[2023-06-27 23:24:38,164] [INFO] DFAST_QC pipeline started.
[2023-06-27 23:24:38,166] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 23:24:38,166] [INFO] DQC Reference Directory: /var/lib/cwl/stg9a89712c-78a2-410b-b3ce-3e1deba0ea07/dqc_reference
[2023-06-27 23:24:39,401] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 23:24:39,402] [INFO] Task started: Prodigal
[2023-06-27 23:24:39,402] [INFO] Running command: gunzip -c /var/lib/cwl/stg16f0e029-fbe4-41fd-ada4-01be7b001909/GCA_002398065.1_ASM239806v1_genomic.fna.gz | prodigal -d GCA_002398065.1_ASM239806v1_genomic.fna/cds.fna -a GCA_002398065.1_ASM239806v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 23:24:45,778] [INFO] Task succeeded: Prodigal
[2023-06-27 23:24:45,779] [INFO] Task started: HMMsearch
[2023-06-27 23:24:45,779] [INFO] Running command: hmmsearch --tblout GCA_002398065.1_ASM239806v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9a89712c-78a2-410b-b3ce-3e1deba0ea07/dqc_reference/reference_markers.hmm GCA_002398065.1_ASM239806v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 23:24:46,037] [INFO] Task succeeded: HMMsearch
[2023-06-27 23:24:46,039] [INFO] Found 6/6 markers.
[2023-06-27 23:24:46,064] [INFO] Query marker FASTA was written to GCA_002398065.1_ASM239806v1_genomic.fna/markers.fasta
[2023-06-27 23:24:46,065] [INFO] Task started: Blastn
[2023-06-27 23:24:46,065] [INFO] Running command: blastn -query GCA_002398065.1_ASM239806v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9a89712c-78a2-410b-b3ce-3e1deba0ea07/dqc_reference/reference_markers.fasta -out GCA_002398065.1_ASM239806v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 23:24:46,632] [INFO] Task succeeded: Blastn
[2023-06-27 23:24:46,637] [INFO] Selected 20 target genomes.
[2023-06-27 23:24:46,637] [INFO] Target genome list was writen to GCA_002398065.1_ASM239806v1_genomic.fna/target_genomes.txt
[2023-06-27 23:24:46,655] [INFO] Task started: fastANI
[2023-06-27 23:24:46,656] [INFO] Running command: fastANI --query /var/lib/cwl/stg16f0e029-fbe4-41fd-ada4-01be7b001909/GCA_002398065.1_ASM239806v1_genomic.fna.gz --refList GCA_002398065.1_ASM239806v1_genomic.fna/target_genomes.txt --output GCA_002398065.1_ASM239806v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 23:24:58,846] [INFO] Task succeeded: fastANI
[2023-06-27 23:24:58,846] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9a89712c-78a2-410b-b3ce-3e1deba0ea07/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 23:24:58,847] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9a89712c-78a2-410b-b3ce-3e1deba0ea07/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 23:24:58,850] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 23:24:58,850] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-27 23:24:58,850] [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
--------------------------------------------------------------------------------
[2023-06-27 23:24:58,852] [INFO] DFAST Taxonomy check result was written to GCA_002398065.1_ASM239806v1_genomic.fna/tc_result.tsv
[2023-06-27 23:24:58,853] [INFO] ===== Taxonomy check completed =====
[2023-06-27 23:24:58,854] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 23:24:58,854] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9a89712c-78a2-410b-b3ce-3e1deba0ea07/dqc_reference/checkm_data
[2023-06-27 23:24:58,859] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 23:24:58,888] [INFO] Task started: CheckM
[2023-06-27 23:24:58,889] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002398065.1_ASM239806v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002398065.1_ASM239806v1_genomic.fna/checkm_input GCA_002398065.1_ASM239806v1_genomic.fna/checkm_result
[2023-06-27 23:25:23,877] [INFO] Task succeeded: CheckM
[2023-06-27 23:25:23,879] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 23:25:23,903] [INFO] ===== Completeness check finished =====
[2023-06-27 23:25:23,903] [INFO] ===== Start GTDB Search =====
[2023-06-27 23:25:23,904] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002398065.1_ASM239806v1_genomic.fna/markers.fasta)
[2023-06-27 23:25:23,904] [INFO] Task started: Blastn
[2023-06-27 23:25:23,904] [INFO] Running command: blastn -query GCA_002398065.1_ASM239806v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9a89712c-78a2-410b-b3ce-3e1deba0ea07/dqc_reference/reference_markers_gtdb.fasta -out GCA_002398065.1_ASM239806v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 23:25:24,641] [INFO] Task succeeded: Blastn
[2023-06-27 23:25:24,648] [INFO] Selected 22 target genomes.
[2023-06-27 23:25:24,648] [INFO] Target genome list was writen to GCA_002398065.1_ASM239806v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 23:25:24,666] [INFO] Task started: fastANI
[2023-06-27 23:25:24,666] [INFO] Running command: fastANI --query /var/lib/cwl/stg16f0e029-fbe4-41fd-ada4-01be7b001909/GCA_002398065.1_ASM239806v1_genomic.fna.gz --refList GCA_002398065.1_ASM239806v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002398065.1_ASM239806v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 23:25:35,179] [INFO] Task succeeded: fastANI
[2023-06-27 23:25:35,188] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 23:25:35,188] [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_002398065.1	s__UBA4874 sp002398065	99.9999	770	780	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Caldicoprobacterales;f__DTU083;g__UBA4874	95.0	99.62	99.56	0.87	0.84	6	conclusive
GCA_002399435.1	s__UBA4874 sp002399435	91.8756	578	780	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Caldicoprobacterales;f__DTU083;g__UBA4874	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012837325.1	s__DURK01 sp012837325	76.3405	60	780	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Caldicoprobacterales;f__DTU083;g__DURK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012839095.1	s__DUOA01 sp012839095	75.7596	53	780	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Caldicoprobacterales;f__DTU083;g__DUOA01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 23:25:35,190] [INFO] GTDB search result was written to GCA_002398065.1_ASM239806v1_genomic.fna/result_gtdb.tsv
[2023-06-27 23:25:35,190] [INFO] ===== GTDB Search completed =====
[2023-06-27 23:25:35,194] [INFO] DFAST_QC result json was written to GCA_002398065.1_ASM239806v1_genomic.fna/dqc_result.json
[2023-06-27 23:25:35,194] [INFO] DFAST_QC completed!
[2023-06-27 23:25:35,194] [INFO] Total running time: 0h0m57s