[2023-06-29 20:34:07,658] [INFO] DFAST_QC pipeline started.
[2023-06-29 20:34:07,660] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 20:34:07,660] [INFO] DQC Reference Directory: /var/lib/cwl/stg63a8a2db-e397-4097-9309-12e17686b54a/dqc_reference
[2023-06-29 20:34:08,905] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 20:34:08,906] [INFO] Task started: Prodigal
[2023-06-29 20:34:08,907] [INFO] Running command: gunzip -c /var/lib/cwl/stg04492958-0b17-4c45-b13d-c92344882ef7/GCA_023127855.1_ASM2312785v1_genomic.fna.gz | prodigal -d GCA_023127855.1_ASM2312785v1_genomic.fna/cds.fna -a GCA_023127855.1_ASM2312785v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 20:34:11,430] [INFO] Task succeeded: Prodigal
[2023-06-29 20:34:11,431] [INFO] Task started: HMMsearch
[2023-06-29 20:34:11,431] [INFO] Running command: hmmsearch --tblout GCA_023127855.1_ASM2312785v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg63a8a2db-e397-4097-9309-12e17686b54a/dqc_reference/reference_markers.hmm GCA_023127855.1_ASM2312785v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 20:34:11,729] [INFO] Task succeeded: HMMsearch
[2023-06-29 20:34:11,733] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg04492958-0b17-4c45-b13d-c92344882ef7/GCA_023127855.1_ASM2312785v1_genomic.fna.gz]
[2023-06-29 20:34:11,760] [INFO] Query marker FASTA was written to GCA_023127855.1_ASM2312785v1_genomic.fna/markers.fasta
[2023-06-29 20:34:11,760] [INFO] Task started: Blastn
[2023-06-29 20:34:11,761] [INFO] Running command: blastn -query GCA_023127855.1_ASM2312785v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg63a8a2db-e397-4097-9309-12e17686b54a/dqc_reference/reference_markers.fasta -out GCA_023127855.1_ASM2312785v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 20:34:12,716] [INFO] Task succeeded: Blastn
[2023-06-29 20:34:12,720] [INFO] Selected 5 target genomes.
[2023-06-29 20:34:12,720] [INFO] Target genome list was writen to GCA_023127855.1_ASM2312785v1_genomic.fna/target_genomes.txt
[2023-06-29 20:34:12,721] [INFO] Task started: fastANI
[2023-06-29 20:34:12,721] [INFO] Running command: fastANI --query /var/lib/cwl/stg04492958-0b17-4c45-b13d-c92344882ef7/GCA_023127855.1_ASM2312785v1_genomic.fna.gz --refList GCA_023127855.1_ASM2312785v1_genomic.fna/target_genomes.txt --output GCA_023127855.1_ASM2312785v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 20:34:14,503] [INFO] Task succeeded: fastANI
[2023-06-29 20:34:14,503] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg63a8a2db-e397-4097-9309-12e17686b54a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 20:34:14,503] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg63a8a2db-e397-4097-9309-12e17686b54a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 20:34:14,505] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 20:34:14,505] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 20:34:14,505] [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
--------------------------------------------------------------------------------
[2023-06-29 20:34:14,507] [INFO] DFAST Taxonomy check result was written to GCA_023127855.1_ASM2312785v1_genomic.fna/tc_result.tsv
[2023-06-29 20:34:14,508] [INFO] ===== Taxonomy check completed =====
[2023-06-29 20:34:14,508] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 20:34:14,508] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg63a8a2db-e397-4097-9309-12e17686b54a/dqc_reference/checkm_data
[2023-06-29 20:34:14,511] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 20:34:14,539] [INFO] Task started: CheckM
[2023-06-29 20:34:14,539] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_023127855.1_ASM2312785v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_023127855.1_ASM2312785v1_genomic.fna/checkm_input GCA_023127855.1_ASM2312785v1_genomic.fna/checkm_result
[2023-06-29 20:34:30,816] [INFO] Task succeeded: CheckM
[2023-06-29 20:34:30,818] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 20:34:30,835] [INFO] ===== Completeness check finished =====
[2023-06-29 20:34:30,836] [INFO] ===== Start GTDB Search =====
[2023-06-29 20:34:30,836] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_023127855.1_ASM2312785v1_genomic.fna/markers.fasta)
[2023-06-29 20:34:30,836] [INFO] Task started: Blastn
[2023-06-29 20:34:30,837] [INFO] Running command: blastn -query GCA_023127855.1_ASM2312785v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg63a8a2db-e397-4097-9309-12e17686b54a/dqc_reference/reference_markers_gtdb.fasta -out GCA_023127855.1_ASM2312785v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 20:34:31,620] [INFO] Task succeeded: Blastn
[2023-06-29 20:34:31,625] [INFO] Selected 12 target genomes.
[2023-06-29 20:34:31,625] [INFO] Target genome list was writen to GCA_023127855.1_ASM2312785v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 20:34:31,633] [INFO] Task started: fastANI
[2023-06-29 20:34:31,633] [INFO] Running command: fastANI --query /var/lib/cwl/stg04492958-0b17-4c45-b13d-c92344882ef7/GCA_023127855.1_ASM2312785v1_genomic.fna.gz --refList GCA_023127855.1_ASM2312785v1_genomic.fna/target_genomes_gtdb.txt --output GCA_023127855.1_ASM2312785v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 20:34:36,362] [INFO] Task succeeded: fastANI
[2023-06-29 20:34:36,418] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 20:34:36,418] [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_004377355.1	s__E29-bin14 sp004377355	76.6929	59	297	d__Bacteria;p__WOR-3;c__UBA3072;o__UBA3072;f__UBA3072;g__E29-bin14	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 20:34:36,421] [INFO] GTDB search result was written to GCA_023127855.1_ASM2312785v1_genomic.fna/result_gtdb.tsv
[2023-06-29 20:34:36,421] [INFO] ===== GTDB Search completed =====
[2023-06-29 20:34:36,425] [INFO] DFAST_QC result json was written to GCA_023127855.1_ASM2312785v1_genomic.fna/dqc_result.json
[2023-06-29 20:34:36,425] [INFO] DFAST_QC completed!
[2023-06-29 20:34:36,425] [INFO] Total running time: 0h0m29s