[2024-01-24 14:55:08,563] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:55:08,567] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:55:08,567] [INFO] DQC Reference Directory: /var/lib/cwl/stg1901e035-480a-4189-a471-0ffa54285773/dqc_reference
[2024-01-24 14:55:10,106] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:55:10,107] [INFO] Task started: Prodigal
[2024-01-24 14:55:10,107] [INFO] Running command: gunzip -c /var/lib/cwl/stg40ff7cf0-6250-46ed-92dd-17c278d92ce6/GCF_016924775.1_ASM1692477v1_genomic.fna.gz | prodigal -d GCF_016924775.1_ASM1692477v1_genomic.fna/cds.fna -a GCF_016924775.1_ASM1692477v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:55:11,542] [INFO] Task succeeded: Prodigal
[2024-01-24 14:55:11,543] [INFO] Task started: HMMsearch
[2024-01-24 14:55:11,543] [INFO] Running command: hmmsearch --tblout GCF_016924775.1_ASM1692477v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1901e035-480a-4189-a471-0ffa54285773/dqc_reference/reference_markers.hmm GCF_016924775.1_ASM1692477v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:55:11,811] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:55:11,813] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg40ff7cf0-6250-46ed-92dd-17c278d92ce6/GCF_016924775.1_ASM1692477v1_genomic.fna.gz]
[2024-01-24 14:55:11,828] [INFO] Query marker FASTA was written to GCF_016924775.1_ASM1692477v1_genomic.fna/markers.fasta
[2024-01-24 14:55:11,829] [INFO] Task started: Blastn
[2024-01-24 14:55:11,829] [INFO] Running command: blastn -query GCF_016924775.1_ASM1692477v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1901e035-480a-4189-a471-0ffa54285773/dqc_reference/reference_markers.fasta -out GCF_016924775.1_ASM1692477v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:14,999] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:15,008] [INFO] Selected 22 target genomes.
[2024-01-24 14:55:15,009] [INFO] Target genome list was writen to GCF_016924775.1_ASM1692477v1_genomic.fna/target_genomes.txt
[2024-01-24 14:55:15,130] [INFO] Task started: fastANI
[2024-01-24 14:55:15,131] [INFO] Running command: fastANI --query /var/lib/cwl/stg40ff7cf0-6250-46ed-92dd-17c278d92ce6/GCF_016924775.1_ASM1692477v1_genomic.fna.gz --refList GCF_016924775.1_ASM1692477v1_genomic.fna/target_genomes.txt --output GCF_016924775.1_ASM1692477v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:55:19,493] [INFO] Task succeeded: fastANI
[2024-01-24 14:55:19,494] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1901e035-480a-4189-a471-0ffa54285773/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:55:19,494] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1901e035-480a-4189-a471-0ffa54285773/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:55:19,496] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:55:19,497] [INFO] The taxonomy check result is classified as 'no_hit'.
[2024-01-24 14:55:19,497] [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
--------------------------------------------------------------------------------
[2024-01-24 14:55:19,499] [INFO] DFAST Taxonomy check result was written to GCF_016924775.1_ASM1692477v1_genomic.fna/tc_result.tsv
[2024-01-24 14:55:19,499] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:55:19,500] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:55:19,500] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1901e035-480a-4189-a471-0ffa54285773/dqc_reference/checkm_data
[2024-01-24 14:55:19,504] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:55:19,516] [INFO] Task started: CheckM
[2024-01-24 14:55:19,517] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016924775.1_ASM1692477v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016924775.1_ASM1692477v1_genomic.fna/checkm_input GCF_016924775.1_ASM1692477v1_genomic.fna/checkm_result
[2024-01-24 14:55:33,704] [INFO] Task succeeded: CheckM
[2024-01-24 14:55:33,704] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:55:33,725] [INFO] ===== Completeness check finished =====
[2024-01-24 14:55:33,726] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:55:33,726] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016924775.1_ASM1692477v1_genomic.fna/markers.fasta)
[2024-01-24 14:55:33,726] [INFO] Task started: Blastn
[2024-01-24 14:55:33,726] [INFO] Running command: blastn -query GCF_016924775.1_ASM1692477v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1901e035-480a-4189-a471-0ffa54285773/dqc_reference/reference_markers_gtdb.fasta -out GCF_016924775.1_ASM1692477v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:34,552] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:34,556] [INFO] Selected 20 target genomes.
[2024-01-24 14:55:34,556] [INFO] Target genome list was writen to GCF_016924775.1_ASM1692477v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:55:34,577] [INFO] Task started: fastANI
[2024-01-24 14:55:34,578] [INFO] Running command: fastANI --query /var/lib/cwl/stg40ff7cf0-6250-46ed-92dd-17c278d92ce6/GCF_016924775.1_ASM1692477v1_genomic.fna.gz --refList GCF_016924775.1_ASM1692477v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016924775.1_ASM1692477v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:55:40,211] [INFO] Task succeeded: fastANI
[2024-01-24 14:55:40,217] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:55:40,217] [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
GCF_016924775.1	s__Metamycoplasma gypis	100.0	277	278	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Metamycoplasma	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_018914005.1	s__Metamycoplasma zalophi	77.8941	70	278	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Metamycoplasma	95.0	99.02	99.02	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:55:40,219] [INFO] GTDB search result was written to GCF_016924775.1_ASM1692477v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:55:40,219] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:55:40,222] [INFO] DFAST_QC result json was written to GCF_016924775.1_ASM1692477v1_genomic.fna/dqc_result.json
[2024-01-24 14:55:40,222] [INFO] DFAST_QC completed!
[2024-01-24 14:55:40,223] [INFO] Total running time: 0h0m32s