[2024-01-24 13:17:34,886] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:34,888] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:34,888] [INFO] DQC Reference Directory: /var/lib/cwl/stg7dccbe39-15de-4a50-800a-1a85d11e8ac9/dqc_reference
[2024-01-24 13:17:36,290] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:36,291] [INFO] Task started: Prodigal
[2024-01-24 13:17:36,291] [INFO] Running command: gunzip -c /var/lib/cwl/stgad1a4ffa-d1e8-4478-9073-98deeac23126/GCF_000276685.1_ASM27668v1_genomic.fna.gz | prodigal -d GCF_000276685.1_ASM27668v1_genomic.fna/cds.fna -a GCF_000276685.1_ASM27668v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:39,770] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:39,770] [INFO] Task started: HMMsearch
[2024-01-24 13:17:39,770] [INFO] Running command: hmmsearch --tblout GCF_000276685.1_ASM27668v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7dccbe39-15de-4a50-800a-1a85d11e8ac9/dqc_reference/reference_markers.hmm GCF_000276685.1_ASM27668v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:40,028] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:40,030] [INFO] Found 6/6 markers.
[2024-01-24 13:17:40,054] [INFO] Query marker FASTA was written to GCF_000276685.1_ASM27668v1_genomic.fna/markers.fasta
[2024-01-24 13:17:40,054] [INFO] Task started: Blastn
[2024-01-24 13:17:40,054] [INFO] Running command: blastn -query GCF_000276685.1_ASM27668v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7dccbe39-15de-4a50-800a-1a85d11e8ac9/dqc_reference/reference_markers.fasta -out GCF_000276685.1_ASM27668v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:40,697] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:40,701] [INFO] Selected 17 target genomes.
[2024-01-24 13:17:40,701] [INFO] Target genome list was writen to GCF_000276685.1_ASM27668v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:40,720] [INFO] Task started: fastANI
[2024-01-24 13:17:40,721] [INFO] Running command: fastANI --query /var/lib/cwl/stgad1a4ffa-d1e8-4478-9073-98deeac23126/GCF_000276685.1_ASM27668v1_genomic.fna.gz --refList GCF_000276685.1_ASM27668v1_genomic.fna/target_genomes.txt --output GCF_000276685.1_ASM27668v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:47,624] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:47,625] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7dccbe39-15de-4a50-800a-1a85d11e8ac9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:47,625] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7dccbe39-15de-4a50-800a-1a85d11e8ac9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:47,632] [INFO] Found 5 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:17:47,632] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:17:47,632] [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
Taylorella equigenitalis	strain=ATCC 35865	GCA_000276685.1	29575	29575	type	True	100.0	577	577	95	conclusive
Taylorella equigenitalis	strain=NCTC11184	GCA_900637125.1	29575	29575	type	True	99.9849	576	577	95	conclusive
Taylorella asinigenitalis	strain=ATCC 700933	GCA_000687755.1	84590	84590	type	True	80.3448	292	577	95	below_threshold
Pelistega ratti	strain=NLN63	GCA_009833965.1	2652177	2652177	type	True	78.3217	52	577	95	below_threshold
Pelistega indica	strain=HM-7	GCA_000506865.1	1414851	1414851	type	True	77.4608	51	577	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:17:47,633] [INFO] DFAST Taxonomy check result was written to GCF_000276685.1_ASM27668v1_genomic.fna/tc_result.tsv
[2024-01-24 13:17:47,634] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:47,634] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:47,634] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7dccbe39-15de-4a50-800a-1a85d11e8ac9/dqc_reference/checkm_data
[2024-01-24 13:17:47,635] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:47,655] [INFO] Task started: CheckM
[2024-01-24 13:17:47,656] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000276685.1_ASM27668v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000276685.1_ASM27668v1_genomic.fna/checkm_input GCF_000276685.1_ASM27668v1_genomic.fna/checkm_result
[2024-01-24 13:18:06,672] [INFO] Task succeeded: CheckM
[2024-01-24 13:18:06,674] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:18:06,694] [INFO] ===== Completeness check finished =====
[2024-01-24 13:18:06,695] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:18:06,695] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000276685.1_ASM27668v1_genomic.fna/markers.fasta)
[2024-01-24 13:18:06,696] [INFO] Task started: Blastn
[2024-01-24 13:18:06,696] [INFO] Running command: blastn -query GCF_000276685.1_ASM27668v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7dccbe39-15de-4a50-800a-1a85d11e8ac9/dqc_reference/reference_markers_gtdb.fasta -out GCF_000276685.1_ASM27668v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:07,710] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:07,714] [INFO] Selected 24 target genomes.
[2024-01-24 13:18:07,714] [INFO] Target genome list was writen to GCF_000276685.1_ASM27668v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:18:07,766] [INFO] Task started: fastANI
[2024-01-24 13:18:07,766] [INFO] Running command: fastANI --query /var/lib/cwl/stgad1a4ffa-d1e8-4478-9073-98deeac23126/GCF_000276685.1_ASM27668v1_genomic.fna.gz --refList GCF_000276685.1_ASM27668v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000276685.1_ASM27668v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:18:15,560] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:15,565] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:18:15,565] [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_000276685.1	s__Taylorella equigenitalis	100.0	577	577	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Taylorella	95.0	99.66	99.39	0.98	0.96	12	conclusive
GCF_000687755.1	s__Taylorella asinigenitalis	80.385	293	577	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Taylorella	95.0	98.23	98.12	0.95	0.94	3	-
GCF_009833965.1	s__Pelistega ratti	78.3358	52	577	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pelistega	95.0	97.82	97.82	0.91	0.91	2	-
GCF_000506865.1	s__Pelistega indica	77.4608	51	577	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pelistega	95.0	99.45	98.91	0.95	0.92	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:18:15,567] [INFO] GTDB search result was written to GCF_000276685.1_ASM27668v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:18:15,568] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:18:15,571] [INFO] DFAST_QC result json was written to GCF_000276685.1_ASM27668v1_genomic.fna/dqc_result.json
[2024-01-24 13:18:15,571] [INFO] DFAST_QC completed!
[2024-01-24 13:18:15,571] [INFO] Total running time: 0h0m41s