[2024-01-24 13:55:57,909] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:57,911] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:57,911] [INFO] DQC Reference Directory: /var/lib/cwl/stgc5e686f7-3538-4f74-a143-c10e2ba348c3/dqc_reference
[2024-01-24 13:55:59,135] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:59,136] [INFO] Task started: Prodigal
[2024-01-24 13:55:59,136] [INFO] Running command: gunzip -c /var/lib/cwl/stg38a6dfee-0fac-423f-a051-e353e6aa338a/GCF_000159235.2_ASM15923v2_genomic.fna.gz | prodigal -d GCF_000159235.2_ASM15923v2_genomic.fna/cds.fna -a GCF_000159235.2_ASM15923v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:56:02,863] [INFO] Task succeeded: Prodigal
[2024-01-24 13:56:02,863] [INFO] Task started: HMMsearch
[2024-01-24 13:56:02,864] [INFO] Running command: hmmsearch --tblout GCF_000159235.2_ASM15923v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc5e686f7-3538-4f74-a143-c10e2ba348c3/dqc_reference/reference_markers.hmm GCF_000159235.2_ASM15923v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:56:03,068] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:56:03,069] [INFO] Found 6/6 markers.
[2024-01-24 13:56:03,087] [INFO] Query marker FASTA was written to GCF_000159235.2_ASM15923v2_genomic.fna/markers.fasta
[2024-01-24 13:56:03,087] [INFO] Task started: Blastn
[2024-01-24 13:56:03,087] [INFO] Running command: blastn -query GCF_000159235.2_ASM15923v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgc5e686f7-3538-4f74-a143-c10e2ba348c3/dqc_reference/reference_markers.fasta -out GCF_000159235.2_ASM15923v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:03,668] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:03,672] [INFO] Selected 9 target genomes.
[2024-01-24 13:56:03,673] [INFO] Target genome list was writen to GCF_000159235.2_ASM15923v2_genomic.fna/target_genomes.txt
[2024-01-24 13:56:03,729] [INFO] Task started: fastANI
[2024-01-24 13:56:03,729] [INFO] Running command: fastANI --query /var/lib/cwl/stg38a6dfee-0fac-423f-a051-e353e6aa338a/GCF_000159235.2_ASM15923v2_genomic.fna.gz --refList GCF_000159235.2_ASM15923v2_genomic.fna/target_genomes.txt --output GCF_000159235.2_ASM15923v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:56:07,020] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:07,021] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc5e686f7-3538-4f74-a143-c10e2ba348c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:56:07,022] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc5e686f7-3538-4f74-a143-c10e2ba348c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:56:07,032] [INFO] Found 4 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 13:56:07,032] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:56:07,032] [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=DSM 15829	GCA_000159235.2	82135	82135	type	True	100.0	474	474	95	conclusive
Fannyhessea vaginae	strain=FDAARGOS_934	GCA_016026575.1	82135	82135	type	True	99.9961	473	474	95	conclusive
Fannyhessea vaginae	strain=NCTC13935	GCA_900445305.1	82135	82135	type	True	99.9947	473	474	95	conclusive
Fannyhessea vaginae	strain=DSM 15829	GCA_000178335.1	82135	82135	type	True	99.914	438	474	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 13:56:07,034] [INFO] DFAST Taxonomy check result was written to GCF_000159235.2_ASM15923v2_genomic.fna/tc_result.tsv
[2024-01-24 13:56:07,035] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:56:07,035] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:56:07,035] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc5e686f7-3538-4f74-a143-c10e2ba348c3/dqc_reference/checkm_data
[2024-01-24 13:56:07,037] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:56:07,055] [INFO] Task started: CheckM
[2024-01-24 13:56:07,055] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000159235.2_ASM15923v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000159235.2_ASM15923v2_genomic.fna/checkm_input GCF_000159235.2_ASM15923v2_genomic.fna/checkm_result
[2024-01-24 13:56:25,278] [INFO] Task succeeded: CheckM
[2024-01-24 13:56:25,280] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:56:25,299] [INFO] ===== Completeness check finished =====
[2024-01-24 13:56:25,299] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:56:25,300] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000159235.2_ASM15923v2_genomic.fna/markers.fasta)
[2024-01-24 13:56:25,300] [INFO] Task started: Blastn
[2024-01-24 13:56:25,301] [INFO] Running command: blastn -query GCF_000159235.2_ASM15923v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgc5e686f7-3538-4f74-a143-c10e2ba348c3/dqc_reference/reference_markers_gtdb.fasta -out GCF_000159235.2_ASM15923v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:26,074] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:26,078] [INFO] Selected 19 target genomes.
[2024-01-24 13:56:26,078] [INFO] Target genome list was writen to GCF_000159235.2_ASM15923v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:56:26,097] [INFO] Task started: fastANI
[2024-01-24 13:56:26,098] [INFO] Running command: fastANI --query /var/lib/cwl/stg38a6dfee-0fac-423f-a051-e353e6aa338a/GCF_000159235.2_ASM15923v2_genomic.fna.gz --refList GCF_000159235.2_ASM15923v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000159235.2_ASM15923v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:56:31,901] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:31,907] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:56:31,907] [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	100.0	474	474	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	79.7942	115	474	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 13:56:31,909] [INFO] GTDB search result was written to GCF_000159235.2_ASM15923v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:56:31,910] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:56:31,912] [INFO] DFAST_QC result json was written to GCF_000159235.2_ASM15923v2_genomic.fna/dqc_result.json
[2024-01-24 13:56:31,912] [INFO] DFAST_QC completed!
[2024-01-24 13:56:31,912] [INFO] Total running time: 0h0m34s