[2023-06-30 20:00:15,065] [INFO] DFAST_QC pipeline started.
[2023-06-30 20:00:15,067] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 20:00:15,067] [INFO] DQC Reference Directory: /var/lib/cwl/stged2579e3-6a48-4991-83c3-afe9af286996/dqc_reference
[2023-06-30 20:00:16,742] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 20:00:16,743] [INFO] Task started: Prodigal
[2023-06-30 20:00:16,743] [INFO] Running command: gunzip -c /var/lib/cwl/stg6c62bb81-ee48-421d-a5f4-bdf6f723ab56/GCA_016779685.1_ASM1677968v1_genomic.fna.gz | prodigal -d GCA_016779685.1_ASM1677968v1_genomic.fna/cds.fna -a GCA_016779685.1_ASM1677968v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 20:00:19,472] [INFO] Task succeeded: Prodigal
[2023-06-30 20:00:19,473] [INFO] Task started: HMMsearch
[2023-06-30 20:00:19,473] [INFO] Running command: hmmsearch --tblout GCA_016779685.1_ASM1677968v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stged2579e3-6a48-4991-83c3-afe9af286996/dqc_reference/reference_markers.hmm GCA_016779685.1_ASM1677968v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 20:00:19,722] [INFO] Task succeeded: HMMsearch
[2023-06-30 20:00:19,723] [INFO] Found 6/6 markers.
[2023-06-30 20:00:19,742] [INFO] Query marker FASTA was written to GCA_016779685.1_ASM1677968v1_genomic.fna/markers.fasta
[2023-06-30 20:00:19,742] [INFO] Task started: Blastn
[2023-06-30 20:00:19,742] [INFO] Running command: blastn -query GCA_016779685.1_ASM1677968v1_genomic.fna/markers.fasta -db /var/lib/cwl/stged2579e3-6a48-4991-83c3-afe9af286996/dqc_reference/reference_markers.fasta -out GCA_016779685.1_ASM1677968v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 20:00:21,460] [INFO] Task succeeded: Blastn
[2023-06-30 20:00:21,466] [INFO] Selected 34 target genomes.
[2023-06-30 20:00:21,466] [INFO] Target genome list was writen to GCA_016779685.1_ASM1677968v1_genomic.fna/target_genomes.txt
[2023-06-30 20:00:21,500] [INFO] Task started: fastANI
[2023-06-30 20:00:21,500] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c62bb81-ee48-421d-a5f4-bdf6f723ab56/GCA_016779685.1_ASM1677968v1_genomic.fna.gz --refList GCA_016779685.1_ASM1677968v1_genomic.fna/target_genomes.txt --output GCA_016779685.1_ASM1677968v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 20:00:40,597] [INFO] Task succeeded: fastANI
[2023-06-30 20:00:40,598] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stged2579e3-6a48-4991-83c3-afe9af286996/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 20:00:40,598] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stged2579e3-6a48-4991-83c3-afe9af286996/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 20:00:40,600] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 20:00:40,600] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 20:00:40,600] [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
--------------------------------------------------------------------------------
[2023-06-30 20:00:40,602] [INFO] DFAST Taxonomy check result was written to GCA_016779685.1_ASM1677968v1_genomic.fna/tc_result.tsv
[2023-06-30 20:00:40,602] [INFO] ===== Taxonomy check completed =====
[2023-06-30 20:00:40,602] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 20:00:40,602] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stged2579e3-6a48-4991-83c3-afe9af286996/dqc_reference/checkm_data
[2023-06-30 20:00:40,605] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 20:00:40,619] [INFO] Task started: CheckM
[2023-06-30 20:00:40,620] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016779685.1_ASM1677968v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016779685.1_ASM1677968v1_genomic.fna/checkm_input GCA_016779685.1_ASM1677968v1_genomic.fna/checkm_result
[2023-06-30 20:00:55,698] [INFO] Task succeeded: CheckM
[2023-06-30 20:00:55,699] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 52.08%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 20:00:55,716] [INFO] ===== Completeness check finished =====
[2023-06-30 20:00:55,716] [INFO] ===== Start GTDB Search =====
[2023-06-30 20:00:55,716] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016779685.1_ASM1677968v1_genomic.fna/markers.fasta)
[2023-06-30 20:00:55,716] [INFO] Task started: Blastn
[2023-06-30 20:00:55,716] [INFO] Running command: blastn -query GCA_016779685.1_ASM1677968v1_genomic.fna/markers.fasta -db /var/lib/cwl/stged2579e3-6a48-4991-83c3-afe9af286996/dqc_reference/reference_markers_gtdb.fasta -out GCA_016779685.1_ASM1677968v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 20:00:56,446] [INFO] Task succeeded: Blastn
[2023-06-30 20:00:56,453] [INFO] Selected 30 target genomes.
[2023-06-30 20:00:56,453] [INFO] Target genome list was writen to GCA_016779685.1_ASM1677968v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 20:00:56,534] [INFO] Task started: fastANI
[2023-06-30 20:00:56,534] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c62bb81-ee48-421d-a5f4-bdf6f723ab56/GCA_016779685.1_ASM1677968v1_genomic.fna.gz --refList GCA_016779685.1_ASM1677968v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016779685.1_ASM1677968v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 20:01:14,802] [INFO] Task succeeded: fastANI
[2023-06-30 20:01:14,804] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 20:01:14,805] [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_016779685.1	s__UBA2521 sp016779685	100.0	343	350	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__UBA2521	95.0	N/A	N/A	N/A	N/A	1	conclusive
--------------------------------------------------------------------------------
[2023-06-30 20:01:14,806] [INFO] GTDB search result was written to GCA_016779685.1_ASM1677968v1_genomic.fna/result_gtdb.tsv
[2023-06-30 20:01:14,807] [INFO] ===== GTDB Search completed =====
[2023-06-30 20:01:14,809] [INFO] DFAST_QC result json was written to GCA_016779685.1_ASM1677968v1_genomic.fna/dqc_result.json
[2023-06-30 20:01:14,809] [INFO] DFAST_QC completed!
[2023-06-30 20:01:14,809] [INFO] Total running time: 0h0m60s