[2023-06-13 14:33:47,531] [INFO] DFAST_QC pipeline started.
[2023-06-13 14:33:47,535] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 14:33:47,535] [INFO] DQC Reference Directory: /var/lib/cwl/stg582a8654-2e6d-4937-8a68-1fccc5faa4a4/dqc_reference
[2023-06-13 14:33:49,855] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 14:33:49,857] [INFO] Task started: Prodigal
[2023-06-13 14:33:49,857] [INFO] Running command: gunzip -c /var/lib/cwl/stgd8f49947-32c8-4c2c-923b-de8109b6c6c8/GCA_022448765.1_ASM2244876v1_genomic.fna.gz | prodigal -d GCA_022448765.1_ASM2244876v1_genomic.fna/cds.fna -a GCA_022448765.1_ASM2244876v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 14:33:56,451] [INFO] Task succeeded: Prodigal
[2023-06-13 14:33:56,451] [INFO] Task started: HMMsearch
[2023-06-13 14:33:56,452] [INFO] Running command: hmmsearch --tblout GCA_022448765.1_ASM2244876v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg582a8654-2e6d-4937-8a68-1fccc5faa4a4/dqc_reference/reference_markers.hmm GCA_022448765.1_ASM2244876v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 14:33:56,739] [INFO] Task succeeded: HMMsearch
[2023-06-13 14:33:56,741] [INFO] Found 6/6 markers.
[2023-06-13 14:33:56,773] [INFO] Query marker FASTA was written to GCA_022448765.1_ASM2244876v1_genomic.fna/markers.fasta
[2023-06-13 14:33:56,774] [INFO] Task started: Blastn
[2023-06-13 14:33:56,774] [INFO] Running command: blastn -query GCA_022448765.1_ASM2244876v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg582a8654-2e6d-4937-8a68-1fccc5faa4a4/dqc_reference/reference_markers.fasta -out GCA_022448765.1_ASM2244876v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 14:33:57,372] [INFO] Task succeeded: Blastn
[2023-06-13 14:33:57,377] [INFO] Selected 29 target genomes.
[2023-06-13 14:33:57,378] [INFO] Target genome list was writen to GCA_022448765.1_ASM2244876v1_genomic.fna/target_genomes.txt
[2023-06-13 14:33:57,386] [INFO] Task started: fastANI
[2023-06-13 14:33:57,386] [INFO] Running command: fastANI --query /var/lib/cwl/stgd8f49947-32c8-4c2c-923b-de8109b6c6c8/GCA_022448765.1_ASM2244876v1_genomic.fna.gz --refList GCA_022448765.1_ASM2244876v1_genomic.fna/target_genomes.txt --output GCA_022448765.1_ASM2244876v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 14:34:13,283] [INFO] Task succeeded: fastANI
[2023-06-13 14:34:13,284] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg582a8654-2e6d-4937-8a68-1fccc5faa4a4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 14:34:13,284] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg582a8654-2e6d-4937-8a68-1fccc5faa4a4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 14:34:13,287] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 14:34:13,287] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 14:34:13,287] [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 14:34:13,296] [INFO] DFAST Taxonomy check result was written to GCA_022448765.1_ASM2244876v1_genomic.fna/tc_result.tsv
[2023-06-13 14:34:13,297] [INFO] ===== Taxonomy check completed =====
[2023-06-13 14:34:13,297] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 14:34:13,297] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg582a8654-2e6d-4937-8a68-1fccc5faa4a4/dqc_reference/checkm_data
[2023-06-13 14:34:13,300] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 14:34:13,349] [INFO] Task started: CheckM
[2023-06-13 14:34:13,349] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022448765.1_ASM2244876v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022448765.1_ASM2244876v1_genomic.fna/checkm_input GCA_022448765.1_ASM2244876v1_genomic.fna/checkm_result
[2023-06-13 14:34:39,971] [INFO] Task succeeded: CheckM
[2023-06-13 14:34:39,973] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.75%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 14:34:40,003] [INFO] ===== Completeness check finished =====
[2023-06-13 14:34:40,004] [INFO] ===== Start GTDB Search =====
[2023-06-13 14:34:40,006] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022448765.1_ASM2244876v1_genomic.fna/markers.fasta)
[2023-06-13 14:34:40,006] [INFO] Task started: Blastn
[2023-06-13 14:34:40,006] [INFO] Running command: blastn -query GCA_022448765.1_ASM2244876v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg582a8654-2e6d-4937-8a68-1fccc5faa4a4/dqc_reference/reference_markers_gtdb.fasta -out GCA_022448765.1_ASM2244876v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 14:34:40,794] [INFO] Task succeeded: Blastn
[2023-06-13 14:34:40,800] [INFO] Selected 31 target genomes.
[2023-06-13 14:34:40,801] [INFO] Target genome list was writen to GCA_022448765.1_ASM2244876v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 14:34:40,832] [INFO] Task started: fastANI
[2023-06-13 14:34:40,833] [INFO] Running command: fastANI --query /var/lib/cwl/stgd8f49947-32c8-4c2c-923b-de8109b6c6c8/GCA_022448765.1_ASM2244876v1_genomic.fna.gz --refList GCA_022448765.1_ASM2244876v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022448765.1_ASM2244876v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 14:34:56,217] [INFO] Task succeeded: fastANI
[2023-06-13 14:34:56,265] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 14:34:56,266] [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_002313255.1	s__UBA11889 sp002313255	79.7849	459	713	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA11889	95.0	98.77	98.77	0.86	0.86	2	-
GCA_002719135.1	s__UBA11889 sp002719135	79.6446	373	713	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA11889	95.0	98.11	97.65	0.74	0.72	3	-
GCA_002715785.1	s__UBA11889 sp002715785	79.1987	326	713	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA11889	95.0	99.18	99.12	0.79	0.76	3	-
--------------------------------------------------------------------------------
[2023-06-13 14:34:56,268] [INFO] GTDB search result was written to GCA_022448765.1_ASM2244876v1_genomic.fna/result_gtdb.tsv
[2023-06-13 14:34:56,268] [INFO] ===== GTDB Search completed =====
[2023-06-13 14:34:56,271] [INFO] DFAST_QC result json was written to GCA_022448765.1_ASM2244876v1_genomic.fna/dqc_result.json
[2023-06-13 14:34:56,271] [INFO] DFAST_QC completed!
[2023-06-13 14:34:56,271] [INFO] Total running time: 0h1m9s