[2024-01-24 11:12:36,238] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:36,243] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:36,244] [INFO] DQC Reference Directory: /var/lib/cwl/stg8ac38285-2ed3-41fc-82d1-2fddabfaa8ab/dqc_reference
[2024-01-24 11:12:38,667] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:38,668] [INFO] Task started: Prodigal
[2024-01-24 11:12:38,668] [INFO] Running command: gunzip -c /var/lib/cwl/stgade03157-2f69-4b71-897d-c9385ce9d551/GCF_002086695.1_ASM208669v1_genomic.fna.gz | prodigal -d GCF_002086695.1_ASM208669v1_genomic.fna/cds.fna -a GCF_002086695.1_ASM208669v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:12:57,326] [INFO] Task succeeded: Prodigal
[2024-01-24 11:12:57,326] [INFO] Task started: HMMsearch
[2024-01-24 11:12:57,326] [INFO] Running command: hmmsearch --tblout GCF_002086695.1_ASM208669v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8ac38285-2ed3-41fc-82d1-2fddabfaa8ab/dqc_reference/reference_markers.hmm GCF_002086695.1_ASM208669v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:12:57,574] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:12:57,575] [INFO] Found 6/6 markers.
[2024-01-24 11:12:57,624] [INFO] Query marker FASTA was written to GCF_002086695.1_ASM208669v1_genomic.fna/markers.fasta
[2024-01-24 11:12:57,625] [INFO] Task started: Blastn
[2024-01-24 11:12:57,625] [INFO] Running command: blastn -query GCF_002086695.1_ASM208669v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8ac38285-2ed3-41fc-82d1-2fddabfaa8ab/dqc_reference/reference_markers.fasta -out GCF_002086695.1_ASM208669v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:12:58,821] [INFO] Task succeeded: Blastn
[2024-01-24 11:12:58,828] [INFO] Selected 10 target genomes.
[2024-01-24 11:12:58,828] [INFO] Target genome list was writen to GCF_002086695.1_ASM208669v1_genomic.fna/target_genomes.txt
[2024-01-24 11:12:58,834] [INFO] Task started: fastANI
[2024-01-24 11:12:58,834] [INFO] Running command: fastANI --query /var/lib/cwl/stgade03157-2f69-4b71-897d-c9385ce9d551/GCF_002086695.1_ASM208669v1_genomic.fna.gz --refList GCF_002086695.1_ASM208669v1_genomic.fna/target_genomes.txt --output GCF_002086695.1_ASM208669v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:13,880] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:13,881] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8ac38285-2ed3-41fc-82d1-2fddabfaa8ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:13,881] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8ac38285-2ed3-41fc-82d1-2fddabfaa8ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:13,890] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:13:13,890] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:13:13,890] [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
Mycolicibacterium rhodesiae	strain=DSM 44223	GCA_002086695.1	36814	36814	type	True	100.0	1979	1981	95	conclusive
Mycolicibacterium aichiense	strain=NCTC10820	GCA_900453085.1	1799	1799	type	True	91.8421	1721	1981	95	below_threshold
Mycolicibacterium aichiense	strain=JCM 6376	GCA_010726245.1	1799	1799	type	True	91.8298	1727	1981	95	below_threshold
Mycolicibacterium aromaticivorans	strain=JS19b1	GCA_000559085.2	318425	318425	type	True	91.1671	1628	1981	95	below_threshold
Mycobacterium crocinum	strain=JCM 16369	GCA_022370635.3	388459	388459	type	True	86.822	1588	1981	95	below_threshold
Mycobacterium pallens	strain=JCM 16370	GCA_019456675.1	370524	370524	type	True	86.7504	1594	1981	95	below_threshold
Mycolicibacterium vinylchloridicum	strain=CECT 8761	GCA_013404075.1	2736928	2736928	type	True	84.4058	1445	1981	95	below_threshold
Mycolicibacterium sphagni	strain=ATCC 33027	GCA_002250655.1	1786	1786	type	True	83.7026	1357	1981	95	below_threshold
Mycolicibacterium anyangense	strain=JCM 30275	GCA_010731855.1	1431246	1431246	type	True	81.8665	1137	1981	95	below_threshold
Mycolicibacterium stellerae	strain=CECT 8783	GCA_003719305.1	2358193	2358193	type	True	79.0891	846	1981	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:13,892] [INFO] DFAST Taxonomy check result was written to GCF_002086695.1_ASM208669v1_genomic.fna/tc_result.tsv
[2024-01-24 11:13:13,892] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:13,893] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:13,893] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8ac38285-2ed3-41fc-82d1-2fddabfaa8ab/dqc_reference/checkm_data
[2024-01-24 11:13:13,894] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:13,946] [INFO] Task started: CheckM
[2024-01-24 11:13:13,946] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002086695.1_ASM208669v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002086695.1_ASM208669v1_genomic.fna/checkm_input GCF_002086695.1_ASM208669v1_genomic.fna/checkm_result
[2024-01-24 11:14:08,220] [INFO] Task succeeded: CheckM
[2024-01-24 11:14:08,221] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:14:08,238] [INFO] ===== Completeness check finished =====
[2024-01-24 11:14:08,238] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:14:08,239] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002086695.1_ASM208669v1_genomic.fna/markers.fasta)
[2024-01-24 11:14:08,239] [INFO] Task started: Blastn
[2024-01-24 11:14:08,239] [INFO] Running command: blastn -query GCF_002086695.1_ASM208669v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8ac38285-2ed3-41fc-82d1-2fddabfaa8ab/dqc_reference/reference_markers_gtdb.fasta -out GCF_002086695.1_ASM208669v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:14:10,190] [INFO] Task succeeded: Blastn
[2024-01-24 11:14:10,196] [INFO] Selected 7 target genomes.
[2024-01-24 11:14:10,197] [INFO] Target genome list was writen to GCF_002086695.1_ASM208669v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:14:10,202] [INFO] Task started: fastANI
[2024-01-24 11:14:10,202] [INFO] Running command: fastANI --query /var/lib/cwl/stgade03157-2f69-4b71-897d-c9385ce9d551/GCF_002086695.1_ASM208669v1_genomic.fna.gz --refList GCF_002086695.1_ASM208669v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002086695.1_ASM208669v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:14:21,182] [INFO] Task succeeded: fastANI
[2024-01-24 11:14:21,189] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:14:21,189] [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_002086695.1	s__Mycobacterium rhodesiae	100.0	1979	1981	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_010726245.1	s__Mycobacterium aichiense	91.8298	1727	1981	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002887815.1	s__Mycobacterium sp002887815	91.4709	1663	1981	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008329905.1	s__Mycobacterium sp008329905	91.2784	1661	1981	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000559085.1	s__Mycobacterium aromaticivorans	91.1585	1629	1981	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001886515.1	s__Mycobacterium sp001886515	86.8167	1573	1981	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.54	98.54	0.94	0.94	2	-
GCF_001021385.1	s__Mycobacterium sp001021385	86.2045	1553	1981	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:14:21,191] [INFO] GTDB search result was written to GCF_002086695.1_ASM208669v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:14:21,191] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:14:21,194] [INFO] DFAST_QC result json was written to GCF_002086695.1_ASM208669v1_genomic.fna/dqc_result.json
[2024-01-24 11:14:21,194] [INFO] DFAST_QC completed!
[2024-01-24 11:14:21,194] [INFO] Total running time: 0h1m45s