[2024-01-25 19:36:20,636] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:36:20,637] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:36:20,637] [INFO] DQC Reference Directory: /var/lib/cwl/stg0511f725-0e6b-4901-9f31-2f62f68b84c1/dqc_reference
[2024-01-25 19:36:21,799] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:36:21,800] [INFO] Task started: Prodigal
[2024-01-25 19:36:21,800] [INFO] Running command: gunzip -c /var/lib/cwl/stg5313b566-1f50-4a10-a35c-f11230192f8b/GCF_002243385.1_ASM224338v1_genomic.fna.gz | prodigal -d GCF_002243385.1_ASM224338v1_genomic.fna/cds.fna -a GCF_002243385.1_ASM224338v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:36:25,495] [INFO] Task succeeded: Prodigal
[2024-01-25 19:36:25,495] [INFO] Task started: HMMsearch
[2024-01-25 19:36:25,495] [INFO] Running command: hmmsearch --tblout GCF_002243385.1_ASM224338v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0511f725-0e6b-4901-9f31-2f62f68b84c1/dqc_reference/reference_markers.hmm GCF_002243385.1_ASM224338v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:36:25,691] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:36:25,692] [INFO] Found 6/6 markers.
[2024-01-25 19:36:25,711] [INFO] Query marker FASTA was written to GCF_002243385.1_ASM224338v1_genomic.fna/markers.fasta
[2024-01-25 19:36:25,712] [INFO] Task started: Blastn
[2024-01-25 19:36:25,712] [INFO] Running command: blastn -query GCF_002243385.1_ASM224338v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0511f725-0e6b-4901-9f31-2f62f68b84c1/dqc_reference/reference_markers.fasta -out GCF_002243385.1_ASM224338v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:36:26,292] [INFO] Task succeeded: Blastn
[2024-01-25 19:36:26,294] [INFO] Selected 8 target genomes.
[2024-01-25 19:36:26,295] [INFO] Target genome list was writen to GCF_002243385.1_ASM224338v1_genomic.fna/target_genomes.txt
[2024-01-25 19:36:26,297] [INFO] Task started: fastANI
[2024-01-25 19:36:26,298] [INFO] Running command: fastANI --query /var/lib/cwl/stg5313b566-1f50-4a10-a35c-f11230192f8b/GCF_002243385.1_ASM224338v1_genomic.fna.gz --refList GCF_002243385.1_ASM224338v1_genomic.fna/target_genomes.txt --output GCF_002243385.1_ASM224338v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:36:29,668] [INFO] Task succeeded: fastANI
[2024-01-25 19:36:29,669] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0511f725-0e6b-4901-9f31-2f62f68b84c1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:36:29,669] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0511f725-0e6b-4901-9f31-2f62f68b84c1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:36:29,673] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:36:29,673] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:36:29,673] [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 pumilum	strain=ATCC 700696	GCA_002243385.1	86332	86332	type	True	99.9947	618	620	95	conclusive
Mogibacterium diversum	strain=CCUG 47132	GCA_002998925.1	114527	114527	type	True	84.7984	416	620	95	below_threshold
Mogibacterium timidum	strain=ATCC 33093	GCA_000525775.1	35519	35519	type	True	81.2481	246	620	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:36:29,675] [INFO] DFAST Taxonomy check result was written to GCF_002243385.1_ASM224338v1_genomic.fna/tc_result.tsv
[2024-01-25 19:36:29,675] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:36:29,675] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:36:29,675] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0511f725-0e6b-4901-9f31-2f62f68b84c1/dqc_reference/checkm_data
[2024-01-25 19:36:29,676] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:36:29,697] [INFO] Task started: CheckM
[2024-01-25 19:36:29,697] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002243385.1_ASM224338v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002243385.1_ASM224338v1_genomic.fna/checkm_input GCF_002243385.1_ASM224338v1_genomic.fna/checkm_result
[2024-01-25 19:36:46,109] [INFO] Task succeeded: CheckM
[2024-01-25 19:36:46,110] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:36:46,126] [INFO] ===== Completeness check finished =====
[2024-01-25 19:36:46,126] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:36:46,126] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002243385.1_ASM224338v1_genomic.fna/markers.fasta)
[2024-01-25 19:36:46,126] [INFO] Task started: Blastn
[2024-01-25 19:36:46,126] [INFO] Running command: blastn -query GCF_002243385.1_ASM224338v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0511f725-0e6b-4901-9f31-2f62f68b84c1/dqc_reference/reference_markers_gtdb.fasta -out GCF_002243385.1_ASM224338v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:36:46,861] [INFO] Task succeeded: Blastn
[2024-01-25 19:36:46,864] [INFO] Selected 15 target genomes.
[2024-01-25 19:36:46,864] [INFO] Target genome list was writen to GCF_002243385.1_ASM224338v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:36:46,876] [INFO] Task started: fastANI
[2024-01-25 19:36:46,876] [INFO] Running command: fastANI --query /var/lib/cwl/stg5313b566-1f50-4a10-a35c-f11230192f8b/GCF_002243385.1_ASM224338v1_genomic.fna.gz --refList GCF_002243385.1_ASM224338v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002243385.1_ASM224338v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:36:52,414] [INFO] Task succeeded: fastANI
[2024-01-25 19:36:52,417] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:36:52,418] [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_002243385.1	s__Mogibacterium pumilum	99.9947	617	620	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__Mogibacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002998925.1	s__Mogibacterium diversum	84.8302	417	620	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__Mogibacterium	95.0	97.57	97.06	0.95	0.90	11	-
GCF_000525775.1	s__Mogibacterium timidum	81.2481	246	620	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__Mogibacterium	95.0	98.94	98.78	0.92	0.88	4	-
--------------------------------------------------------------------------------
[2024-01-25 19:36:52,419] [INFO] GTDB search result was written to GCF_002243385.1_ASM224338v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:36:52,419] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:36:52,421] [INFO] DFAST_QC result json was written to GCF_002243385.1_ASM224338v1_genomic.fna/dqc_result.json
[2024-01-25 19:36:52,421] [INFO] DFAST_QC completed!
[2024-01-25 19:36:52,421] [INFO] Total running time: 0h0m32s