[2023-06-18 10:35:32,847] [INFO] DFAST_QC pipeline started.
[2023-06-18 10:35:32,852] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 10:35:32,852] [INFO] DQC Reference Directory: /var/lib/cwl/stgbd8acd52-b62e-48f4-b86d-0886a124bc69/dqc_reference
[2023-06-18 10:35:34,432] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 10:35:34,433] [INFO] Task started: Prodigal
[2023-06-18 10:35:34,433] [INFO] Running command: gunzip -c /var/lib/cwl/stge3e9bab0-e308-44bb-93d9-77091ce0afa0/GCA_018701715.1_ASM1870171v1_genomic.fna.gz | prodigal -d GCA_018701715.1_ASM1870171v1_genomic.fna/cds.fna -a GCA_018701715.1_ASM1870171v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 10:35:37,594] [INFO] Task succeeded: Prodigal
[2023-06-18 10:35:37,594] [INFO] Task started: HMMsearch
[2023-06-18 10:35:37,594] [INFO] Running command: hmmsearch --tblout GCA_018701715.1_ASM1870171v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbd8acd52-b62e-48f4-b86d-0886a124bc69/dqc_reference/reference_markers.hmm GCA_018701715.1_ASM1870171v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 10:35:37,788] [INFO] Task succeeded: HMMsearch
[2023-06-18 10:35:37,789] [INFO] Found 6/6 markers.
[2023-06-18 10:35:37,807] [INFO] Query marker FASTA was written to GCA_018701715.1_ASM1870171v1_genomic.fna/markers.fasta
[2023-06-18 10:35:37,808] [INFO] Task started: Blastn
[2023-06-18 10:35:37,808] [INFO] Running command: blastn -query GCA_018701715.1_ASM1870171v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbd8acd52-b62e-48f4-b86d-0886a124bc69/dqc_reference/reference_markers.fasta -out GCA_018701715.1_ASM1870171v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 10:35:38,399] [INFO] Task succeeded: Blastn
[2023-06-18 10:35:38,404] [INFO] Selected 10 target genomes.
[2023-06-18 10:35:38,404] [INFO] Target genome list was writen to GCA_018701715.1_ASM1870171v1_genomic.fna/target_genomes.txt
[2023-06-18 10:35:38,409] [INFO] Task started: fastANI
[2023-06-18 10:35:38,410] [INFO] Running command: fastANI --query /var/lib/cwl/stge3e9bab0-e308-44bb-93d9-77091ce0afa0/GCA_018701715.1_ASM1870171v1_genomic.fna.gz --refList GCA_018701715.1_ASM1870171v1_genomic.fna/target_genomes.txt --output GCA_018701715.1_ASM1870171v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 10:35:43,288] [INFO] Task succeeded: fastANI
[2023-06-18 10:35:43,288] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbd8acd52-b62e-48f4-b86d-0886a124bc69/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 10:35:43,289] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbd8acd52-b62e-48f4-b86d-0886a124bc69/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 10:35:43,293] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 10:35:43,293] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-18 10:35:43,293] [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
--------------------------------------------------------------------------------
[2023-06-18 10:35:43,296] [INFO] DFAST Taxonomy check result was written to GCA_018701715.1_ASM1870171v1_genomic.fna/tc_result.tsv
[2023-06-18 10:35:43,297] [INFO] ===== Taxonomy check completed =====
[2023-06-18 10:35:43,297] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 10:35:43,297] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbd8acd52-b62e-48f4-b86d-0886a124bc69/dqc_reference/checkm_data
[2023-06-18 10:35:43,299] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 10:35:43,333] [INFO] Task started: CheckM
[2023-06-18 10:35:43,334] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018701715.1_ASM1870171v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018701715.1_ASM1870171v1_genomic.fna/checkm_input GCA_018701715.1_ASM1870171v1_genomic.fna/checkm_result
[2023-06-18 10:36:00,635] [INFO] Task succeeded: CheckM
[2023-06-18 10:36:00,638] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 76.04%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 10:36:00,704] [INFO] ===== Completeness check finished =====
[2023-06-18 10:36:00,704] [INFO] ===== Start GTDB Search =====
[2023-06-18 10:36:00,705] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018701715.1_ASM1870171v1_genomic.fna/markers.fasta)
[2023-06-18 10:36:00,705] [INFO] Task started: Blastn
[2023-06-18 10:36:00,705] [INFO] Running command: blastn -query GCA_018701715.1_ASM1870171v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbd8acd52-b62e-48f4-b86d-0886a124bc69/dqc_reference/reference_markers_gtdb.fasta -out GCA_018701715.1_ASM1870171v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 10:36:01,506] [INFO] Task succeeded: Blastn
[2023-06-18 10:36:01,512] [INFO] Selected 15 target genomes.
[2023-06-18 10:36:01,512] [INFO] Target genome list was writen to GCA_018701715.1_ASM1870171v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 10:36:01,587] [INFO] Task started: fastANI
[2023-06-18 10:36:01,587] [INFO] Running command: fastANI --query /var/lib/cwl/stge3e9bab0-e308-44bb-93d9-77091ce0afa0/GCA_018701715.1_ASM1870171v1_genomic.fna.gz --refList GCA_018701715.1_ASM1870171v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018701715.1_ASM1870171v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 10:36:04,825] [INFO] Task succeeded: fastANI
[2023-06-18 10:36:04,828] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 10:36:04,828] [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_018651085.1	s__JABIEQ01 sp018651085	99.8673	193	198	d__Bacteria;p__Patescibacteria;c__ABY1;o__Magasanikbacterales;f__UBA922;g__JABIEQ01	95.0	99.91	99.83	0.95	0.83	7	conclusive
--------------------------------------------------------------------------------
[2023-06-18 10:36:04,835] [INFO] GTDB search result was written to GCA_018701715.1_ASM1870171v1_genomic.fna/result_gtdb.tsv
[2023-06-18 10:36:04,836] [INFO] ===== GTDB Search completed =====
[2023-06-18 10:36:04,839] [INFO] DFAST_QC result json was written to GCA_018701715.1_ASM1870171v1_genomic.fna/dqc_result.json
[2023-06-18 10:36:04,839] [INFO] DFAST_QC completed!
[2023-06-18 10:36:04,839] [INFO] Total running time: 0h0m32s