[2023-06-18 17:33:59,897] [INFO] DFAST_QC pipeline started.
[2023-06-18 17:33:59,900] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 17:33:59,900] [INFO] DQC Reference Directory: /var/lib/cwl/stg07d955e3-d5e6-43ba-9262-a9abf3abd9d9/dqc_reference
[2023-06-18 17:34:01,220] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 17:34:01,221] [INFO] Task started: Prodigal
[2023-06-18 17:34:01,222] [INFO] Running command: gunzip -c /var/lib/cwl/stg4c8b67bc-2b08-4f5c-8499-a5fbfc71c068/GCA_018400085.1_ASM1840008v1_genomic.fna.gz | prodigal -d GCA_018400085.1_ASM1840008v1_genomic.fna/cds.fna -a GCA_018400085.1_ASM1840008v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 17:34:06,586] [INFO] Task succeeded: Prodigal
[2023-06-18 17:34:06,587] [INFO] Task started: HMMsearch
[2023-06-18 17:34:06,587] [INFO] Running command: hmmsearch --tblout GCA_018400085.1_ASM1840008v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg07d955e3-d5e6-43ba-9262-a9abf3abd9d9/dqc_reference/reference_markers.hmm GCA_018400085.1_ASM1840008v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 17:34:06,819] [INFO] Task succeeded: HMMsearch
[2023-06-18 17:34:06,821] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg4c8b67bc-2b08-4f5c-8499-a5fbfc71c068/GCA_018400085.1_ASM1840008v1_genomic.fna.gz]
[2023-06-18 17:34:06,847] [INFO] Query marker FASTA was written to GCA_018400085.1_ASM1840008v1_genomic.fna/markers.fasta
[2023-06-18 17:34:06,847] [INFO] Task started: Blastn
[2023-06-18 17:34:06,848] [INFO] Running command: blastn -query GCA_018400085.1_ASM1840008v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg07d955e3-d5e6-43ba-9262-a9abf3abd9d9/dqc_reference/reference_markers.fasta -out GCA_018400085.1_ASM1840008v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 17:34:07,402] [INFO] Task succeeded: Blastn
[2023-06-18 17:34:07,408] [INFO] Selected 5 target genomes.
[2023-06-18 17:34:07,409] [INFO] Target genome list was writen to GCA_018400085.1_ASM1840008v1_genomic.fna/target_genomes.txt
[2023-06-18 17:34:07,412] [INFO] Task started: fastANI
[2023-06-18 17:34:07,412] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c8b67bc-2b08-4f5c-8499-a5fbfc71c068/GCA_018400085.1_ASM1840008v1_genomic.fna.gz --refList GCA_018400085.1_ASM1840008v1_genomic.fna/target_genomes.txt --output GCA_018400085.1_ASM1840008v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 17:34:10,566] [INFO] Task succeeded: fastANI
[2023-06-18 17:34:10,566] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg07d955e3-d5e6-43ba-9262-a9abf3abd9d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 17:34:10,566] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg07d955e3-d5e6-43ba-9262-a9abf3abd9d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 17:34:10,571] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 17:34:10,572] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-18 17:34:10,572] [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 17:34:10,580] [INFO] DFAST Taxonomy check result was written to GCA_018400085.1_ASM1840008v1_genomic.fna/tc_result.tsv
[2023-06-18 17:34:10,581] [INFO] ===== Taxonomy check completed =====
[2023-06-18 17:34:10,581] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 17:34:10,581] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg07d955e3-d5e6-43ba-9262-a9abf3abd9d9/dqc_reference/checkm_data
[2023-06-18 17:34:10,584] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 17:34:10,606] [INFO] Task started: CheckM
[2023-06-18 17:34:10,606] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018400085.1_ASM1840008v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018400085.1_ASM1840008v1_genomic.fna/checkm_input GCA_018400085.1_ASM1840008v1_genomic.fna/checkm_result
[2023-06-18 17:34:29,927] [INFO] Task succeeded: CheckM
[2023-06-18 17:34:29,929] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 61.09%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 17:34:29,963] [INFO] ===== Completeness check finished =====
[2023-06-18 17:34:29,964] [INFO] ===== Start GTDB Search =====
[2023-06-18 17:34:29,965] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018400085.1_ASM1840008v1_genomic.fna/markers.fasta)
[2023-06-18 17:34:29,965] [INFO] Task started: Blastn
[2023-06-18 17:34:29,965] [INFO] Running command: blastn -query GCA_018400085.1_ASM1840008v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg07d955e3-d5e6-43ba-9262-a9abf3abd9d9/dqc_reference/reference_markers_gtdb.fasta -out GCA_018400085.1_ASM1840008v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 17:34:30,664] [INFO] Task succeeded: Blastn
[2023-06-18 17:34:30,668] [INFO] Selected 8 target genomes.
[2023-06-18 17:34:30,669] [INFO] Target genome list was writen to GCA_018400085.1_ASM1840008v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 17:34:30,697] [INFO] Task started: fastANI
[2023-06-18 17:34:30,697] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c8b67bc-2b08-4f5c-8499-a5fbfc71c068/GCA_018400085.1_ASM1840008v1_genomic.fna.gz --refList GCA_018400085.1_ASM1840008v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018400085.1_ASM1840008v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 17:34:33,634] [INFO] Task succeeded: fastANI
[2023-06-18 17:34:33,637] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-18 17:34:33,637] [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
--------------------------------------------------------------------------------
[2023-06-18 17:34:33,644] [INFO] GTDB search result was written to GCA_018400085.1_ASM1840008v1_genomic.fna/result_gtdb.tsv
[2023-06-18 17:34:33,645] [INFO] ===== GTDB Search completed =====
[2023-06-18 17:34:33,651] [INFO] DFAST_QC result json was written to GCA_018400085.1_ASM1840008v1_genomic.fna/dqc_result.json
[2023-06-18 17:34:33,651] [INFO] DFAST_QC completed!
[2023-06-18 17:34:33,652] [INFO] Total running time: 0h0m34s