[2023-06-29 13:53:42,161] [INFO] DFAST_QC pipeline started.
[2023-06-29 13:53:42,164] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 13:53:42,165] [INFO] DQC Reference Directory: /var/lib/cwl/stgf4042aa2-4841-490a-a393-d6ebe50b49cb/dqc_reference
[2023-06-29 13:53:43,429] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 13:53:43,430] [INFO] Task started: Prodigal
[2023-06-29 13:53:43,430] [INFO] Running command: gunzip -c /var/lib/cwl/stg6561f6f4-ac49-4f19-802c-051cb9bee91f/GCA_021836465.1_ASM2183646v1_genomic.fna.gz | prodigal -d GCA_021836465.1_ASM2183646v1_genomic.fna/cds.fna -a GCA_021836465.1_ASM2183646v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 13:53:46,665] [INFO] Task succeeded: Prodigal
[2023-06-29 13:53:46,665] [INFO] Task started: HMMsearch
[2023-06-29 13:53:46,666] [INFO] Running command: hmmsearch --tblout GCA_021836465.1_ASM2183646v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf4042aa2-4841-490a-a393-d6ebe50b49cb/dqc_reference/reference_markers.hmm GCA_021836465.1_ASM2183646v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 13:53:46,873] [INFO] Task succeeded: HMMsearch
[2023-06-29 13:53:46,875] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg6561f6f4-ac49-4f19-802c-051cb9bee91f/GCA_021836465.1_ASM2183646v1_genomic.fna.gz]
[2023-06-29 13:53:46,903] [INFO] Query marker FASTA was written to GCA_021836465.1_ASM2183646v1_genomic.fna/markers.fasta
[2023-06-29 13:53:46,904] [INFO] Task started: Blastn
[2023-06-29 13:53:46,904] [INFO] Running command: blastn -query GCA_021836465.1_ASM2183646v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf4042aa2-4841-490a-a393-d6ebe50b49cb/dqc_reference/reference_markers.fasta -out GCA_021836465.1_ASM2183646v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 13:53:47,451] [INFO] Task succeeded: Blastn
[2023-06-29 13:53:47,456] [INFO] Selected 6 target genomes.
[2023-06-29 13:53:47,457] [INFO] Target genome list was writen to GCA_021836465.1_ASM2183646v1_genomic.fna/target_genomes.txt
[2023-06-29 13:53:47,460] [INFO] Task started: fastANI
[2023-06-29 13:53:47,460] [INFO] Running command: fastANI --query /var/lib/cwl/stg6561f6f4-ac49-4f19-802c-051cb9bee91f/GCA_021836465.1_ASM2183646v1_genomic.fna.gz --refList GCA_021836465.1_ASM2183646v1_genomic.fna/target_genomes.txt --output GCA_021836465.1_ASM2183646v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 13:53:51,504] [INFO] Task succeeded: fastANI
[2023-06-29 13:53:51,505] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf4042aa2-4841-490a-a393-d6ebe50b49cb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 13:53:51,505] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf4042aa2-4841-490a-a393-d6ebe50b49cb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 13:53:51,507] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 13:53:51,507] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 13:53:51,507] [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 13:53:51,510] [INFO] DFAST Taxonomy check result was written to GCA_021836465.1_ASM2183646v1_genomic.fna/tc_result.tsv
[2023-06-29 13:53:51,510] [INFO] ===== Taxonomy check completed =====
[2023-06-29 13:53:51,510] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 13:53:51,511] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf4042aa2-4841-490a-a393-d6ebe50b49cb/dqc_reference/checkm_data
[2023-06-29 13:53:51,514] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 13:53:51,529] [INFO] Task started: CheckM
[2023-06-29 13:53:51,529] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021836465.1_ASM2183646v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021836465.1_ASM2183646v1_genomic.fna/checkm_input GCA_021836465.1_ASM2183646v1_genomic.fna/checkm_result
[2023-06-29 13:54:08,830] [INFO] Task succeeded: CheckM
[2023-06-29 13:54:08,832] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.87%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 13:54:08,853] [INFO] ===== Completeness check finished =====
[2023-06-29 13:54:08,854] [INFO] ===== Start GTDB Search =====
[2023-06-29 13:54:08,854] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021836465.1_ASM2183646v1_genomic.fna/markers.fasta)
[2023-06-29 13:54:08,855] [INFO] Task started: Blastn
[2023-06-29 13:54:08,855] [INFO] Running command: blastn -query GCA_021836465.1_ASM2183646v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf4042aa2-4841-490a-a393-d6ebe50b49cb/dqc_reference/reference_markers_gtdb.fasta -out GCA_021836465.1_ASM2183646v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 13:54:09,624] [INFO] Task succeeded: Blastn
[2023-06-29 13:54:09,628] [INFO] Selected 18 target genomes.
[2023-06-29 13:54:09,629] [INFO] Target genome list was writen to GCA_021836465.1_ASM2183646v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 13:54:09,636] [INFO] Task started: fastANI
[2023-06-29 13:54:09,637] [INFO] Running command: fastANI --query /var/lib/cwl/stg6561f6f4-ac49-4f19-802c-051cb9bee91f/GCA_021836465.1_ASM2183646v1_genomic.fna.gz --refList GCA_021836465.1_ASM2183646v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021836465.1_ASM2183646v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 13:54:13,538] [INFO] Task succeeded: fastANI
[2023-06-29 13:54:13,541] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 13:54:13,542] [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
--------------------------------------------------------------------------------
[2023-06-29 13:54:13,544] [INFO] GTDB search result was written to GCA_021836465.1_ASM2183646v1_genomic.fna/result_gtdb.tsv
[2023-06-29 13:54:13,545] [INFO] ===== GTDB Search completed =====
[2023-06-29 13:54:13,548] [INFO] DFAST_QC result json was written to GCA_021836465.1_ASM2183646v1_genomic.fna/dqc_result.json
[2023-06-29 13:54:13,549] [INFO] DFAST_QC completed!
[2023-06-29 13:54:13,549] [INFO] Total running time: 0h0m31s