[2024-01-24 14:06:30,610] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:30,612] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:30,612] [INFO] DQC Reference Directory: /var/lib/cwl/stga4a31c64-2622-4029-8927-7c9e6237413d/dqc_reference
[2024-01-24 14:06:32,245] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:32,250] [INFO] Task started: Prodigal
[2024-01-24 14:06:32,250] [INFO] Running command: gunzip -c /var/lib/cwl/stgd66b9ecd-15f2-43b4-9425-c673b90e0765/GCF_001591785.1_ASM159178v1_genomic.fna.gz | prodigal -d GCF_001591785.1_ASM159178v1_genomic.fna/cds.fna -a GCF_001591785.1_ASM159178v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:45,132] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:45,133] [INFO] Task started: HMMsearch
[2024-01-24 14:06:45,133] [INFO] Running command: hmmsearch --tblout GCF_001591785.1_ASM159178v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga4a31c64-2622-4029-8927-7c9e6237413d/dqc_reference/reference_markers.hmm GCF_001591785.1_ASM159178v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:45,494] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:45,496] [INFO] Found 6/6 markers.
[2024-01-24 14:06:45,555] [INFO] Query marker FASTA was written to GCF_001591785.1_ASM159178v1_genomic.fna/markers.fasta
[2024-01-24 14:06:45,555] [INFO] Task started: Blastn
[2024-01-24 14:06:45,556] [INFO] Running command: blastn -query GCF_001591785.1_ASM159178v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga4a31c64-2622-4029-8927-7c9e6237413d/dqc_reference/reference_markers.fasta -out GCF_001591785.1_ASM159178v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:46,244] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:46,247] [INFO] Selected 8 target genomes.
[2024-01-24 14:06:46,247] [INFO] Target genome list was writen to GCF_001591785.1_ASM159178v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:46,273] [INFO] Task started: fastANI
[2024-01-24 14:06:46,274] [INFO] Running command: fastANI --query /var/lib/cwl/stgd66b9ecd-15f2-43b4-9425-c673b90e0765/GCF_001591785.1_ASM159178v1_genomic.fna.gz --refList GCF_001591785.1_ASM159178v1_genomic.fna/target_genomes.txt --output GCF_001591785.1_ASM159178v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:55,834] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:55,834] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga4a31c64-2622-4029-8927-7c9e6237413d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:55,835] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga4a31c64-2622-4029-8927-7c9e6237413d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:55,842] [INFO] Found 6 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:06:55,842] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:55,842] [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
Peribacillus simplex	strain=NBRC 15720	GCA_001591785.1	1478	1478	suspected-type	True	100.0	1776	1780	95	conclusive
Peribacillus simplex	strain=DSM 1321	GCA_002243645.1	1478	1478	suspected-type	True	99.9975	1780	1780	95	conclusive
Peribacillus frigoritolerans	strain=DSM 8801	GCA_024169475.1	450367	450367	type	True	93.2611	1479	1780	95	below_threshold
Peribacillus frigoritolerans	strain=FJAT-2396	GCA_001636405.1	450367	450367	type	True	93.1601	1502	1780	95	below_threshold
Peribacillus butanolivorans	strain=DSM 18926	GCA_001273755.1	421767	421767	type	True	85.4465	1311	1780	95	below_threshold
Peribacillus muralis	strain=DSM 16288	GCA_001439925.1	264697	264697	type	True	85.089	1174	1780	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:55,844] [INFO] DFAST Taxonomy check result was written to GCF_001591785.1_ASM159178v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:55,844] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:55,844] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:55,845] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga4a31c64-2622-4029-8927-7c9e6237413d/dqc_reference/checkm_data
[2024-01-24 14:06:55,846] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:55,899] [INFO] Task started: CheckM
[2024-01-24 14:06:55,899] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001591785.1_ASM159178v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001591785.1_ASM159178v1_genomic.fna/checkm_input GCF_001591785.1_ASM159178v1_genomic.fna/checkm_result
[2024-01-24 14:07:38,468] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:38,469] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:38,489] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:38,489] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:38,490] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001591785.1_ASM159178v1_genomic.fna/markers.fasta)
[2024-01-24 14:07:38,490] [INFO] Task started: Blastn
[2024-01-24 14:07:38,491] [INFO] Running command: blastn -query GCF_001591785.1_ASM159178v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga4a31c64-2622-4029-8927-7c9e6237413d/dqc_reference/reference_markers_gtdb.fasta -out GCF_001591785.1_ASM159178v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:39,251] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:39,255] [INFO] Selected 7 target genomes.
[2024-01-24 14:07:39,255] [INFO] Target genome list was writen to GCF_001591785.1_ASM159178v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:39,262] [INFO] Task started: fastANI
[2024-01-24 14:07:39,263] [INFO] Running command: fastANI --query /var/lib/cwl/stgd66b9ecd-15f2-43b4-9425-c673b90e0765/GCF_001591785.1_ASM159178v1_genomic.fna.gz --refList GCF_001591785.1_ASM159178v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001591785.1_ASM159178v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:49,790] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:49,797] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:49,798] [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_002243645.1	s__Peribacillus simplex	99.9975	1780	1780	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Peribacillus	95.0	99.44	98.94	0.96	0.92	4	conclusive
GCF_017355165.1	s__Peribacillus sp017355165	94.5813	1404	1780	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Peribacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018613325.1	s__Peribacillus sp018613325	94.1179	1459	1780	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Peribacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002835675.1	s__Peribacillus sp002835675	93.9472	1505	1780	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Peribacillus	95.0	96.47	96.35	0.90	0.87	3	-
GCF_900156045.1	s__Peribacillus simplex_D	93.8675	1559	1780	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Peribacillus	95.0	95.46	95.05	0.86	0.84	7	-
GCF_001636405.1	s__Peribacillus frigoritolerans	93.1601	1502	1780	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Peribacillus	95.0	97.03	95.65	0.88	0.82	39	-
GCF_001578185.1	s__Peribacillus simplex_A	91.1149	1378	1780	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Peribacillus	95.0	97.63	97.17	0.91	0.91	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:07:49,800] [INFO] GTDB search result was written to GCF_001591785.1_ASM159178v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:49,800] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:49,803] [INFO] DFAST_QC result json was written to GCF_001591785.1_ASM159178v1_genomic.fna/dqc_result.json
[2024-01-24 14:07:49,804] [INFO] DFAST_QC completed!
[2024-01-24 14:07:49,804] [INFO] Total running time: 0h1m19s