	type	True	75.7283	70	1875	95	below_threshold
Chitinophaga ginsengisegetis	strain=DSM 18108	GCA_900168065.1	393003	393003	type	True	75.383	58	1875	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:14:47,846] [INFO] DFAST Taxonomy check result was written to GCF_001654455.1_ASM165445v1_genomic.fna/tc_result.tsv
[2024-01-24 14:14:47,846] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:14:47,846] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:14:47,847] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0c398332-3e84-4360-9ede-f39d2982c390/dqc_reference/checkm_data
[2024-01-24 14:14:47,848] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:14:47,904] [INFO] Task started: CheckM
[2024-01-24 14:14:47,904] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001654455.1_ASM165445v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001654455.1_ASM165445v1_genomic.fna/checkm_input GCF_001654455.1_ASM165445v1_genomic.fna/checkm_result
[2024-01-24 14:16:01,295] [INFO] Task succeeded: CheckM
[2024-01-24 14:16:01,296] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:16:01,311] [INFO] ===== Completeness check finished =====
[2024-01-24 14:16:01,311] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:16:01,312] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001654455.1_ASM165445v1_genomic.fna/markers.fasta)
[2024-01-24 14:16:01,312] [INFO] Task started: Blastn
[2024-01-24 14:16:01,312] [INFO] Running command: blastn -query GCF_001654455.1_ASM165445v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0c398332-3e84-4360-9ede-f39d2982c390/dqc_reference/reference_markers_gtdb.fasta -out GCF_001654455.1_ASM165445v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:16:02,162] [INFO] Task succeeded: Blastn
[2024-01-24 14:16:02,167] [INFO] Selected 14 target genomes.
[2024-01-24 14:16:02,167] [INFO] Target genome list was writen to GCF_001654455.1_ASM165445v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:16:02,196] [INFO] Task started: fastANI
[2024-01-24 14:16:02,197] [INFO] Running command: fastANI --query /var/lib/cwl/stg448b5243-5ed1-4bdb-932a-685b9b174730/GCF_001654455.1_ASM165445v1_genomic.fna.gz --refList GCF_001654455.1_ASM165445v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001654455.1_ASM165445v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:16:17,211] [INFO] Task succeeded: fastANI
[2024-01-24 14:16:17,234] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:16:17,234] [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_001654455.1	s__Niabella ginsenosidivorans	100.0	1875	1875	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niabella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000243115.2	s__Niabella soli	78.2237	541	1875	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niabella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101395.1	s__Niabella drilacis	77.9629	474	1875	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niabella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744715.1	s__Niabella sp017744715	77.9453	501	1875	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niabella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374125.1	s__Niabella aurantiaca	77.8969	504	1875	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niabella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744795.1	s__Niabella sp017744795	77.8319	460	1875	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niabella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016708305.1	s__Niabella sp016708305	76.6395	69	1875	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niabella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003349965.1	s__Niabella yanshanensis	76.4706	149	1875	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niabella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826165.1	s__JJ008 sp902826165	76.2886	78	1875	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001899685.1	s__Agriterribacter sp001899685	76.0267	93	1875	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Agriterribacter	95.0	99.97	99.97	0.97	0.97	2	-
GCA_003243445.1	s__46-32 sp003243445	75.8485	69	1875	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__46-32	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004341975.1	s__Niastella sp004341975	75.5868	83	1875	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niastella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:16:17,236] [INFO] GTDB search result was written to GCF_001654455.1_ASM165445v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:16:17,237] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:16:17,240] [INFO] DFAST_QC result json was written to GCF_001654455.1_ASM165445v1_genomic.fna/dqc_result.json
[2024-01-24 14:16:17,240] [INFO] DFAST_QC completed!
[2024-01-24 14:16:17,240] [INFO] Total running time: 0h2m11s