[2024-01-25 18:02:20,749] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:02:20,750] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:02:20,750] [INFO] DQC Reference Directory: /var/lib/cwl/stgf8ec3b70-3e46-45ba-885b-a95b5fb39589/dqc_reference
[2024-01-25 18:02:21,885] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:02:21,886] [INFO] Task started: Prodigal
[2024-01-25 18:02:21,886] [INFO] Running command: gunzip -c /var/lib/cwl/stg7be75721-a776-44f7-b3a2-d0c81211097c/GCF_014652335.1_ASM1465233v1_genomic.fna.gz | prodigal -d GCF_014652335.1_ASM1465233v1_genomic.fna/cds.fna -a GCF_014652335.1_ASM1465233v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:02:30,793] [INFO] Task succeeded: Prodigal
[2024-01-25 18:02:30,793] [INFO] Task started: HMMsearch
[2024-01-25 18:02:30,793] [INFO] Running command: hmmsearch --tblout GCF_014652335.1_ASM1465233v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf8ec3b70-3e46-45ba-885b-a95b5fb39589/dqc_reference/reference_markers.hmm GCF_014652335.1_ASM1465233v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:02:31,008] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:02:31,009] [INFO] Found 6/6 markers.
[2024-01-25 18:02:31,035] [INFO] Query marker FASTA was written to GCF_014652335.1_ASM1465233v1_genomic.fna/markers.fasta
[2024-01-25 18:02:31,035] [INFO] Task started: Blastn
[2024-01-25 18:02:31,036] [INFO] Running command: blastn -query GCF_014652335.1_ASM1465233v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf8ec3b70-3e46-45ba-885b-a95b5fb39589/dqc_reference/reference_markers.fasta -out GCF_014652335.1_ASM1465233v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:02:31,972] [INFO] Task succeeded: Blastn
[2024-01-25 18:02:31,975] [INFO] Selected 12 target genomes.
[2024-01-25 18:02:31,976] [INFO] Target genome list was writen to GCF_014652335.1_ASM1465233v1_genomic.fna/target_genomes.txt
[2024-01-25 18:02:31,987] [INFO] Task started: fastANI
[2024-01-25 18:02:31,988] [INFO] Running command: fastANI --query /var/lib/cwl/stg7be75721-a776-44f7-b3a2-d0c81211097c/GCF_014652335.1_ASM1465233v1_genomic.fna.gz --refList GCF_014652335.1_ASM1465233v1_genomic.fna/target_genomes.txt --output GCF_014652335.1_ASM1465233v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:02:43,009] [INFO] Task succeeded: fastANI
[2024-01-25 18:02:43,010] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf8ec3b70-3e46-45ba-885b-a95b5fb39589/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:02:43,010] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf8ec3b70-3e46-45ba-885b-a95b5fb39589/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:02:43,018] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:02:43,018] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:02:43,018] [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
Vogesella fluminis	strain=KCTC 23713	GCA_014652335.1	1069161	1069161	type	True	100.0	1039	1042	95	conclusive
Vogesella alkaliphila	strain=KCTC 32041	GCA_014652475.1	1193621	1193621	type	True	93.9375	860	1042	95	below_threshold
Vogesella indigofera	strain=DSM 3303	GCA_003633895.1	45465	45465	type	True	93.2004	863	1042	95	below_threshold
Vogesella urethralis	strain=YM-1	GCA_007644045.2	2592656	2592656	type	True	83.3162	689	1042	95	below_threshold
Vogesella mureinivorans	strain=389	GCA_007644035.2	657276	657276	type	True	82.0838	662	1042	95	below_threshold
Crenobacter luteus	strain=DSM 27258	GCA_004345725.1	1452487	1452487	type	True	81.2413	528	1042	95	below_threshold
Chromobacterium piscinae	strain=DSM 23278	GCA_021129175.1	686831	686831	type	True	81.0226	566	1042	95	below_threshold
Chromobacterium sinusclupearum	strain=MWU13-2610	GCA_002902845.1	2077146	2077146	type	True	80.9482	525	1042	95	below_threshold
Chromobacterium aquaticum	strain=DSM 19852	GCA_021129195.1	467180	467180	type	True	80.8983	554	1042	95	below_threshold
Chromobacterium alticapitis	strain=MWU14-2602	GCA_002924365.1	2073169	2073169	type	True	80.7521	522	1042	95	below_threshold
Crenobacter cavernae	strain=K1W11S-77	GCA_003355495.1	2290923	2290923	type	True	80.5367	519	1042	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	76.9565	291	1042	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:02:43,019] [INFO] DFAST Taxonomy check result was written to GCF_014652335.1_ASM1465233v1_genomic.fna/tc_result.tsv
[2024-01-25 18:02:43,020] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:02:43,020] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:02:43,020] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf8ec3b70-3e46-45ba-885b-a95b5fb39589/dqc_reference/checkm_data
[2024-01-25 18:02:43,021] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:02:43,056] [INFO] Task started: CheckM
[2024-01-25 18:02:43,056] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014652335.1_ASM1465233v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014652335.1_ASM1465233v1_genomic.fna/checkm_input GCF_014652335.1_ASM1465233v1_genomic.fna/checkm_result
[2024-01-25 18:03:11,576] [INFO] Task succeeded: CheckM
[2024-01-25 18:03:11,577] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:03:11,597] [INFO] ===== Completeness check finished =====
[2024-01-25 18:03:11,597] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:03:11,597] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014652335.1_ASM1465233v1_genomic.fna/markers.fasta)
[2024-01-25 18:03:11,597] [INFO] Task started: Blastn
[2024-01-25 18:03:11,597] [INFO] Running command: blastn -query GCF_014652335.1_ASM1465233v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf8ec3b70-3e46-45ba-885b-a95b5fb39589/dqc_reference/reference_markers_gtdb.fasta -out GCF_014652335.1_ASM1465233v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:03:13,468] [INFO] Task succeeded: Blastn
[2024-01-25 18:03:13,471] [INFO] Selected 10 target genomes.
[2024-01-25 18:03:13,471] [INFO] Target genome list was writen to GCF_014652335.1_ASM1465233v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:03:13,481] [INFO] Task started: fastANI
[2024-01-25 18:03:13,482] [INFO] Running command: fastANI --query /var/lib/cwl/stg7be75721-a776-44f7-b3a2-d0c81211097c/GCF_014652335.1_ASM1465233v1_genomic.fna.gz --refList GCF_014652335.1_ASM1465233v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014652335.1_ASM1465233v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:03:21,646] [INFO] Task succeeded: fastANI
[2024-01-25 18:03:21,653] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:03:21,653] [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_014652335.1	s__Vogesella fluminis	100.0	1039	1042	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Vogesella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014652475.1	s__Vogesella alkaliphila	93.9375	860	1042	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Vogesella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003633895.1	s__Vogesella indigofera	93.1874	864	1042	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Vogesella	95.0	97.25	97.21	0.95	0.93	3	-
GCF_900090205.1	s__Vogesella sp900090205	84.1948	716	1042	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Vogesella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902829295.1	s__Vogesella oryzae	83.5973	673	1042	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Vogesella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007644045.2	s__Vogesella urethralis	83.3086	690	1042	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Vogesella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000335715.1	s__Vogesella sp000335715	82.4643	639	1042	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Vogesella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017998615.1	s__Vogesella sp017998615	81.7944	465	1042	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Vogesella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016192025.1	s__Pseudogulbenkiania sp016192025	81.4682	460	1042	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Pseudogulbenkiania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003355495.1	s__Crenobacter cavernae	80.528	519	1042	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Crenobacter	95.0	96.17	96.17	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:03:21,654] [INFO] GTDB search result was written to GCF_014652335.1_ASM1465233v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:03:21,655] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:03:21,659] [INFO] DFAST_QC result json was written to GCF_014652335.1_ASM1465233v1_genomic.fna/dqc_result.json
[2024-01-25 18:03:21,659] [INFO] DFAST_QC completed!
[2024-01-25 18:03:21,659] [INFO] Total running time: 0h1m1s