[2023-06-29 12:41:08,608] [INFO] DFAST_QC pipeline started.
[2023-06-29 12:41:08,611] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 12:41:08,611] [INFO] DQC Reference Directory: /var/lib/cwl/stg797d7f4c-e923-467b-9bfe-a48e92557d1d/dqc_reference
[2023-06-29 12:41:09,907] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 12:41:09,908] [INFO] Task started: Prodigal
[2023-06-29 12:41:09,909] [INFO] Running command: gunzip -c /var/lib/cwl/stg3f294f77-7a3c-4531-804a-11930c9c9918/GCA_023257375.1_ASM2325737v1_genomic.fna.gz | prodigal -d GCA_023257375.1_ASM2325737v1_genomic.fna/cds.fna -a GCA_023257375.1_ASM2325737v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 12:41:14,640] [INFO] Task succeeded: Prodigal
[2023-06-29 12:41:14,641] [INFO] Task started: HMMsearch
[2023-06-29 12:41:14,641] [INFO] Running command: hmmsearch --tblout GCA_023257375.1_ASM2325737v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg797d7f4c-e923-467b-9bfe-a48e92557d1d/dqc_reference/reference_markers.hmm GCA_023257375.1_ASM2325737v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 12:41:14,805] [INFO] Task succeeded: HMMsearch
[2023-06-29 12:41:14,806] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg3f294f77-7a3c-4531-804a-11930c9c9918/GCA_023257375.1_ASM2325737v1_genomic.fna.gz]
[2023-06-29 12:41:14,826] [INFO] Query marker FASTA was written to GCA_023257375.1_ASM2325737v1_genomic.fna/markers.fasta
[2023-06-29 12:41:14,826] [INFO] Task started: Blastn
[2023-06-29 12:41:14,826] [INFO] Running command: blastn -query GCA_023257375.1_ASM2325737v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg797d7f4c-e923-467b-9bfe-a48e92557d1d/dqc_reference/reference_markers.fasta -out GCA_023257375.1_ASM2325737v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 12:41:15,370] [INFO] Task succeeded: Blastn
[2023-06-29 12:41:15,374] [INFO] Selected 10 target genomes.
[2023-06-29 12:41:15,374] [INFO] Target genome list was writen to GCA_023257375.1_ASM2325737v1_genomic.fna/target_genomes.txt
[2023-06-29 12:41:15,376] [INFO] Task started: fastANI
[2023-06-29 12:41:15,376] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f294f77-7a3c-4531-804a-11930c9c9918/GCA_023257375.1_ASM2325737v1_genomic.fna.gz --refList GCA_023257375.1_ASM2325737v1_genomic.fna/target_genomes.txt --output GCA_023257375.1_ASM2325737v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 12:41:22,815] [INFO] Task succeeded: fastANI
[2023-06-29 12:41:22,815] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg797d7f4c-e923-467b-9bfe-a48e92557d1d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 12:41:22,816] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg797d7f4c-e923-467b-9bfe-a48e92557d1d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 12:41:22,817] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 12:41:22,817] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 12:41:22,817] [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
--------------------------------------------------------------------------------
[2023-06-29 12:41:22,821] [INFO] DFAST Taxonomy check result was written to GCA_023257375.1_ASM2325737v1_genomic.fna/tc_result.tsv
[2023-06-29 12:41:22,825] [INFO] ===== Taxonomy check completed =====
[2023-06-29 12:41:22,826] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 12:41:22,826] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg797d7f4c-e923-467b-9bfe-a48e92557d1d/dqc_reference/checkm_data
[2023-06-29 12:41:22,830] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 12:41:22,846] [INFO] Task started: CheckM
[2023-06-29 12:41:22,846] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_023257375.1_ASM2325737v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_023257375.1_ASM2325737v1_genomic.fna/checkm_input GCA_023257375.1_ASM2325737v1_genomic.fna/checkm_result
[2023-06-29 12:41:43,820] [INFO] Task succeeded: CheckM
[2023-06-29 12:41:43,822] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 67.30%
Contamintation: 6.63%
Strain heterogeneity: 75.00%
--------------------------------------------------------------------------------
[2023-06-29 12:41:43,846] [INFO] ===== Completeness check finished =====
[2023-06-29 12:41:43,847] [INFO] ===== Start GTDB Search =====
[2023-06-29 12:41:43,847] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_023257375.1_ASM2325737v1_genomic.fna/markers.fasta)
[2023-06-29 12:41:43,848] [INFO] Task started: Blastn
[2023-06-29 12:41:43,848] [INFO] Running command: blastn -query GCA_023257375.1_ASM2325737v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg797d7f4c-e923-467b-9bfe-a48e92557d1d/dqc_reference/reference_markers_gtdb.fasta -out GCA_023257375.1_ASM2325737v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 12:41:44,434] [INFO] Task succeeded: Blastn
[2023-06-29 12:41:44,438] [INFO] Selected 8 target genomes.
[2023-06-29 12:41:44,438] [INFO] Target genome list was writen to GCA_023257375.1_ASM2325737v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 12:41:44,457] [INFO] Task started: fastANI
[2023-06-29 12:41:44,457] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f294f77-7a3c-4531-804a-11930c9c9918/GCA_023257375.1_ASM2325737v1_genomic.fna.gz --refList GCA_023257375.1_ASM2325737v1_genomic.fna/target_genomes_gtdb.txt --output GCA_023257375.1_ASM2325737v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 12:41:47,945] [INFO] Task succeeded: fastANI
[2023-06-29 12:41:47,952] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 12:41:47,952] [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_018883025.1	s__67-14 sp018883025	98.663	57	58	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__70-9;g__67-14	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_903891285.1	s__67-14 sp903891285	93.5387	54	58	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__70-9;g__67-14	95.0	99.08	99.08	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2023-06-29 12:41:47,955] [INFO] GTDB search result was written to GCA_023257375.1_ASM2325737v1_genomic.fna/result_gtdb.tsv
[2023-06-29 12:41:47,956] [INFO] ===== GTDB Search completed =====
[2023-06-29 12:41:47,959] [INFO] DFAST_QC result json was written to GCA_023257375.1_ASM2325737v1_genomic.fna/dqc_result.json
[2023-06-29 12:41:47,960] [INFO] DFAST_QC completed!
[2023-06-29 12:41:47,960] [INFO] Total running time: 0h0m39s