[2024-01-24 13:55:14,705] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:14,707] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:14,707] [INFO] DQC Reference Directory: /var/lib/cwl/stg7c680502-7e05-437b-afcd-2f77e4125625/dqc_reference
[2024-01-24 13:55:16,063] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:16,064] [INFO] Task started: Prodigal
[2024-01-24 13:55:16,064] [INFO] Running command: gunzip -c /var/lib/cwl/stg994d1b49-cd42-4c2d-8734-62ed61aada9a/GCF_009695865.1_ASM969586v1_genomic.fna.gz | prodigal -d GCF_009695865.1_ASM969586v1_genomic.fna/cds.fna -a GCF_009695865.1_ASM969586v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:55:21,063] [INFO] Task succeeded: Prodigal
[2024-01-24 13:55:21,064] [INFO] Task started: HMMsearch
[2024-01-24 13:55:21,064] [INFO] Running command: hmmsearch --tblout GCF_009695865.1_ASM969586v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7c680502-7e05-437b-afcd-2f77e4125625/dqc_reference/reference_markers.hmm GCF_009695865.1_ASM969586v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:55:21,313] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:55:21,315] [INFO] Found 6/6 markers.
[2024-01-24 13:55:21,337] [INFO] Query marker FASTA was written to GCF_009695865.1_ASM969586v1_genomic.fna/markers.fasta
[2024-01-24 13:55:21,338] [INFO] Task started: Blastn
[2024-01-24 13:55:21,338] [INFO] Running command: blastn -query GCF_009695865.1_ASM969586v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7c680502-7e05-437b-afcd-2f77e4125625/dqc_reference/reference_markers.fasta -out GCF_009695865.1_ASM969586v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:55:21,942] [INFO] Task succeeded: Blastn
[2024-01-24 13:55:21,947] [INFO] Selected 20 target genomes.
[2024-01-24 13:55:21,948] [INFO] Target genome list was writen to GCF_009695865.1_ASM969586v1_genomic.fna/target_genomes.txt
[2024-01-24 13:55:21,980] [INFO] Task started: fastANI
[2024-01-24 13:55:21,981] [INFO] Running command: fastANI --query /var/lib/cwl/stg994d1b49-cd42-4c2d-8734-62ed61aada9a/GCF_009695865.1_ASM969586v1_genomic.fna.gz --refList GCF_009695865.1_ASM969586v1_genomic.fna/target_genomes.txt --output GCF_009695865.1_ASM969586v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:55:34,161] [INFO] Task succeeded: fastANI
[2024-01-24 13:55:34,161] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7c680502-7e05-437b-afcd-2f77e4125625/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:55:34,161] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7c680502-7e05-437b-afcd-2f77e4125625/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:55:34,165] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:55:34,165] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:55:34,166] [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
Mogibacterium kristiansenii	strain=WCA-MUC-591-APC-4B	GCA_009695905.1	2606708	2606708	type	True	77.5925	53	663	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:55:34,167] [INFO] DFAST Taxonomy check result was written to GCF_009695865.1_ASM969586v1_genomic.fna/tc_result.tsv
[2024-01-24 13:55:34,168] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:55:34,168] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:55:34,168] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7c680502-7e05-437b-afcd-2f77e4125625/dqc_reference/checkm_data
[2024-01-24 13:55:34,170] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:55:34,192] [INFO] Task started: CheckM
[2024-01-24 13:55:34,193] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009695865.1_ASM969586v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009695865.1_ASM969586v1_genomic.fna/checkm_input GCF_009695865.1_ASM969586v1_genomic.fna/checkm_result
[2024-01-24 13:55:57,308] [INFO] Task succeeded: CheckM
[2024-01-24 13:55:57,310] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:55:57,330] [INFO] ===== Completeness check finished =====
[2024-01-24 13:55:57,331] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:55:57,331] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009695865.1_ASM969586v1_genomic.fna/markers.fasta)
[2024-01-24 13:55:57,332] [INFO] Task started: Blastn
[2024-01-24 13:55:57,332] [INFO] Running command: blastn -query GCF_009695865.1_ASM969586v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7c680502-7e05-437b-afcd-2f77e4125625/dqc_reference/reference_markers_gtdb.fasta -out GCF_009695865.1_ASM969586v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:55:58,212] [INFO] Task succeeded: Blastn
[2024-01-24 13:55:58,217] [INFO] Selected 19 target genomes.
[2024-01-24 13:55:58,218] [INFO] Target genome list was writen to GCF_009695865.1_ASM969586v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:55:58,237] [INFO] Task started: fastANI
[2024-01-24 13:55:58,238] [INFO] Running command: fastANI --query /var/lib/cwl/stg994d1b49-cd42-4c2d-8734-62ed61aada9a/GCF_009695865.1_ASM969586v1_genomic.fna.gz --refList GCF_009695865.1_ASM969586v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009695865.1_ASM969586v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:56:05,224] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:05,231] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:56:05,231] [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_009695865.1	s__Baileyella intestinalis	100.0	663	663	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__Baileyella	95.0	98.65	98.64	0.97	0.95	3	conclusive
GCF_900155555.1	s__Baileyella timonense	80.3066	244	663	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__Baileyella	95.0	97.95	97.92	0.94	0.90	4	-
--------------------------------------------------------------------------------
[2024-01-24 13:56:05,233] [INFO] GTDB search result was written to GCF_009695865.1_ASM969586v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:56:05,233] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:56:05,235] [INFO] DFAST_QC result json was written to GCF_009695865.1_ASM969586v1_genomic.fna/dqc_result.json
[2024-01-24 13:56:05,235] [INFO] DFAST_QC completed!
[2024-01-24 13:56:05,235] [INFO] Total running time: 0h0m51s