[2023-06-13 21:08:21,192] [INFO] DFAST_QC pipeline started.
[2023-06-13 21:08:21,195] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 21:08:21,195] [INFO] DQC Reference Directory: /var/lib/cwl/stg43c87649-a242-4cf3-8a69-270bed91f228/dqc_reference
[2023-06-13 21:08:22,425] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 21:08:22,426] [INFO] Task started: Prodigal
[2023-06-13 21:08:22,426] [INFO] Running command: gunzip -c /var/lib/cwl/stg8cea3180-78c3-4d3e-b2ec-a8b5cd3c396b/GCA_022600955.1_ASM2260095v1_genomic.fna.gz | prodigal -d GCA_022600955.1_ASM2260095v1_genomic.fna/cds.fna -a GCA_022600955.1_ASM2260095v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 21:08:33,882] [INFO] Task succeeded: Prodigal
[2023-06-13 21:08:33,883] [INFO] Task started: HMMsearch
[2023-06-13 21:08:33,883] [INFO] Running command: hmmsearch --tblout GCA_022600955.1_ASM2260095v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg43c87649-a242-4cf3-8a69-270bed91f228/dqc_reference/reference_markers.hmm GCA_022600955.1_ASM2260095v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 21:08:34,137] [INFO] Task succeeded: HMMsearch
[2023-06-13 21:08:34,139] [INFO] Found 6/6 markers.
[2023-06-13 21:08:34,174] [INFO] Query marker FASTA was written to GCA_022600955.1_ASM2260095v1_genomic.fna/markers.fasta
[2023-06-13 21:08:34,174] [INFO] Task started: Blastn
[2023-06-13 21:08:34,174] [INFO] Running command: blastn -query GCA_022600955.1_ASM2260095v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg43c87649-a242-4cf3-8a69-270bed91f228/dqc_reference/reference_markers.fasta -out GCA_022600955.1_ASM2260095v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 21:08:34,847] [INFO] Task succeeded: Blastn
[2023-06-13 21:08:34,853] [INFO] Selected 29 target genomes.
[2023-06-13 21:08:34,853] [INFO] Target genome list was writen to GCA_022600955.1_ASM2260095v1_genomic.fna/target_genomes.txt
[2023-06-13 21:08:34,856] [INFO] Task started: fastANI
[2023-06-13 21:08:34,856] [INFO] Running command: fastANI --query /var/lib/cwl/stg8cea3180-78c3-4d3e-b2ec-a8b5cd3c396b/GCA_022600955.1_ASM2260095v1_genomic.fna.gz --refList GCA_022600955.1_ASM2260095v1_genomic.fna/target_genomes.txt --output GCA_022600955.1_ASM2260095v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 21:08:56,939] [INFO] Task succeeded: fastANI
[2023-06-13 21:08:56,940] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg43c87649-a242-4cf3-8a69-270bed91f228/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 21:08:56,940] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg43c87649-a242-4cf3-8a69-270bed91f228/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 21:08:56,944] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 21:08:56,944] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 21:08:56,944] [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
Woeseia oceani	strain=XK5	GCA_001677435.1	1548547	1548547	type	True	76.3141	79	1272	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 21:08:56,947] [INFO] DFAST Taxonomy check result was written to GCA_022600955.1_ASM2260095v1_genomic.fna/tc_result.tsv
[2023-06-13 21:08:56,947] [INFO] ===== Taxonomy check completed =====
[2023-06-13 21:08:56,947] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 21:08:56,948] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg43c87649-a242-4cf3-8a69-270bed91f228/dqc_reference/checkm_data
[2023-06-13 21:08:56,948] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 21:08:56,989] [INFO] Task started: CheckM
[2023-06-13 21:08:56,989] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022600955.1_ASM2260095v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022600955.1_ASM2260095v1_genomic.fna/checkm_input GCA_022600955.1_ASM2260095v1_genomic.fna/checkm_result
[2023-06-13 21:09:34,089] [INFO] Task succeeded: CheckM
[2023-06-13 21:09:34,090] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 21:09:34,115] [INFO] ===== Completeness check finished =====
[2023-06-13 21:09:34,116] [INFO] ===== Start GTDB Search =====
[2023-06-13 21:09:34,116] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022600955.1_ASM2260095v1_genomic.fna/markers.fasta)
[2023-06-13 21:09:34,116] [INFO] Task started: Blastn
[2023-06-13 21:09:34,117] [INFO] Running command: blastn -query GCA_022600955.1_ASM2260095v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg43c87649-a242-4cf3-8a69-270bed91f228/dqc_reference/reference_markers_gtdb.fasta -out GCA_022600955.1_ASM2260095v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 21:09:35,229] [INFO] Task succeeded: Blastn
[2023-06-13 21:09:35,233] [INFO] Selected 26 target genomes.
[2023-06-13 21:09:35,233] [INFO] Target genome list was writen to GCA_022600955.1_ASM2260095v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 21:09:35,239] [INFO] Task started: fastANI
[2023-06-13 21:09:35,239] [INFO] Running command: fastANI --query /var/lib/cwl/stg8cea3180-78c3-4d3e-b2ec-a8b5cd3c396b/GCA_022600955.1_ASM2260095v1_genomic.fna.gz --refList GCA_022600955.1_ASM2260095v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022600955.1_ASM2260095v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 21:09:48,530] [INFO] Task succeeded: fastANI
[2023-06-13 21:09:48,545] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 21:09:48,545] [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
GCA_009937445.1	s__UBA1847 sp009937445	78.0441	186	1272	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__UBA1847	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018699395.1	s__UBA1847 sp018699395	77.8651	64	1272	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__UBA1847	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013001045.1	s__UBA1847 sp013001045	76.8554	112	1272	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__UBA1847	95.0	99.51	99.51	0.75	0.75	2	-
GCA_004282875.1	s__UBA1847 sp004282875	76.7722	129	1272	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__UBA1847	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013043165.1	s__UBA1847 sp013043165	76.6537	163	1272	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__UBA1847	95.0	99.92	99.83	0.96	0.93	3	-
GCA_905480255.1	s__SZUA-117 sp905480255	76.4646	52	1272	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__SZUA-117	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009937605.1	s__UBA1847 sp009937605	76.46	119	1272	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__UBA1847	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001677435.1	s__Woeseia oceani	76.309	78	1272	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__Woeseia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009937525.1	s__JAACFE01 sp009937525	76.2952	81	1272	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__JAACFE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009937505.1	s__JAACFE01 sp009937505	76.2093	79	1272	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__JAACFE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009937615.1	s__JAACFB01 sp009937615	76.1269	87	1272	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__JAACFB01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 21:09:48,547] [INFO] GTDB search result was written to GCA_022600955.1_ASM2260095v1_genomic.fna/result_gtdb.tsv
[2023-06-13 21:09:48,548] [INFO] ===== GTDB Search completed =====
[2023-06-13 21:09:48,551] [INFO] DFAST_QC result json was written to GCA_022600955.1_ASM2260095v1_genomic.fna/dqc_result.json
[2023-06-13 21:09:48,551] [INFO] DFAST_QC completed!
[2023-06-13 21:09:48,552] [INFO] Total running time: 0h1m27s