[2023-06-18 20:29:46,887] [INFO] DFAST_QC pipeline started.
[2023-06-18 20:29:46,895] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 20:29:46,895] [INFO] DQC Reference Directory: /var/lib/cwl/stgbf12af15-0aac-4fae-9cb4-6e146c43dcea/dqc_reference
[2023-06-18 20:29:50,722] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 20:29:50,723] [INFO] Task started: Prodigal
[2023-06-18 20:29:50,724] [INFO] Running command: gunzip -c /var/lib/cwl/stg1d838c77-d898-4b66-a815-8a797f139160/GCA_018607745.1_ASM1860774v1_genomic.fna.gz | prodigal -d GCA_018607745.1_ASM1860774v1_genomic.fna/cds.fna -a GCA_018607745.1_ASM1860774v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 20:29:57,114] [INFO] Task succeeded: Prodigal
[2023-06-18 20:29:57,115] [INFO] Task started: HMMsearch
[2023-06-18 20:29:57,115] [INFO] Running command: hmmsearch --tblout GCA_018607745.1_ASM1860774v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbf12af15-0aac-4fae-9cb4-6e146c43dcea/dqc_reference/reference_markers.hmm GCA_018607745.1_ASM1860774v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 20:29:57,465] [INFO] Task succeeded: HMMsearch
[2023-06-18 20:29:57,466] [INFO] Found 6/6 markers.
[2023-06-18 20:29:57,506] [INFO] Query marker FASTA was written to GCA_018607745.1_ASM1860774v1_genomic.fna/markers.fasta
[2023-06-18 20:29:57,506] [INFO] Task started: Blastn
[2023-06-18 20:29:57,506] [INFO] Running command: blastn -query GCA_018607745.1_ASM1860774v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbf12af15-0aac-4fae-9cb4-6e146c43dcea/dqc_reference/reference_markers.fasta -out GCA_018607745.1_ASM1860774v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 20:29:58,215] [INFO] Task succeeded: Blastn
[2023-06-18 20:29:58,219] [INFO] Selected 30 target genomes.
[2023-06-18 20:29:58,219] [INFO] Target genome list was writen to GCA_018607745.1_ASM1860774v1_genomic.fna/target_genomes.txt
[2023-06-18 20:29:58,224] [INFO] Task started: fastANI
[2023-06-18 20:29:58,224] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d838c77-d898-4b66-a815-8a797f139160/GCA_018607745.1_ASM1860774v1_genomic.fna.gz --refList GCA_018607745.1_ASM1860774v1_genomic.fna/target_genomes.txt --output GCA_018607745.1_ASM1860774v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 20:30:15,651] [INFO] Task succeeded: fastANI
[2023-06-18 20:30:15,651] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbf12af15-0aac-4fae-9cb4-6e146c43dcea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 20:30:15,652] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbf12af15-0aac-4fae-9cb4-6e146c43dcea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 20:30:15,653] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 20:30:15,653] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-18 20:30:15,654] [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
--------------------------------------------------------------------------------
[2023-06-18 20:30:15,658] [INFO] DFAST Taxonomy check result was written to GCA_018607745.1_ASM1860774v1_genomic.fna/tc_result.tsv
[2023-06-18 20:30:15,663] [INFO] ===== Taxonomy check completed =====
[2023-06-18 20:30:15,663] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 20:30:15,663] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbf12af15-0aac-4fae-9cb4-6e146c43dcea/dqc_reference/checkm_data
[2023-06-18 20:30:15,666] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 20:30:15,698] [INFO] Task started: CheckM
[2023-06-18 20:30:15,698] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018607745.1_ASM1860774v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018607745.1_ASM1860774v1_genomic.fna/checkm_input GCA_018607745.1_ASM1860774v1_genomic.fna/checkm_result
[2023-06-18 20:30:41,289] [INFO] Task succeeded: CheckM
[2023-06-18 20:30:41,291] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.31%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 20:30:41,314] [INFO] ===== Completeness check finished =====
[2023-06-18 20:30:41,315] [INFO] ===== Start GTDB Search =====
[2023-06-18 20:30:41,315] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018607745.1_ASM1860774v1_genomic.fna/markers.fasta)
[2023-06-18 20:30:41,315] [INFO] Task started: Blastn
[2023-06-18 20:30:41,316] [INFO] Running command: blastn -query GCA_018607745.1_ASM1860774v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbf12af15-0aac-4fae-9cb4-6e146c43dcea/dqc_reference/reference_markers_gtdb.fasta -out GCA_018607745.1_ASM1860774v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 20:30:42,112] [INFO] Task succeeded: Blastn
[2023-06-18 20:30:42,117] [INFO] Selected 32 target genomes.
[2023-06-18 20:30:42,118] [INFO] Target genome list was writen to GCA_018607745.1_ASM1860774v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 20:30:42,134] [INFO] Task started: fastANI
[2023-06-18 20:30:42,134] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d838c77-d898-4b66-a815-8a797f139160/GCA_018607745.1_ASM1860774v1_genomic.fna.gz --refList GCA_018607745.1_ASM1860774v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018607745.1_ASM1860774v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 20:30:56,476] [INFO] Task succeeded: fastANI
[2023-06-18 20:30:56,483] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 20:30:56,483] [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_905479205.1	s__Luminiphilus sp905479205	99.2645	593	780	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	99.27	99.27	0.81	0.81	2	conclusive
GCA_002389505.1	s__Luminiphilus sp002389505	85.8338	112	780	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	99.90	99.90	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2023-06-18 20:30:56,485] [INFO] GTDB search result was written to GCA_018607745.1_ASM1860774v1_genomic.fna/result_gtdb.tsv
[2023-06-18 20:30:56,485] [INFO] ===== GTDB Search completed =====
[2023-06-18 20:30:56,488] [INFO] DFAST_QC result json was written to GCA_018607745.1_ASM1860774v1_genomic.fna/dqc_result.json
[2023-06-18 20:30:56,488] [INFO] DFAST_QC completed!
[2023-06-18 20:30:56,488] [INFO] Total running time: 0h1m10s