[2023-06-13 14:45:23,620] [INFO] DFAST_QC pipeline started.
[2023-06-13 14:45:23,626] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 14:45:23,626] [INFO] DQC Reference Directory: /var/lib/cwl/stg0f05d962-5576-4b42-9a2d-9dca877cfb3f/dqc_reference
[2023-06-13 14:45:24,991] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 14:45:24,991] [INFO] Task started: Prodigal
[2023-06-13 14:45:24,992] [INFO] Running command: gunzip -c /var/lib/cwl/stgfe66d150-233d-448b-8547-0e0fd8611bd2/GCA_022425005.1_ASM2242500v1_genomic.fna.gz | prodigal -d GCA_022425005.1_ASM2242500v1_genomic.fna/cds.fna -a GCA_022425005.1_ASM2242500v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 14:45:26,355] [INFO] Task succeeded: Prodigal
[2023-06-13 14:45:26,355] [INFO] Task started: HMMsearch
[2023-06-13 14:45:26,356] [INFO] Running command: hmmsearch --tblout GCA_022425005.1_ASM2242500v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0f05d962-5576-4b42-9a2d-9dca877cfb3f/dqc_reference/reference_markers.hmm GCA_022425005.1_ASM2242500v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 14:45:26,568] [INFO] Task succeeded: HMMsearch
[2023-06-13 14:45:26,569] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgfe66d150-233d-448b-8547-0e0fd8611bd2/GCA_022425005.1_ASM2242500v1_genomic.fna.gz]
[2023-06-13 14:45:26,585] [INFO] Query marker FASTA was written to GCA_022425005.1_ASM2242500v1_genomic.fna/markers.fasta
[2023-06-13 14:45:26,585] [INFO] Task started: Blastn
[2023-06-13 14:45:26,585] [INFO] Running command: blastn -query GCA_022425005.1_ASM2242500v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f05d962-5576-4b42-9a2d-9dca877cfb3f/dqc_reference/reference_markers.fasta -out GCA_022425005.1_ASM2242500v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 14:45:28,495] [INFO] Task succeeded: Blastn
[2023-06-13 14:45:28,500] [INFO] Selected 21 target genomes.
[2023-06-13 14:45:28,501] [INFO] Target genome list was writen to GCA_022425005.1_ASM2242500v1_genomic.fna/target_genomes.txt
[2023-06-13 14:45:28,516] [INFO] Task started: fastANI
[2023-06-13 14:45:28,517] [INFO] Running command: fastANI --query /var/lib/cwl/stgfe66d150-233d-448b-8547-0e0fd8611bd2/GCA_022425005.1_ASM2242500v1_genomic.fna.gz --refList GCA_022425005.1_ASM2242500v1_genomic.fna/target_genomes.txt --output GCA_022425005.1_ASM2242500v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 14:45:36,829] [INFO] Task succeeded: fastANI
[2023-06-13 14:45:36,829] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0f05d962-5576-4b42-9a2d-9dca877cfb3f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 14:45:36,830] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0f05d962-5576-4b42-9a2d-9dca877cfb3f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 14:45:36,831] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 14:45:36,831] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 14:45:36,831] [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
--------------------------------------------------------------------------------
[2023-06-13 14:45:36,833] [INFO] DFAST Taxonomy check result was written to GCA_022425005.1_ASM2242500v1_genomic.fna/tc_result.tsv
[2023-06-13 14:45:36,834] [INFO] ===== Taxonomy check completed =====
[2023-06-13 14:45:36,834] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 14:45:36,834] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0f05d962-5576-4b42-9a2d-9dca877cfb3f/dqc_reference/checkm_data
[2023-06-13 14:45:36,837] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 14:45:36,849] [INFO] Task started: CheckM
[2023-06-13 14:45:36,849] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022425005.1_ASM2242500v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022425005.1_ASM2242500v1_genomic.fna/checkm_input GCA_022425005.1_ASM2242500v1_genomic.fna/checkm_result
[2023-06-13 14:45:50,462] [INFO] Task succeeded: CheckM
[2023-06-13 14:45:50,467] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 80.73%
Contamintation: 15.05%
Strain heterogeneity: 40.00%
--------------------------------------------------------------------------------
[2023-06-13 14:45:50,493] [INFO] ===== Completeness check finished =====
[2023-06-13 14:45:50,493] [INFO] ===== Start GTDB Search =====
[2023-06-13 14:45:50,494] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022425005.1_ASM2242500v1_genomic.fna/markers.fasta)
[2023-06-13 14:45:50,494] [INFO] Task started: Blastn
[2023-06-13 14:45:50,494] [INFO] Running command: blastn -query GCA_022425005.1_ASM2242500v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f05d962-5576-4b42-9a2d-9dca877cfb3f/dqc_reference/reference_markers_gtdb.fasta -out GCA_022425005.1_ASM2242500v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 14:45:51,361] [INFO] Task succeeded: Blastn
[2023-06-13 14:45:51,367] [INFO] Selected 21 target genomes.
[2023-06-13 14:45:51,367] [INFO] Target genome list was writen to GCA_022425005.1_ASM2242500v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 14:45:51,428] [INFO] Task started: fastANI
[2023-06-13 14:45:51,429] [INFO] Running command: fastANI --query /var/lib/cwl/stgfe66d150-233d-448b-8547-0e0fd8611bd2/GCA_022425005.1_ASM2242500v1_genomic.fna.gz --refList GCA_022425005.1_ASM2242500v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022425005.1_ASM2242500v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 14:45:57,363] [INFO] Task succeeded: fastANI
[2023-06-13 14:45:57,368] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 14:45:57,368] [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_016779485.1	s__CACLCV01 sp016779485	95.8465	122	169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-002705445;f__GCA-002716945;g__CACLCV01	95.0	99.98	99.97	0.94	0.91	3	conclusive
GCA_902605525.1	s__CACLCV01 sp902605525	79.2709	55	169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-002705445;f__GCA-002716945;g__CACLCV01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 14:45:57,370] [INFO] GTDB search result was written to GCA_022425005.1_ASM2242500v1_genomic.fna/result_gtdb.tsv
[2023-06-13 14:45:57,371] [INFO] ===== GTDB Search completed =====
[2023-06-13 14:45:57,376] [INFO] DFAST_QC result json was written to GCA_022425005.1_ASM2242500v1_genomic.fna/dqc_result.json
[2023-06-13 14:45:57,376] [INFO] DFAST_QC completed!
[2023-06-13 14:45:57,377] [INFO] Total running time: 0h0m34s