[2023-06-13 10:49:25,501] [INFO] DFAST_QC pipeline started.
[2023-06-13 10:49:25,504] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 10:49:25,504] [INFO] DQC Reference Directory: /var/lib/cwl/stg8a62d126-8fa5-42f2-bae7-a18541f593d4/dqc_reference
[2023-06-13 10:49:27,769] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 10:49:27,770] [INFO] Task started: Prodigal
[2023-06-13 10:49:27,771] [INFO] Running command: gunzip -c /var/lib/cwl/stg0ccce0d4-a2f2-48a2-bbb9-7e1904c252ce/GCA_022448785.1_ASM2244878v1_genomic.fna.gz | prodigal -d GCA_022448785.1_ASM2244878v1_genomic.fna/cds.fna -a GCA_022448785.1_ASM2244878v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 10:49:33,287] [INFO] Task succeeded: Prodigal
[2023-06-13 10:49:33,287] [INFO] Task started: HMMsearch
[2023-06-13 10:49:33,288] [INFO] Running command: hmmsearch --tblout GCA_022448785.1_ASM2244878v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8a62d126-8fa5-42f2-bae7-a18541f593d4/dqc_reference/reference_markers.hmm GCA_022448785.1_ASM2244878v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 10:49:33,461] [INFO] Task succeeded: HMMsearch
[2023-06-13 10:49:33,462] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg0ccce0d4-a2f2-48a2-bbb9-7e1904c252ce/GCA_022448785.1_ASM2244878v1_genomic.fna.gz]
[2023-06-13 10:49:33,487] [INFO] Query marker FASTA was written to GCA_022448785.1_ASM2244878v1_genomic.fna/markers.fasta
[2023-06-13 10:49:33,487] [INFO] Task started: Blastn
[2023-06-13 10:49:33,487] [INFO] Running command: blastn -query GCA_022448785.1_ASM2244878v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8a62d126-8fa5-42f2-bae7-a18541f593d4/dqc_reference/reference_markers.fasta -out GCA_022448785.1_ASM2244878v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 10:49:34,045] [INFO] Task succeeded: Blastn
[2023-06-13 10:49:34,049] [INFO] Selected 6 target genomes.
[2023-06-13 10:49:34,049] [INFO] Target genome list was writen to GCA_022448785.1_ASM2244878v1_genomic.fna/target_genomes.txt
[2023-06-13 10:49:34,068] [INFO] Task started: fastANI
[2023-06-13 10:49:34,068] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ccce0d4-a2f2-48a2-bbb9-7e1904c252ce/GCA_022448785.1_ASM2244878v1_genomic.fna.gz --refList GCA_022448785.1_ASM2244878v1_genomic.fna/target_genomes.txt --output GCA_022448785.1_ASM2244878v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 10:49:37,317] [INFO] Task succeeded: fastANI
[2023-06-13 10:49:37,318] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8a62d126-8fa5-42f2-bae7-a18541f593d4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 10:49:37,318] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8a62d126-8fa5-42f2-bae7-a18541f593d4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 10:49:37,319] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 10:49:37,320] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 10:49:37,320] [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 10:49:37,324] [INFO] DFAST Taxonomy check result was written to GCA_022448785.1_ASM2244878v1_genomic.fna/tc_result.tsv
[2023-06-13 10:49:37,324] [INFO] ===== Taxonomy check completed =====
[2023-06-13 10:49:37,324] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 10:49:37,324] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8a62d126-8fa5-42f2-bae7-a18541f593d4/dqc_reference/checkm_data
[2023-06-13 10:49:37,327] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 10:49:37,355] [INFO] Task started: CheckM
[2023-06-13 10:49:37,355] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022448785.1_ASM2244878v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022448785.1_ASM2244878v1_genomic.fna/checkm_input GCA_022448785.1_ASM2244878v1_genomic.fna/checkm_result
[2023-06-13 10:50:00,321] [INFO] Task succeeded: CheckM
[2023-06-13 10:50:00,322] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 74.77%
Contamintation: 0.93%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 10:50:00,343] [INFO] ===== Completeness check finished =====
[2023-06-13 10:50:00,343] [INFO] ===== Start GTDB Search =====
[2023-06-13 10:50:00,344] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022448785.1_ASM2244878v1_genomic.fna/markers.fasta)
[2023-06-13 10:50:00,344] [INFO] Task started: Blastn
[2023-06-13 10:50:00,344] [INFO] Running command: blastn -query GCA_022448785.1_ASM2244878v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8a62d126-8fa5-42f2-bae7-a18541f593d4/dqc_reference/reference_markers_gtdb.fasta -out GCA_022448785.1_ASM2244878v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 10:50:01,051] [INFO] Task succeeded: Blastn
[2023-06-13 10:50:01,055] [INFO] Selected 13 target genomes.
[2023-06-13 10:50:01,055] [INFO] Target genome list was writen to GCA_022448785.1_ASM2244878v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 10:50:01,061] [INFO] Task started: fastANI
[2023-06-13 10:50:01,062] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ccce0d4-a2f2-48a2-bbb9-7e1904c252ce/GCA_022448785.1_ASM2244878v1_genomic.fna.gz --refList GCA_022448785.1_ASM2244878v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022448785.1_ASM2244878v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 10:50:09,000] [INFO] Task succeeded: fastANI
[2023-06-13 10:50:09,007] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 10:50:09,007] [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_002377605.1	s__UBA9145 sp002377605	89.4426	557	804	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002723195.1	s__UBA9145 sp002723195	79.8852	141	804	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012103535.1	s__UBA9145 sp012103535	77.8079	254	804	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002730035.1	s__UBA9145 sp002730035	76.3724	60	804	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	99.69	99.69	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2023-06-13 10:50:09,009] [INFO] GTDB search result was written to GCA_022448785.1_ASM2244878v1_genomic.fna/result_gtdb.tsv
[2023-06-13 10:50:09,011] [INFO] ===== GTDB Search completed =====
[2023-06-13 10:50:09,015] [INFO] DFAST_QC result json was written to GCA_022448785.1_ASM2244878v1_genomic.fna/dqc_result.json
[2023-06-13 10:50:09,015] [INFO] DFAST_QC completed!
[2023-06-13 10:50:09,015] [INFO] Total running time: 0h0m44s