[2023-06-16 22:40:18,924] [INFO] DFAST_QC pipeline started.
[2023-06-16 22:40:18,927] [INFO] DFAST_QC version: 0.5.7
[2023-06-16 22:40:18,927] [INFO] DQC Reference Directory: /var/lib/cwl/stge7d6598f-cbe1-458f-8323-7cd24db37061/dqc_reference
[2023-06-16 22:40:20,272] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-16 22:40:20,273] [INFO] Task started: Prodigal
[2023-06-16 22:40:20,274] [INFO] Running command: gunzip -c /var/lib/cwl/stg2898f1f1-7de8-406d-a82c-fa38744075c0/GCA_003648065.1_ASM364806v1_genomic.fna.gz | prodigal -d GCA_003648065.1_ASM364806v1_genomic.fna/cds.fna -a GCA_003648065.1_ASM364806v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-16 22:40:27,266] [INFO] Task succeeded: Prodigal
[2023-06-16 22:40:27,267] [INFO] Task started: HMMsearch
[2023-06-16 22:40:27,267] [INFO] Running command: hmmsearch --tblout GCA_003648065.1_ASM364806v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge7d6598f-cbe1-458f-8323-7cd24db37061/dqc_reference/reference_markers.hmm GCA_003648065.1_ASM364806v1_genomic.fna/protein.faa > /dev/null
[2023-06-16 22:40:27,528] [INFO] Task succeeded: HMMsearch
[2023-06-16 22:40:27,530] [INFO] Found 6/6 markers.
[2023-06-16 22:40:27,563] [INFO] Query marker FASTA was written to GCA_003648065.1_ASM364806v1_genomic.fna/markers.fasta
[2023-06-16 22:40:27,563] [INFO] Task started: Blastn
[2023-06-16 22:40:27,564] [INFO] Running command: blastn -query GCA_003648065.1_ASM364806v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge7d6598f-cbe1-458f-8323-7cd24db37061/dqc_reference/reference_markers.fasta -out GCA_003648065.1_ASM364806v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 22:40:28,150] [INFO] Task succeeded: Blastn
[2023-06-16 22:40:28,155] [INFO] Selected 14 target genomes.
[2023-06-16 22:40:28,155] [INFO] Target genome list was writen to GCA_003648065.1_ASM364806v1_genomic.fna/target_genomes.txt
[2023-06-16 22:40:28,161] [INFO] Task started: fastANI
[2023-06-16 22:40:28,161] [INFO] Running command: fastANI --query /var/lib/cwl/stg2898f1f1-7de8-406d-a82c-fa38744075c0/GCA_003648065.1_ASM364806v1_genomic.fna.gz --refList GCA_003648065.1_ASM364806v1_genomic.fna/target_genomes.txt --output GCA_003648065.1_ASM364806v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-16 22:40:36,263] [INFO] Task succeeded: fastANI
[2023-06-16 22:40:36,264] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge7d6598f-cbe1-458f-8323-7cd24db37061/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-16 22:40:36,264] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge7d6598f-cbe1-458f-8323-7cd24db37061/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-16 22:40:36,266] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-16 22:40:36,266] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-16 22:40:36,266] [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
--------------------------------------------------------------------------------
[2023-06-16 22:40:36,268] [INFO] DFAST Taxonomy check result was written to GCA_003648065.1_ASM364806v1_genomic.fna/tc_result.tsv
[2023-06-16 22:40:36,269] [INFO] ===== Taxonomy check completed =====
[2023-06-16 22:40:36,269] [INFO] ===== Start completeness check using CheckM =====
[2023-06-16 22:40:36,269] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge7d6598f-cbe1-458f-8323-7cd24db37061/dqc_reference/checkm_data
[2023-06-16 22:40:36,273] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-16 22:40:36,314] [INFO] Task started: CheckM
[2023-06-16 22:40:36,314] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_003648065.1_ASM364806v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_003648065.1_ASM364806v1_genomic.fna/checkm_input GCA_003648065.1_ASM364806v1_genomic.fna/checkm_result
[2023-06-16 22:41:03,236] [INFO] Task succeeded: CheckM
[2023-06-16 22:41:03,237] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.20%
Contamintation: 23.61%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-16 22:41:03,264] [INFO] ===== Completeness check finished =====
[2023-06-16 22:41:03,264] [INFO] ===== Start GTDB Search =====
[2023-06-16 22:41:03,264] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_003648065.1_ASM364806v1_genomic.fna/markers.fasta)
[2023-06-16 22:41:03,265] [INFO] Task started: Blastn
[2023-06-16 22:41:03,265] [INFO] Running command: blastn -query GCA_003648065.1_ASM364806v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge7d6598f-cbe1-458f-8323-7cd24db37061/dqc_reference/reference_markers_gtdb.fasta -out GCA_003648065.1_ASM364806v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 22:41:04,071] [INFO] Task succeeded: Blastn
[2023-06-16 22:41:04,075] [INFO] Selected 19 target genomes.
[2023-06-16 22:41:04,076] [INFO] Target genome list was writen to GCA_003648065.1_ASM364806v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-16 22:41:04,086] [INFO] Task started: fastANI
[2023-06-16 22:41:04,086] [INFO] Running command: fastANI --query /var/lib/cwl/stg2898f1f1-7de8-406d-a82c-fa38744075c0/GCA_003648065.1_ASM364806v1_genomic.fna.gz --refList GCA_003648065.1_ASM364806v1_genomic.fna/target_genomes_gtdb.txt --output GCA_003648065.1_ASM364806v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-16 22:41:14,376] [INFO] Task succeeded: fastANI
[2023-06-16 22:41:14,381] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-16 22:41:14,381] [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_011041825.1	s__HyVt-206 sp011041825	97.7764	346	654	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__SpSt-600;f__SpSt-600;g__HyVt-206	95.0	N/A	N/A	N/A	N/A	1	conclusive
--------------------------------------------------------------------------------
[2023-06-16 22:41:14,384] [INFO] GTDB search result was written to GCA_003648065.1_ASM364806v1_genomic.fna/result_gtdb.tsv
[2023-06-16 22:41:14,384] [INFO] ===== GTDB Search completed =====
[2023-06-16 22:41:14,387] [INFO] DFAST_QC result json was written to GCA_003648065.1_ASM364806v1_genomic.fna/dqc_result.json
[2023-06-16 22:41:14,388] [INFO] DFAST_QC completed!
[2023-06-16 22:41:14,388] [INFO] Total running time: 0h0m55s