[2023-06-14 01:06:57,155] [INFO] DFAST_QC pipeline started.
[2023-06-14 01:06:57,158] [INFO] DFAST_QC version: 0.5.7
[2023-06-14 01:06:57,158] [INFO] DQC Reference Directory: /var/lib/cwl/stgbd81a41a-0a33-4802-9a37-550ab8c144f7/dqc_reference
[2023-06-14 01:06:58,497] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-14 01:06:58,502] [INFO] Task started: Prodigal
[2023-06-14 01:06:58,502] [INFO] Running command: gunzip -c /var/lib/cwl/stg9eee9fa1-062f-4f8d-a7c0-32418ad4b135/GCA_022563615.1_ASM2256361v1_genomic.fna.gz | prodigal -d GCA_022563615.1_ASM2256361v1_genomic.fna/cds.fna -a GCA_022563615.1_ASM2256361v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-14 01:07:06,992] [INFO] Task succeeded: Prodigal
[2023-06-14 01:07:06,992] [INFO] Task started: HMMsearch
[2023-06-14 01:07:06,992] [INFO] Running command: hmmsearch --tblout GCA_022563615.1_ASM2256361v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbd81a41a-0a33-4802-9a37-550ab8c144f7/dqc_reference/reference_markers.hmm GCA_022563615.1_ASM2256361v1_genomic.fna/protein.faa > /dev/null
[2023-06-14 01:07:07,268] [INFO] Task succeeded: HMMsearch
[2023-06-14 01:07:07,270] [INFO] Found 6/6 markers.
[2023-06-14 01:07:07,310] [INFO] Query marker FASTA was written to GCA_022563615.1_ASM2256361v1_genomic.fna/markers.fasta
[2023-06-14 01:07:07,310] [INFO] Task started: Blastn
[2023-06-14 01:07:07,311] [INFO] Running command: blastn -query GCA_022563615.1_ASM2256361v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbd81a41a-0a33-4802-9a37-550ab8c144f7/dqc_reference/reference_markers.fasta -out GCA_022563615.1_ASM2256361v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-14 01:07:07,916] [INFO] Task succeeded: Blastn
[2023-06-14 01:07:07,920] [INFO] Selected 14 target genomes.
[2023-06-14 01:07:07,920] [INFO] Target genome list was writen to GCA_022563615.1_ASM2256361v1_genomic.fna/target_genomes.txt
[2023-06-14 01:07:07,926] [INFO] Task started: fastANI
[2023-06-14 01:07:07,927] [INFO] Running command: fastANI --query /var/lib/cwl/stg9eee9fa1-062f-4f8d-a7c0-32418ad4b135/GCA_022563615.1_ASM2256361v1_genomic.fna.gz --refList GCA_022563615.1_ASM2256361v1_genomic.fna/target_genomes.txt --output GCA_022563615.1_ASM2256361v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-14 01:07:16,648] [INFO] Task succeeded: fastANI
[2023-06-14 01:07:16,649] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbd81a41a-0a33-4802-9a37-550ab8c144f7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-14 01:07:16,649] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbd81a41a-0a33-4802-9a37-550ab8c144f7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-14 01:07:16,659] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-14 01:07:16,659] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-14 01:07:16,659] [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
--------------------------------------------------------------------------------
[2023-06-14 01:07:16,669] [INFO] DFAST Taxonomy check result was written to GCA_022563615.1_ASM2256361v1_genomic.fna/tc_result.tsv
[2023-06-14 01:07:16,673] [INFO] ===== Taxonomy check completed =====
[2023-06-14 01:07:16,674] [INFO] ===== Start completeness check using CheckM =====
[2023-06-14 01:07:16,674] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbd81a41a-0a33-4802-9a37-550ab8c144f7/dqc_reference/checkm_data
[2023-06-14 01:07:16,676] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-14 01:07:16,710] [INFO] Task started: CheckM
[2023-06-14 01:07:16,710] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022563615.1_ASM2256361v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022563615.1_ASM2256361v1_genomic.fna/checkm_input GCA_022563615.1_ASM2256361v1_genomic.fna/checkm_result
[2023-06-14 01:07:47,548] [INFO] Task succeeded: CheckM
[2023-06-14 01:07:47,551] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.52%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-14 01:07:47,573] [INFO] ===== Completeness check finished =====
[2023-06-14 01:07:47,574] [INFO] ===== Start GTDB Search =====
[2023-06-14 01:07:47,574] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022563615.1_ASM2256361v1_genomic.fna/markers.fasta)
[2023-06-14 01:07:47,574] [INFO] Task started: Blastn
[2023-06-14 01:07:47,575] [INFO] Running command: blastn -query GCA_022563615.1_ASM2256361v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbd81a41a-0a33-4802-9a37-550ab8c144f7/dqc_reference/reference_markers_gtdb.fasta -out GCA_022563615.1_ASM2256361v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-14 01:07:48,478] [INFO] Task succeeded: Blastn
[2023-06-14 01:07:48,483] [INFO] Selected 26 target genomes.
[2023-06-14 01:07:48,483] [INFO] Target genome list was writen to GCA_022563615.1_ASM2256361v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-14 01:07:48,557] [INFO] Task started: fastANI
[2023-06-14 01:07:48,557] [INFO] Running command: fastANI --query /var/lib/cwl/stg9eee9fa1-062f-4f8d-a7c0-32418ad4b135/GCA_022563615.1_ASM2256361v1_genomic.fna.gz --refList GCA_022563615.1_ASM2256361v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022563615.1_ASM2256361v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-14 01:08:04,432] [INFO] Task succeeded: fastANI
[2023-06-14 01:08:04,437] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-14 01:08:04,437] [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_016208685.1	s__JACQXM01 sp016208685	75.9566	56	848	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__UBA1845;f__UBA1845;g__JACQXM01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-14 01:08:04,439] [INFO] GTDB search result was written to GCA_022563615.1_ASM2256361v1_genomic.fna/result_gtdb.tsv
[2023-06-14 01:08:04,440] [INFO] ===== GTDB Search completed =====
[2023-06-14 01:08:04,452] [INFO] DFAST_QC result json was written to GCA_022563615.1_ASM2256361v1_genomic.fna/dqc_result.json
[2023-06-14 01:08:04,453] [INFO] DFAST_QC completed!
[2023-06-14 01:08:04,453] [INFO] Total running time: 0h1m7s