[2024-01-24 10:56:34,527] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:56:34,529] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:56:34,529] [INFO] DQC Reference Directory: /var/lib/cwl/stgd04b965d-2b71-4822-83ca-2f738e8a1489/dqc_reference
[2024-01-24 10:56:36,718] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:56:36,719] [INFO] Task started: Prodigal
[2024-01-24 10:56:36,719] [INFO] Running command: gunzip -c /var/lib/cwl/stgd7c3409b-c6ce-47d5-87db-37d75c31bb93/GCF_900445305.1_58174_B01_genomic.fna.gz | prodigal -d GCF_900445305.1_58174_B01_genomic.fna/cds.fna -a GCF_900445305.1_58174_B01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:56:40,662] [INFO] Task succeeded: Prodigal
[2024-01-24 10:56:40,663] [INFO] Task started: HMMsearch
[2024-01-24 10:56:40,663] [INFO] Running command: hmmsearch --tblout GCF_900445305.1_58174_B01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd04b965d-2b71-4822-83ca-2f738e8a1489/dqc_reference/reference_markers.hmm GCF_900445305.1_58174_B01_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:56:40,951] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:56:40,953] [INFO] Found 6/6 markers.
[2024-01-24 10:56:40,969] [INFO] Query marker FASTA was written to GCF_900445305.1_58174_B01_genomic.fna/markers.fasta
[2024-01-24 10:56:40,970] [INFO] Task started: Blastn
[2024-01-24 10:56:40,970] [INFO] Running command: blastn -query GCF_900445305.1_58174_B01_genomic.fna/markers.fasta -db /var/lib/cwl/stgd04b965d-2b71-4822-83ca-2f738e8a1489/dqc_reference/reference_markers.fasta -out GCF_900445305.1_58174_B01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:56:43,530] [INFO] Task succeeded: Blastn
[2024-01-24 10:56:43,534] [INFO] Selected 9 target genomes.
[2024-01-24 10:56:43,534] [INFO] Target genome list was writen to GCF_900445305.1_58174_B01_genomic.fna/target_genomes.txt
[2024-01-24 10:56:43,678] [INFO] Task started: fastANI
[2024-01-24 10:56:43,678] [INFO] Running command: fastANI --query /var/lib/cwl/stgd7c3409b-c6ce-47d5-87db-37d75c31bb93/GCF_900445305.1_58174_B01_genomic.fna.gz --refList GCF_900445305.1_58174_B01_genomic.fna/target_genomes.txt --output GCF_900445305.1_58174_B01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:56:47,019] [INFO] Task succeeded: fastANI
[2024-01-24 10:56:47,020] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd04b965d-2b71-4822-83ca-2f738e8a1489/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:56:47,020] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd04b965d-2b71-4822-83ca-2f738e8a1489/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:56:47,106] [INFO] Found 4 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 10:56:47,106] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:56:47,106] [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
Fannyhessea vaginae	strain=NCTC13935	GCA_900445305.1	82135	82135	type	True	100.0	480	482	95	conclusive
Fannyhessea vaginae	strain=FDAARGOS_934	GCA_016026575.1	82135	82135	type	True	99.9997	478	482	95	conclusive
Fannyhessea vaginae	strain=DSM 15829	GCA_000159235.2	82135	82135	type	True	99.9898	471	482	95	conclusive
Fannyhessea vaginae	strain=DSM 15829	GCA_000178335.1	82135	82135	type	True	99.9202	439	482	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 10:56:47,108] [INFO] DFAST Taxonomy check result was written to GCF_900445305.1_58174_B01_genomic.fna/tc_result.tsv
[2024-01-24 10:56:47,108] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:56:47,108] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:56:47,108] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd04b965d-2b71-4822-83ca-2f738e8a1489/dqc_reference/checkm_data
[2024-01-24 10:56:47,114] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:56:47,130] [INFO] Task started: CheckM
[2024-01-24 10:56:47,130] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900445305.1_58174_B01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900445305.1_58174_B01_genomic.fna/checkm_input GCF_900445305.1_58174_B01_genomic.fna/checkm_result
[2024-01-24 10:57:10,421] [INFO] Task succeeded: CheckM
[2024-01-24 10:57:10,422] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:57:10,436] [INFO] ===== Completeness check finished =====
[2024-01-24 10:57:10,436] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:57:10,437] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900445305.1_58174_B01_genomic.fna/markers.fasta)
[2024-01-24 10:57:10,438] [INFO] Task started: Blastn
[2024-01-24 10:57:10,438] [INFO] Running command: blastn -query GCF_900445305.1_58174_B01_genomic.fna/markers.fasta -db /var/lib/cwl/stgd04b965d-2b71-4822-83ca-2f738e8a1489/dqc_reference/reference_markers_gtdb.fasta -out GCF_900445305.1_58174_B01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:11,723] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:11,728] [INFO] Selected 19 target genomes.
[2024-01-24 10:57:11,728] [INFO] Target genome list was writen to GCF_900445305.1_58174_B01_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:57:11,762] [INFO] Task started: fastANI
[2024-01-24 10:57:11,762] [INFO] Running command: fastANI --query /var/lib/cwl/stgd7c3409b-c6ce-47d5-87db-37d75c31bb93/GCF_900445305.1_58174_B01_genomic.fna.gz --refList GCF_900445305.1_58174_B01_genomic.fna/target_genomes_gtdb.txt --output GCF_900445305.1_58174_B01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:57:18,150] [INFO] Task succeeded: fastANI
[2024-01-24 10:57:18,161] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:57:18,161] [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_000159235.2	s__Fannyhessea vaginae	99.9898	471	482	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Fannyhessea	95.0	98.56	95.72	0.97	0.92	6	conclusive
GCF_900343135.1	s__Fannyhessea massiliense	79.3967	122	482	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Fannyhessea	95.0	96.69	96.69	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2024-01-24 10:57:18,163] [INFO] GTDB search result was written to GCF_900445305.1_58174_B01_genomic.fna/result_gtdb.tsv
[2024-01-24 10:57:18,164] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:57:18,166] [INFO] DFAST_QC result json was written to GCF_900445305.1_58174_B01_genomic.fna/dqc_result.json
[2024-01-24 10:57:18,167] [INFO] DFAST_QC completed!
[2024-01-24 10:57:18,167] [INFO] Total running time: 0h0m44s