[2023-06-13 23:18:02,384] [INFO] DFAST_QC pipeline started.
[2023-06-13 23:18:02,387] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 23:18:02,388] [INFO] DQC Reference Directory: /var/lib/cwl/stga8398b4f-7ea3-4e65-900d-bae099835a92/dqc_reference
[2023-06-13 23:18:04,366] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 23:18:04,370] [INFO] Task started: Prodigal
[2023-06-13 23:18:04,370] [INFO] Running command: gunzip -c /var/lib/cwl/stgf1b81134-b787-4d1d-a261-5ee314def144/GCA_022600255.1_ASM2260025v1_genomic.fna.gz | prodigal -d GCA_022600255.1_ASM2260025v1_genomic.fna/cds.fna -a GCA_022600255.1_ASM2260025v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 23:18:10,783] [INFO] Task succeeded: Prodigal
[2023-06-13 23:18:10,783] [INFO] Task started: HMMsearch
[2023-06-13 23:18:10,783] [INFO] Running command: hmmsearch --tblout GCA_022600255.1_ASM2260025v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga8398b4f-7ea3-4e65-900d-bae099835a92/dqc_reference/reference_markers.hmm GCA_022600255.1_ASM2260025v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 23:18:11,008] [INFO] Task succeeded: HMMsearch
[2023-06-13 23:18:11,009] [INFO] Found 6/6 markers.
[2023-06-13 23:18:11,040] [INFO] Query marker FASTA was written to GCA_022600255.1_ASM2260025v1_genomic.fna/markers.fasta
[2023-06-13 23:18:11,040] [INFO] Task started: Blastn
[2023-06-13 23:18:11,040] [INFO] Running command: blastn -query GCA_022600255.1_ASM2260025v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga8398b4f-7ea3-4e65-900d-bae099835a92/dqc_reference/reference_markers.fasta -out GCA_022600255.1_ASM2260025v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 23:18:11,730] [INFO] Task succeeded: Blastn
[2023-06-13 23:18:11,734] [INFO] Selected 31 target genomes.
[2023-06-13 23:18:11,734] [INFO] Target genome list was writen to GCA_022600255.1_ASM2260025v1_genomic.fna/target_genomes.txt
[2023-06-13 23:18:11,772] [INFO] Task started: fastANI
[2023-06-13 23:18:11,772] [INFO] Running command: fastANI --query /var/lib/cwl/stgf1b81134-b787-4d1d-a261-5ee314def144/GCA_022600255.1_ASM2260025v1_genomic.fna.gz --refList GCA_022600255.1_ASM2260025v1_genomic.fna/target_genomes.txt --output GCA_022600255.1_ASM2260025v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 23:18:41,336] [INFO] Task succeeded: fastANI
[2023-06-13 23:18:41,337] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga8398b4f-7ea3-4e65-900d-bae099835a92/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 23:18:41,337] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga8398b4f-7ea3-4e65-900d-bae099835a92/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 23:18:41,339] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 23:18:41,339] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 23:18:41,339] [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
--------------------------------------------------------------------------------
[2023-06-13 23:18:41,341] [INFO] DFAST Taxonomy check result was written to GCA_022600255.1_ASM2260025v1_genomic.fna/tc_result.tsv
[2023-06-13 23:18:41,342] [INFO] ===== Taxonomy check completed =====
[2023-06-13 23:18:41,342] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 23:18:41,342] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga8398b4f-7ea3-4e65-900d-bae099835a92/dqc_reference/checkm_data
[2023-06-13 23:18:41,345] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 23:18:41,373] [INFO] Task started: CheckM
[2023-06-13 23:18:41,374] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022600255.1_ASM2260025v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022600255.1_ASM2260025v1_genomic.fna/checkm_input GCA_022600255.1_ASM2260025v1_genomic.fna/checkm_result
[2023-06-13 23:19:04,400] [INFO] Task succeeded: CheckM
[2023-06-13 23:19:04,402] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.74%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 23:19:04,424] [INFO] ===== Completeness check finished =====
[2023-06-13 23:19:04,425] [INFO] ===== Start GTDB Search =====
[2023-06-13 23:19:04,426] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022600255.1_ASM2260025v1_genomic.fna/markers.fasta)
[2023-06-13 23:19:04,426] [INFO] Task started: Blastn
[2023-06-13 23:19:04,426] [INFO] Running command: blastn -query GCA_022600255.1_ASM2260025v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga8398b4f-7ea3-4e65-900d-bae099835a92/dqc_reference/reference_markers_gtdb.fasta -out GCA_022600255.1_ASM2260025v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 23:19:05,478] [INFO] Task succeeded: Blastn
[2023-06-13 23:19:05,482] [INFO] Selected 30 target genomes.
[2023-06-13 23:19:05,482] [INFO] Target genome list was writen to GCA_022600255.1_ASM2260025v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 23:19:05,753] [INFO] Task started: fastANI
[2023-06-13 23:19:05,754] [INFO] Running command: fastANI --query /var/lib/cwl/stgf1b81134-b787-4d1d-a261-5ee314def144/GCA_022600255.1_ASM2260025v1_genomic.fna.gz --refList GCA_022600255.1_ASM2260025v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022600255.1_ASM2260025v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 23:19:28,846] [INFO] Task succeeded: fastANI
[2023-06-13 23:19:28,848] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 23:19:28,848] [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
--------------------------------------------------------------------------------
[2023-06-13 23:19:28,849] [INFO] GTDB search result was written to GCA_022600255.1_ASM2260025v1_genomic.fna/result_gtdb.tsv
[2023-06-13 23:19:28,850] [INFO] ===== GTDB Search completed =====
[2023-06-13 23:19:28,852] [INFO] DFAST_QC result json was written to GCA_022600255.1_ASM2260025v1_genomic.fna/dqc_result.json
[2023-06-13 23:19:28,852] [INFO] DFAST_QC completed!
[2023-06-13 23:19:28,852] [INFO] Total running time: 0h1m26s