[2023-06-17 11:08:16,137] [INFO] DFAST_QC pipeline started.
[2023-06-17 11:08:16,140] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 11:08:16,140] [INFO] DQC Reference Directory: /var/lib/cwl/stga0b7296f-552a-4a5d-8eff-94fcc44359d7/dqc_reference
[2023-06-17 11:08:17,407] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 11:08:17,408] [INFO] Task started: Prodigal
[2023-06-17 11:08:17,409] [INFO] Running command: gunzip -c /var/lib/cwl/stg2bccea40-6bde-4b6c-8387-84168554d1a0/GCA_013545915.1_ASM1354591v1_genomic.fna.gz | prodigal -d GCA_013545915.1_ASM1354591v1_genomic.fna/cds.fna -a GCA_013545915.1_ASM1354591v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 11:08:18,576] [INFO] Task succeeded: Prodigal
[2023-06-17 11:08:18,577] [INFO] Task started: HMMsearch
[2023-06-17 11:08:18,577] [INFO] Running command: hmmsearch --tblout GCA_013545915.1_ASM1354591v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga0b7296f-552a-4a5d-8eff-94fcc44359d7/dqc_reference/reference_markers.hmm GCA_013545915.1_ASM1354591v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 11:08:18,731] [INFO] Task succeeded: HMMsearch
[2023-06-17 11:08:18,733] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg2bccea40-6bde-4b6c-8387-84168554d1a0/GCA_013545915.1_ASM1354591v1_genomic.fna.gz]
[2023-06-17 11:08:18,746] [INFO] Query marker FASTA was written to GCA_013545915.1_ASM1354591v1_genomic.fna/markers.fasta
[2023-06-17 11:08:18,747] [INFO] Task started: Blastn
[2023-06-17 11:08:18,747] [INFO] Running command: blastn -query GCA_013545915.1_ASM1354591v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga0b7296f-552a-4a5d-8eff-94fcc44359d7/dqc_reference/reference_markers.fasta -out GCA_013545915.1_ASM1354591v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 11:08:19,296] [INFO] Task succeeded: Blastn
[2023-06-17 11:08:19,300] [INFO] Selected 4 target genomes.
[2023-06-17 11:08:19,301] [INFO] Target genome list was writen to GCA_013545915.1_ASM1354591v1_genomic.fna/target_genomes.txt
[2023-06-17 11:08:19,302] [INFO] Task started: fastANI
[2023-06-17 11:08:19,302] [INFO] Running command: fastANI --query /var/lib/cwl/stg2bccea40-6bde-4b6c-8387-84168554d1a0/GCA_013545915.1_ASM1354591v1_genomic.fna.gz --refList GCA_013545915.1_ASM1354591v1_genomic.fna/target_genomes.txt --output GCA_013545915.1_ASM1354591v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 11:08:21,029] [INFO] Task succeeded: fastANI
[2023-06-17 11:08:21,030] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga0b7296f-552a-4a5d-8eff-94fcc44359d7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 11:08:21,030] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga0b7296f-552a-4a5d-8eff-94fcc44359d7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 11:08:21,032] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 11:08:21,032] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-17 11:08:21,032] [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
--------------------------------------------------------------------------------
[2023-06-17 11:08:21,035] [INFO] DFAST Taxonomy check result was written to GCA_013545915.1_ASM1354591v1_genomic.fna/tc_result.tsv
[2023-06-17 11:08:21,035] [INFO] ===== Taxonomy check completed =====
[2023-06-17 11:08:21,036] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 11:08:21,036] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga0b7296f-552a-4a5d-8eff-94fcc44359d7/dqc_reference/checkm_data
[2023-06-17 11:08:21,041] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 11:08:21,051] [INFO] Task started: CheckM
[2023-06-17 11:08:21,052] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013545915.1_ASM1354591v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013545915.1_ASM1354591v1_genomic.fna/checkm_input GCA_013545915.1_ASM1354591v1_genomic.fna/checkm_result
[2023-06-17 11:08:32,951] [INFO] Task succeeded: CheckM
[2023-06-17 11:08:32,953] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 16.67%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 11:08:32,972] [INFO] ===== Completeness check finished =====
[2023-06-17 11:08:32,972] [INFO] ===== Start GTDB Search =====
[2023-06-17 11:08:32,972] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013545915.1_ASM1354591v1_genomic.fna/markers.fasta)
[2023-06-17 11:08:32,973] [INFO] Task started: Blastn
[2023-06-17 11:08:32,973] [INFO] Running command: blastn -query GCA_013545915.1_ASM1354591v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga0b7296f-552a-4a5d-8eff-94fcc44359d7/dqc_reference/reference_markers_gtdb.fasta -out GCA_013545915.1_ASM1354591v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 11:08:33,622] [INFO] Task succeeded: Blastn
[2023-06-17 11:08:33,626] [INFO] Selected 10 target genomes.
[2023-06-17 11:08:33,627] [INFO] Target genome list was writen to GCA_013545915.1_ASM1354591v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 11:08:33,642] [INFO] Task started: fastANI
[2023-06-17 11:08:33,643] [INFO] Running command: fastANI --query /var/lib/cwl/stg2bccea40-6bde-4b6c-8387-84168554d1a0/GCA_013545915.1_ASM1354591v1_genomic.fna.gz --refList GCA_013545915.1_ASM1354591v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013545915.1_ASM1354591v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 11:08:35,289] [INFO] Task succeeded: fastANI
[2023-06-17 11:08:35,291] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-17 11:08:35,292] [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
--------------------------------------------------------------------------------
[2023-06-17 11:08:35,294] [INFO] GTDB search result was written to GCA_013545915.1_ASM1354591v1_genomic.fna/result_gtdb.tsv
[2023-06-17 11:08:35,295] [INFO] ===== GTDB Search completed =====
[2023-06-17 11:08:35,298] [INFO] DFAST_QC result json was written to GCA_013545915.1_ASM1354591v1_genomic.fna/dqc_result.json
[2023-06-17 11:08:35,299] [INFO] DFAST_QC completed!
[2023-06-17 11:08:35,299] [INFO] Total running time: 0h0m19s