[2023-06-30 07:45:05,686] [INFO] DFAST_QC pipeline started.
[2023-06-30 07:45:05,688] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 07:45:05,689] [INFO] DQC Reference Directory: /var/lib/cwl/stgdc98f2af-6477-4d75-b9b8-84789661ce75/dqc_reference
[2023-06-30 07:45:07,055] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 07:45:07,056] [INFO] Task started: Prodigal
[2023-06-30 07:45:07,056] [INFO] Running command: gunzip -c /var/lib/cwl/stgadc8c857-241f-45d7-8b4e-2987c237786a/GCA_024679535.1_ASM2467953v1_genomic.fna.gz | prodigal -d GCA_024679535.1_ASM2467953v1_genomic.fna/cds.fna -a GCA_024679535.1_ASM2467953v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 07:45:16,897] [INFO] Task succeeded: Prodigal
[2023-06-30 07:45:16,898] [INFO] Task started: HMMsearch
[2023-06-30 07:45:16,898] [INFO] Running command: hmmsearch --tblout GCA_024679535.1_ASM2467953v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdc98f2af-6477-4d75-b9b8-84789661ce75/dqc_reference/reference_markers.hmm GCA_024679535.1_ASM2467953v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 07:45:17,209] [INFO] Task succeeded: HMMsearch
[2023-06-30 07:45:17,210] [INFO] Found 6/6 markers.
[2023-06-30 07:45:17,261] [INFO] Query marker FASTA was written to GCA_024679535.1_ASM2467953v1_genomic.fna/markers.fasta
[2023-06-30 07:45:17,261] [INFO] Task started: Blastn
[2023-06-30 07:45:17,261] [INFO] Running command: blastn -query GCA_024679535.1_ASM2467953v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc98f2af-6477-4d75-b9b8-84789661ce75/dqc_reference/reference_markers.fasta -out GCA_024679535.1_ASM2467953v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 07:45:18,030] [INFO] Task succeeded: Blastn
[2023-06-30 07:45:18,060] [INFO] Selected 32 target genomes.
[2023-06-30 07:45:18,061] [INFO] Target genome list was writen to GCA_024679535.1_ASM2467953v1_genomic.fna/target_genomes.txt
[2023-06-30 07:45:18,062] [INFO] Task started: fastANI
[2023-06-30 07:45:18,063] [INFO] Running command: fastANI --query /var/lib/cwl/stgadc8c857-241f-45d7-8b4e-2987c237786a/GCA_024679535.1_ASM2467953v1_genomic.fna.gz --refList GCA_024679535.1_ASM2467953v1_genomic.fna/target_genomes.txt --output GCA_024679535.1_ASM2467953v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 07:45:38,397] [INFO] Task succeeded: fastANI
[2023-06-30 07:45:38,398] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdc98f2af-6477-4d75-b9b8-84789661ce75/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 07:45:38,398] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdc98f2af-6477-4d75-b9b8-84789661ce75/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 07:45:38,404] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 07:45:38,405] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 07:45:38,405] [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	76.0683	80	1042	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 07:45:38,407] [INFO] DFAST Taxonomy check result was written to GCA_024679535.1_ASM2467953v1_genomic.fna/tc_result.tsv
[2023-06-30 07:45:38,408] [INFO] ===== Taxonomy check completed =====
[2023-06-30 07:45:38,408] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 07:45:38,408] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdc98f2af-6477-4d75-b9b8-84789661ce75/dqc_reference/checkm_data
[2023-06-30 07:45:38,410] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 07:45:38,444] [INFO] Task started: CheckM
[2023-06-30 07:45:38,445] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024679535.1_ASM2467953v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024679535.1_ASM2467953v1_genomic.fna/checkm_input GCA_024679535.1_ASM2467953v1_genomic.fna/checkm_result
[2023-06-30 07:46:11,318] [INFO] Task succeeded: CheckM
[2023-06-30 07:46:11,319] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.98%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-30 07:46:11,344] [INFO] ===== Completeness check finished =====
[2023-06-30 07:46:11,344] [INFO] ===== Start GTDB Search =====
[2023-06-30 07:46:11,345] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024679535.1_ASM2467953v1_genomic.fna/markers.fasta)
[2023-06-30 07:46:11,345] [INFO] Task started: Blastn
[2023-06-30 07:46:11,345] [INFO] Running command: blastn -query GCA_024679535.1_ASM2467953v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc98f2af-6477-4d75-b9b8-84789661ce75/dqc_reference/reference_markers_gtdb.fasta -out GCA_024679535.1_ASM2467953v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 07:46:12,650] [INFO] Task succeeded: Blastn
[2023-06-30 07:46:12,655] [INFO] Selected 22 target genomes.
[2023-06-30 07:46:12,655] [INFO] Target genome list was writen to GCA_024679535.1_ASM2467953v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 07:46:12,685] [INFO] Task started: fastANI
[2023-06-30 07:46:12,686] [INFO] Running command: fastANI --query /var/lib/cwl/stgadc8c857-241f-45d7-8b4e-2987c237786a/GCA_024679535.1_ASM2467953v1_genomic.fna.gz --refList GCA_024679535.1_ASM2467953v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024679535.1_ASM2467953v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 07:46:23,708] [INFO] Task succeeded: fastANI
[2023-06-30 07:46:23,721] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 07:46:23,722] [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_004282875.1	s__UBA1847 sp004282875	78.5294	396	1042	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__UBA1847	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009937605.1	s__UBA1847 sp009937605	77.7891	320	1042	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__UBA1847	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013042375.1	s__UBA1847 sp013042375	77.378	269	1042	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__UBA1847	95.0	99.79	99.73	0.92	0.88	6	-
GCA_013043165.1	s__UBA1847 sp013043165	77.1599	185	1042	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__UBA1847	95.0	99.92	99.83	0.96	0.93	3	-
GCA_013001045.1	s__UBA1847 sp013001045	76.9943	138	1042	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__UBA1847	95.0	99.51	99.51	0.75	0.75	2	-
GCA_009937445.1	s__UBA1847 sp009937445	76.8835	118	1042	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__UBA1847	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011772865.1	s__JAACFB01 sp011772865	76.6923	148	1042	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__JAACFB01	95.0	99.97	99.97	0.99	0.99	3	-
GCA_002338605.1	s__UBA1847 sp002338605	76.5295	119	1042	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__UBA1847	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009937525.1	s__JAACFE01 sp009937525	76.4857	142	1042	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	76.2849	132	1042	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__JAACFB01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 07:46:23,724] [INFO] GTDB search result was written to GCA_024679535.1_ASM2467953v1_genomic.fna/result_gtdb.tsv
[2023-06-30 07:46:23,724] [INFO] ===== GTDB Search completed =====
[2023-06-30 07:46:23,727] [INFO] DFAST_QC result json was written to GCA_024679535.1_ASM2467953v1_genomic.fna/dqc_result.json
[2023-06-30 07:46:23,728] [INFO] DFAST_QC completed!
[2023-06-30 07:46:23,728] [INFO] Total running time: 0h1m18s