[2024-01-24 13:48:43,401] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:48:43,403] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:48:43,403] [INFO] DQC Reference Directory: /var/lib/cwl/stga4b0d8ea-ef04-458e-a22c-9b4d8cdb8db9/dqc_reference
[2024-01-24 13:48:44,682] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:48:44,683] [INFO] Task started: Prodigal
[2024-01-24 13:48:44,683] [INFO] Running command: gunzip -c /var/lib/cwl/stg5cb8169b-fcec-4dfa-b8be-1bec28def535/GCF_002243645.1_ASM224364v1_genomic.fna.gz | prodigal -d GCF_002243645.1_ASM224364v1_genomic.fna/cds.fna -a GCF_002243645.1_ASM224364v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:48:57,835] [INFO] Task succeeded: Prodigal
[2024-01-24 13:48:57,835] [INFO] Task started: HMMsearch
[2024-01-24 13:48:57,835] [INFO] Running command: hmmsearch --tblout GCF_002243645.1_ASM224364v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga4b0d8ea-ef04-458e-a22c-9b4d8cdb8db9/dqc_reference/reference_markers.hmm GCF_002243645.1_ASM224364v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:48:58,154] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:48:58,156] [INFO] Found 6/6 markers.
[2024-01-24 13:48:58,204] [INFO] Query marker FASTA was written to GCF_002243645.1_ASM224364v1_genomic.fna/markers.fasta
[2024-01-24 13:48:58,205] [INFO] Task started: Blastn
[2024-01-24 13:48:58,205] [INFO] Running command: blastn -query GCF_002243645.1_ASM224364v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga4b0d8ea-ef04-458e-a22c-9b4d8cdb8db9/dqc_reference/reference_markers.fasta -out GCF_002243645.1_ASM224364v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:48:58,798] [INFO] Task succeeded: Blastn
[2024-01-24 13:48:58,803] [INFO] Selected 8 target genomes.
[2024-01-24 13:48:58,804] [INFO] Target genome list was writen to GCF_002243645.1_ASM224364v1_genomic.fna/target_genomes.txt
[2024-01-24 13:48:58,808] [INFO] Task started: fastANI
[2024-01-24 13:48:58,808] [INFO] Running command: fastANI --query /var/lib/cwl/stg5cb8169b-fcec-4dfa-b8be-1bec28def535/GCF_002243645.1_ASM224364v1_genomic.fna.gz --refList GCF_002243645.1_ASM224364v1_genomic.fna/target_genomes.txt --output GCF_002243645.1_ASM224364v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:08,728] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:08,729] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga4b0d8ea-ef04-458e-a22c-9b4d8cdb8db9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:08,729] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga4b0d8ea-ef04-458e-a22c-9b4d8cdb8db9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:08,739] [INFO] Found 6 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:49:08,739] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:08,739] [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=DSM 1321	GCA_002243645.1	1478	1478	suspected-type	True	100.0	1879	1881	95	conclusive
Peribacillus simplex	strain=NBRC 15720	GCA_001591785.1	1478	1478	suspected-type	True	99.939	1781	1881	95	conclusive
Peribacillus frigoritolerans	strain=DSM 8801	GCA_024169475.1	450367	450367	type	True	93.1949	1541	1881	95	below_threshold
Peribacillus frigoritolerans	strain=FJAT-2396	GCA_001636405.1	450367	450367	type	True	93.1262	1556	1881	95	below_threshold
Peribacillus butanolivorans	strain=DSM 18926	GCA_001273755.1	421767	421767	type	True	85.5395	1328	1881	95	below_threshold
Peribacillus muralis	strain=DSM 16288	GCA_001439925.1	264697	264697	type	True	85.092	1208	1881	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:08,741] [INFO] DFAST Taxonomy check result was written to GCF_002243645.1_ASM224364v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:08,741] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:08,741] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:08,742] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga4b0d8ea-ef04-458e-a22c-9b4d8cdb8db9/dqc_reference/checkm_data
[2024-01-24 13:49:08,742] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:08,801] [INFO] Task started: CheckM
[2024-01-24 13:49:08,802] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002243645.1_ASM224364v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002243645.1_ASM224364v1_genomic.fna/checkm_input GCF_002243645.1_ASM224364v1_genomic.fna/checkm_result
[2024-01-24 13:49:52,355] [INFO] Task succeeded: CheckM
[2024-01-24 13:49:52,356] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:49:52,375] [INFO] ===== Completeness check finished =====
[2024-01-24 13:49:52,375] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:49:52,376] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002243645.1_ASM224364v1_genomic.fna/markers.fasta)
[2024-01-24 13:49:52,376] [INFO] Task started: Blastn
[2024-01-24 13:49:52,376] [INFO] Running command: blastn -query GCF_002243645.1_ASM224364v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga4b0d8ea-ef04-458e-a22c-9b4d8cdb8db9/dqc_reference/reference_markers_gtdb.fasta -out GCF_002243645.1_ASM224364v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:53,219] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:53,222] [INFO] Selected 7 target genomes.
[2024-01-24 13:49:53,222] [INFO] Target genome list was writen to GCF_002243645.1_ASM224364v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:49:53,227] [INFO] Task started: fastANI
[2024-01-24 13:49:53,227] [INFO] Running command: fastANI --query /var/lib/cwl/stg5cb8169b-fcec-4dfa-b8be-1bec28def535/GCF_002243645.1_ASM224364v1_genomic.fna.gz --refList GCF_002243645.1_ASM224364v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002243645.1_ASM224364v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:05,761] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:05,769] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:05,770] [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	100.0	1880	1881	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	94.4523	1441	1881	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	94.1102	1473	1881	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	93.8718	1547	1881	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	93.7982	1594	1881	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	93.1191	1554	1881	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	91.0229	1426	1881	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 13:50:05,771] [INFO] GTDB search result was written to GCF_002243645.1_ASM224364v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:05,772] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:05,775] [INFO] DFAST_QC result json was written to GCF_002243645.1_ASM224364v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:05,776] [INFO] DFAST_QC completed!
[2024-01-24 13:50:05,776] [INFO] Total running time: 0h1m22s