[2023-06-08 01:48:47,606] [INFO] DFAST_QC pipeline started.
[2023-06-08 01:48:47,608] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 01:48:47,608] [INFO] DQC Reference Directory: /var/lib/cwl/stgc77e2853-eefe-48f5-b654-f027b9a3bfb1/dqc_reference
[2023-06-08 01:48:48,890] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 01:48:48,891] [INFO] Task started: Prodigal
[2023-06-08 01:48:48,891] [INFO] Running command: gunzip -c /var/lib/cwl/stg9e4651fb-6de5-4f7a-997e-74d3d715d47e/GCA_945877565.1_TH-08apr19-51_genomic.fna.gz | prodigal -d GCA_945877565.1_TH-08apr19-51_genomic.fna/cds.fna -a GCA_945877565.1_TH-08apr19-51_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 01:48:54,931] [INFO] Task succeeded: Prodigal
[2023-06-08 01:48:54,931] [INFO] Task started: HMMsearch
[2023-06-08 01:48:54,932] [INFO] Running command: hmmsearch --tblout GCA_945877565.1_TH-08apr19-51_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc77e2853-eefe-48f5-b654-f027b9a3bfb1/dqc_reference/reference_markers.hmm GCA_945877565.1_TH-08apr19-51_genomic.fna/protein.faa > /dev/null
[2023-06-08 01:48:55,163] [INFO] Task succeeded: HMMsearch
[2023-06-08 01:48:55,165] [INFO] Found 6/6 markers.
[2023-06-08 01:48:55,192] [INFO] Query marker FASTA was written to GCA_945877565.1_TH-08apr19-51_genomic.fna/markers.fasta
[2023-06-08 01:48:55,192] [INFO] Task started: Blastn
[2023-06-08 01:48:55,192] [INFO] Running command: blastn -query GCA_945877565.1_TH-08apr19-51_genomic.fna/markers.fasta -db /var/lib/cwl/stgc77e2853-eefe-48f5-b654-f027b9a3bfb1/dqc_reference/reference_markers.fasta -out GCA_945877565.1_TH-08apr19-51_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 01:48:55,821] [INFO] Task succeeded: Blastn
[2023-06-08 01:48:55,826] [INFO] Selected 25 target genomes.
[2023-06-08 01:48:55,827] [INFO] Target genome list was writen to GCA_945877565.1_TH-08apr19-51_genomic.fna/target_genomes.txt
[2023-06-08 01:48:55,831] [INFO] Task started: fastANI
[2023-06-08 01:48:55,832] [INFO] Running command: fastANI --query /var/lib/cwl/stg9e4651fb-6de5-4f7a-997e-74d3d715d47e/GCA_945877565.1_TH-08apr19-51_genomic.fna.gz --refList GCA_945877565.1_TH-08apr19-51_genomic.fna/target_genomes.txt --output GCA_945877565.1_TH-08apr19-51_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 01:49:13,104] [INFO] Task succeeded: fastANI
[2023-06-08 01:49:13,105] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc77e2853-eefe-48f5-b654-f027b9a3bfb1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 01:49:13,106] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc77e2853-eefe-48f5-b654-f027b9a3bfb1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 01:49:13,108] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 01:49:13,108] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 01:49:13,108] [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
--------------------------------------------------------------------------------
[2023-06-08 01:49:13,114] [INFO] DFAST Taxonomy check result was written to GCA_945877565.1_TH-08apr19-51_genomic.fna/tc_result.tsv
[2023-06-08 01:49:13,115] [INFO] ===== Taxonomy check completed =====
[2023-06-08 01:49:13,116] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 01:49:13,116] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc77e2853-eefe-48f5-b654-f027b9a3bfb1/dqc_reference/checkm_data
[2023-06-08 01:49:13,120] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 01:49:13,146] [INFO] Task started: CheckM
[2023-06-08 01:49:13,146] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945877565.1_TH-08apr19-51_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945877565.1_TH-08apr19-51_genomic.fna/checkm_input GCA_945877565.1_TH-08apr19-51_genomic.fna/checkm_result
[2023-06-08 01:49:36,221] [INFO] Task succeeded: CheckM
[2023-06-08 01:49:36,222] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 01:49:36,244] [INFO] ===== Completeness check finished =====
[2023-06-08 01:49:36,245] [INFO] ===== Start GTDB Search =====
[2023-06-08 01:49:36,245] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945877565.1_TH-08apr19-51_genomic.fna/markers.fasta)
[2023-06-08 01:49:36,246] [INFO] Task started: Blastn
[2023-06-08 01:49:36,246] [INFO] Running command: blastn -query GCA_945877565.1_TH-08apr19-51_genomic.fna/markers.fasta -db /var/lib/cwl/stgc77e2853-eefe-48f5-b654-f027b9a3bfb1/dqc_reference/reference_markers_gtdb.fasta -out GCA_945877565.1_TH-08apr19-51_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 01:49:37,213] [INFO] Task succeeded: Blastn
[2023-06-08 01:49:37,218] [INFO] Selected 11 target genomes.
[2023-06-08 01:49:37,218] [INFO] Target genome list was writen to GCA_945877565.1_TH-08apr19-51_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 01:49:37,224] [INFO] Task started: fastANI
[2023-06-08 01:49:37,224] [INFO] Running command: fastANI --query /var/lib/cwl/stg9e4651fb-6de5-4f7a-997e-74d3d715d47e/GCA_945877565.1_TH-08apr19-51_genomic.fna.gz --refList GCA_945877565.1_TH-08apr19-51_genomic.fna/target_genomes_gtdb.txt --output GCA_945877565.1_TH-08apr19-51_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 01:49:44,669] [INFO] Task succeeded: fastANI
[2023-06-08 01:49:44,681] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 01:49:44,681] [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_009692115.1	s__JABFSM01 sp009692115	98.066	643	671	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__GWC2-71-9;g__JABFSM01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016794825.1	s__JABFSM01 sp016794825	78.1901	284	671	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__GWC2-71-9;g__JABFSM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826755.1	s__JABFSM01 sp902826755	77.634	221	671	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__GWC2-71-9;g__JABFSM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016874005.1	s__JABFSM01 sp016874005	77.0155	200	671	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__GWC2-71-9;g__JABFSM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013140635.1	s__JABFSM01 sp013140635	76.6788	87	671	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__GWC2-71-9;g__JABFSM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016713785.1	s__JADJOM01 sp016713785	76.2708	113	671	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__GWC2-71-9;g__JADJOM01	95.0	99.05	98.46	0.95	0.91	10	-
GCA_013820855.1	s__JACDDX01 sp013820855	76.2503	85	671	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__GWC2-71-9;g__JACDDX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013813675.1	s__JACDDX01 sp013813675	76.0074	59	671	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__GWC2-71-9;g__JACDDX01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 01:49:44,690] [INFO] GTDB search result was written to GCA_945877565.1_TH-08apr19-51_genomic.fna/result_gtdb.tsv
[2023-06-08 01:49:44,691] [INFO] ===== GTDB Search completed =====
[2023-06-08 01:49:44,697] [INFO] DFAST_QC result json was written to GCA_945877565.1_TH-08apr19-51_genomic.fna/dqc_result.json
[2023-06-08 01:49:44,697] [INFO] DFAST_QC completed!
[2023-06-08 01:49:44,697] [INFO] Total running time: 0h0m57s