[2023-06-04 17:30:21,827] [INFO] DFAST_QC pipeline started.
[2023-06-04 17:30:21,830] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 17:30:21,830] [INFO] DQC Reference Directory: /var/lib/cwl/stg4b5cecc5-c43d-4be9-b8cd-4242f408e45d/dqc_reference
[2023-06-04 17:30:23,757] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 17:30:23,759] [INFO] Task started: Prodigal
[2023-06-04 17:30:23,759] [INFO] Running command: gunzip -c /var/lib/cwl/stgd7516a79-1b3f-469b-baaf-80b281beb6e1/GCA_934874875.1_MTG243_bin.54.fa_genomic.fna.gz | prodigal -d GCA_934874875.1_MTG243_bin.54.fa_genomic.fna/cds.fna -a GCA_934874875.1_MTG243_bin.54.fa_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 17:30:27,861] [INFO] Task succeeded: Prodigal
[2023-06-04 17:30:27,861] [INFO] Task started: HMMsearch
[2023-06-04 17:30:27,862] [INFO] Running command: hmmsearch --tblout GCA_934874875.1_MTG243_bin.54.fa_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4b5cecc5-c43d-4be9-b8cd-4242f408e45d/dqc_reference/reference_markers.hmm GCA_934874875.1_MTG243_bin.54.fa_genomic.fna/protein.faa > /dev/null
[2023-06-04 17:30:28,077] [INFO] Task succeeded: HMMsearch
[2023-06-04 17:30:28,079] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgd7516a79-1b3f-469b-baaf-80b281beb6e1/GCA_934874875.1_MTG243_bin.54.fa_genomic.fna.gz]
[2023-06-04 17:30:28,102] [INFO] Query marker FASTA was written to GCA_934874875.1_MTG243_bin.54.fa_genomic.fna/markers.fasta
[2023-06-04 17:30:28,102] [INFO] Task started: Blastn
[2023-06-04 17:30:28,103] [INFO] Running command: blastn -query GCA_934874875.1_MTG243_bin.54.fa_genomic.fna/markers.fasta -db /var/lib/cwl/stg4b5cecc5-c43d-4be9-b8cd-4242f408e45d/dqc_reference/reference_markers.fasta -out GCA_934874875.1_MTG243_bin.54.fa_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 17:30:30,328] [INFO] Task succeeded: Blastn
[2023-06-04 17:30:30,332] [INFO] Selected 17 target genomes.
[2023-06-04 17:30:30,333] [INFO] Target genome list was writen to GCA_934874875.1_MTG243_bin.54.fa_genomic.fna/target_genomes.txt
[2023-06-04 17:30:37,323] [INFO] Task started: fastANI
[2023-06-04 17:30:37,323] [INFO] Running command: fastANI --query /var/lib/cwl/stgd7516a79-1b3f-469b-baaf-80b281beb6e1/GCA_934874875.1_MTG243_bin.54.fa_genomic.fna.gz --refList GCA_934874875.1_MTG243_bin.54.fa_genomic.fna/target_genomes.txt --output GCA_934874875.1_MTG243_bin.54.fa_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 17:30:48,228] [INFO] Task succeeded: fastANI
[2023-06-04 17:30:48,228] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4b5cecc5-c43d-4be9-b8cd-4242f408e45d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 17:30:48,229] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4b5cecc5-c43d-4be9-b8cd-4242f408e45d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 17:30:48,231] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 17:30:48,231] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-04 17:30:48,231] [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
--------------------------------------------------------------------------------
[2023-06-04 17:30:48,233] [INFO] DFAST Taxonomy check result was written to GCA_934874875.1_MTG243_bin.54.fa_genomic.fna/tc_result.tsv
[2023-06-04 17:30:48,234] [INFO] ===== Taxonomy check completed =====
[2023-06-04 17:30:48,234] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 17:30:48,234] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4b5cecc5-c43d-4be9-b8cd-4242f408e45d/dqc_reference/checkm_data
[2023-06-04 17:30:48,236] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 17:30:48,260] [INFO] Task started: CheckM
[2023-06-04 17:30:48,260] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934874875.1_MTG243_bin.54.fa_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934874875.1_MTG243_bin.54.fa_genomic.fna/checkm_input GCA_934874875.1_MTG243_bin.54.fa_genomic.fna/checkm_result
[2023-06-04 17:31:07,491] [INFO] Task succeeded: CheckM
[2023-06-04 17:31:07,493] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 17:31:07,523] [INFO] ===== Completeness check finished =====
[2023-06-04 17:31:07,524] [INFO] ===== Start GTDB Search =====
[2023-06-04 17:31:07,524] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934874875.1_MTG243_bin.54.fa_genomic.fna/markers.fasta)
[2023-06-04 17:31:07,525] [INFO] Task started: Blastn
[2023-06-04 17:31:07,525] [INFO] Running command: blastn -query GCA_934874875.1_MTG243_bin.54.fa_genomic.fna/markers.fasta -db /var/lib/cwl/stg4b5cecc5-c43d-4be9-b8cd-4242f408e45d/dqc_reference/reference_markers_gtdb.fasta -out GCA_934874875.1_MTG243_bin.54.fa_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 17:31:08,358] [INFO] Task succeeded: Blastn
[2023-06-04 17:31:08,367] [INFO] Selected 23 target genomes.
[2023-06-04 17:31:08,368] [INFO] Target genome list was writen to GCA_934874875.1_MTG243_bin.54.fa_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 17:31:08,931] [INFO] Task started: fastANI
[2023-06-04 17:31:08,931] [INFO] Running command: fastANI --query /var/lib/cwl/stgd7516a79-1b3f-469b-baaf-80b281beb6e1/GCA_934874875.1_MTG243_bin.54.fa_genomic.fna.gz --refList GCA_934874875.1_MTG243_bin.54.fa_genomic.fna/target_genomes_gtdb.txt --output GCA_934874875.1_MTG243_bin.54.fa_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 17:31:19,609] [INFO] Task succeeded: fastANI
[2023-06-04 17:31:19,614] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 17:31:19,614] [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_000436335.1	s__CAG-217 sp000436335	97.649	336	353	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-217	95.0	97.66	96.86	0.92	0.85	21	conclusive
--------------------------------------------------------------------------------
[2023-06-04 17:31:19,617] [INFO] GTDB search result was written to GCA_934874875.1_MTG243_bin.54.fa_genomic.fna/result_gtdb.tsv
[2023-06-04 17:31:19,618] [INFO] ===== GTDB Search completed =====
[2023-06-04 17:31:19,620] [INFO] DFAST_QC result json was written to GCA_934874875.1_MTG243_bin.54.fa_genomic.fna/dqc_result.json
[2023-06-04 17:31:19,621] [INFO] DFAST_QC completed!
[2023-06-04 17:31:19,621] [INFO] Total running time: 0h0m58s