[2023-06-19 09:52:39,125] [INFO] DFAST_QC pipeline started.
[2023-06-19 09:52:39,128] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 09:52:39,128] [INFO] DQC Reference Directory: /var/lib/cwl/stg834112e1-11c8-497b-b494-cf392eb32da4/dqc_reference
[2023-06-19 09:52:41,823] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 09:52:41,824] [INFO] Task started: Prodigal
[2023-06-19 09:52:41,825] [INFO] Running command: gunzip -c /var/lib/cwl/stga768fa87-ccbf-4194-8e8d-11dd6bd9136c/GCA_013042905.1_ASM1304290v1_genomic.fna.gz | prodigal -d GCA_013042905.1_ASM1304290v1_genomic.fna/cds.fna -a GCA_013042905.1_ASM1304290v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 09:52:45,302] [INFO] Task succeeded: Prodigal
[2023-06-19 09:52:45,302] [INFO] Task started: HMMsearch
[2023-06-19 09:52:45,302] [INFO] Running command: hmmsearch --tblout GCA_013042905.1_ASM1304290v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg834112e1-11c8-497b-b494-cf392eb32da4/dqc_reference/reference_markers.hmm GCA_013042905.1_ASM1304290v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 09:52:45,520] [INFO] Task succeeded: HMMsearch
[2023-06-19 09:52:45,521] [WARNING] Found 3/6 markers. [/var/lib/cwl/stga768fa87-ccbf-4194-8e8d-11dd6bd9136c/GCA_013042905.1_ASM1304290v1_genomic.fna.gz]
[2023-06-19 09:52:45,542] [INFO] Query marker FASTA was written to GCA_013042905.1_ASM1304290v1_genomic.fna/markers.fasta
[2023-06-19 09:52:45,542] [INFO] Task started: Blastn
[2023-06-19 09:52:45,542] [INFO] Running command: blastn -query GCA_013042905.1_ASM1304290v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg834112e1-11c8-497b-b494-cf392eb32da4/dqc_reference/reference_markers.fasta -out GCA_013042905.1_ASM1304290v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 09:52:46,074] [INFO] Task succeeded: Blastn
[2023-06-19 09:52:46,078] [INFO] Selected 20 target genomes.
[2023-06-19 09:52:46,078] [INFO] Target genome list was writen to GCA_013042905.1_ASM1304290v1_genomic.fna/target_genomes.txt
[2023-06-19 09:52:46,080] [INFO] Task started: fastANI
[2023-06-19 09:52:46,080] [INFO] Running command: fastANI --query /var/lib/cwl/stga768fa87-ccbf-4194-8e8d-11dd6bd9136c/GCA_013042905.1_ASM1304290v1_genomic.fna.gz --refList GCA_013042905.1_ASM1304290v1_genomic.fna/target_genomes.txt --output GCA_013042905.1_ASM1304290v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 09:52:58,469] [INFO] Task succeeded: fastANI
[2023-06-19 09:52:58,469] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg834112e1-11c8-497b-b494-cf392eb32da4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 09:52:58,470] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg834112e1-11c8-497b-b494-cf392eb32da4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 09:52:58,472] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 09:52:58,472] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 09:52:58,472] [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
--------------------------------------------------------------------------------
[2023-06-19 09:52:58,475] [INFO] DFAST Taxonomy check result was written to GCA_013042905.1_ASM1304290v1_genomic.fna/tc_result.tsv
[2023-06-19 09:52:58,475] [INFO] ===== Taxonomy check completed =====
[2023-06-19 09:52:58,476] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 09:52:58,476] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg834112e1-11c8-497b-b494-cf392eb32da4/dqc_reference/checkm_data
[2023-06-19 09:52:58,480] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 09:52:58,505] [INFO] Task started: CheckM
[2023-06-19 09:52:58,505] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013042905.1_ASM1304290v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013042905.1_ASM1304290v1_genomic.fna/checkm_input GCA_013042905.1_ASM1304290v1_genomic.fna/checkm_result
[2023-06-19 09:53:16,756] [INFO] Task succeeded: CheckM
[2023-06-19 09:53:16,759] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 48.73%
Contamintation: 0.52%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-19 09:53:16,780] [INFO] ===== Completeness check finished =====
[2023-06-19 09:53:16,781] [INFO] ===== Start GTDB Search =====
[2023-06-19 09:53:16,781] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013042905.1_ASM1304290v1_genomic.fna/markers.fasta)
[2023-06-19 09:53:16,781] [INFO] Task started: Blastn
[2023-06-19 09:53:16,782] [INFO] Running command: blastn -query GCA_013042905.1_ASM1304290v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg834112e1-11c8-497b-b494-cf392eb32da4/dqc_reference/reference_markers_gtdb.fasta -out GCA_013042905.1_ASM1304290v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 09:53:17,326] [INFO] Task succeeded: Blastn
[2023-06-19 09:53:17,330] [INFO] Selected 19 target genomes.
[2023-06-19 09:53:17,331] [INFO] Target genome list was writen to GCA_013042905.1_ASM1304290v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 09:53:17,339] [INFO] Task started: fastANI
[2023-06-19 09:53:17,339] [INFO] Running command: fastANI --query /var/lib/cwl/stga768fa87-ccbf-4194-8e8d-11dd6bd9136c/GCA_013042905.1_ASM1304290v1_genomic.fna.gz --refList GCA_013042905.1_ASM1304290v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013042905.1_ASM1304290v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 09:53:25,242] [INFO] Task succeeded: fastANI
[2023-06-19 09:53:25,246] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-19 09:53:25,246] [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_013042055.1	s__JABDQW01 sp013042055	77.5022	91	359	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SZUA-229;f__SZUA-229;g__JABDQW01	95.0	99.07	99.07	0.84	0.84	2	-
--------------------------------------------------------------------------------
[2023-06-19 09:53:25,249] [INFO] GTDB search result was written to GCA_013042905.1_ASM1304290v1_genomic.fna/result_gtdb.tsv
[2023-06-19 09:53:25,250] [INFO] ===== GTDB Search completed =====
[2023-06-19 09:53:25,252] [INFO] DFAST_QC result json was written to GCA_013042905.1_ASM1304290v1_genomic.fna/dqc_result.json
[2023-06-19 09:53:25,253] [INFO] DFAST_QC completed!
[2023-06-19 09:53:25,253] [INFO] Total running time: 0h0m46s