[2024-01-24 11:44:38,163] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:44:38,165] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:44:38,165] [INFO] DQC Reference Directory: /var/lib/cwl/stg360bcdd2-7c55-4f2e-96f8-f9f5d4441af7/dqc_reference
[2024-01-24 11:44:41,490] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:44:41,491] [INFO] Task started: Prodigal
[2024-01-24 11:44:41,491] [INFO] Running command: gunzip -c /var/lib/cwl/stg73d9d496-c07e-47df-9b15-e828e23bec24/GCF_024169475.1_ASM2416947v1_genomic.fna.gz | prodigal -d GCF_024169475.1_ASM2416947v1_genomic.fna/cds.fna -a GCF_024169475.1_ASM2416947v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:44:54,644] [INFO] Task succeeded: Prodigal
[2024-01-24 11:44:54,645] [INFO] Task started: HMMsearch
[2024-01-24 11:44:54,645] [INFO] Running command: hmmsearch --tblout GCF_024169475.1_ASM2416947v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg360bcdd2-7c55-4f2e-96f8-f9f5d4441af7/dqc_reference/reference_markers.hmm GCF_024169475.1_ASM2416947v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:54,969] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:54,970] [INFO] Found 6/6 markers.
[2024-01-24 11:44:55,030] [INFO] Query marker FASTA was written to GCF_024169475.1_ASM2416947v1_genomic.fna/markers.fasta
[2024-01-24 11:44:55,030] [INFO] Task started: Blastn
[2024-01-24 11:44:55,031] [INFO] Running command: blastn -query GCF_024169475.1_ASM2416947v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg360bcdd2-7c55-4f2e-96f8-f9f5d4441af7/dqc_reference/reference_markers.fasta -out GCF_024169475.1_ASM2416947v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:55,604] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:55,608] [INFO] Selected 9 target genomes.
[2024-01-24 11:44:55,609] [INFO] Target genome list was writen to GCF_024169475.1_ASM2416947v1_genomic.fna/target_genomes.txt
[2024-01-24 11:44:55,650] [INFO] Task started: fastANI
[2024-01-24 11:44:55,651] [INFO] Running command: fastANI --query /var/lib/cwl/stg73d9d496-c07e-47df-9b15-e828e23bec24/GCF_024169475.1_ASM2416947v1_genomic.fna.gz --refList GCF_024169475.1_ASM2416947v1_genomic.fna/target_genomes.txt --output GCF_024169475.1_ASM2416947v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:45:08,430] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:08,431] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg360bcdd2-7c55-4f2e-96f8-f9f5d4441af7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:45:08,431] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg360bcdd2-7c55-4f2e-96f8-f9f5d4441af7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:45:08,444] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:45:08,444] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:45:08,444] [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 frigoritolerans	strain=DSM 8801	GCA_024169475.1	450367	450367	type	True	100.0	1829	1832	95	conclusive
Peribacillus frigoritolerans	strain=FJAT-2396	GCA_001636405.1	450367	450367	type	True	96.9065	1615	1832	95	conclusive
Peribacillus simplex	strain=NBRC 15720	GCA_001591785.1	1478	1478	suspected-type	True	93.2564	1490	1832	95	below_threshold
Peribacillus simplex	strain=DSM 1321	GCA_002243645.1	1478	1478	suspected-type	True	93.2492	1545	1832	95	below_threshold
Peribacillus muralis	strain=DSM 16288	GCA_001439925.1	264697	264697	type	True	84.6769	1164	1832	95	below_threshold
Peribacillus butanolivorans	strain=DSM 18926	GCA_001273755.1	421767	421767	type	True	84.4096	1251	1832	95	below_threshold
Bacillus anthracis	strain=Vollum	GCA_022221345.1	1392	1392	type	True	81.0116	77	1832	95	below_threshold
Bacillus licheniformis	strain=DSM 13	GCA_022630555.1	1402	1402	type	True	79.9208	69	1832	95	below_threshold
Cytobacillus solani	strain=FJAT-18043	GCA_001420595.1	1637975	1637975	type	True	79.0523	124	1832	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:45:08,446] [INFO] DFAST Taxonomy check result was written to GCF_024169475.1_ASM2416947v1_genomic.fna/tc_result.tsv
[2024-01-24 11:45:08,447] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:45:08,447] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:45:08,447] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg360bcdd2-7c55-4f2e-96f8-f9f5d4441af7/dqc_reference/checkm_data
[2024-01-24 11:45:08,448] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:45:08,512] [INFO] Task started: CheckM
[2024-01-24 11:45:08,513] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024169475.1_ASM2416947v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024169475.1_ASM2416947v1_genomic.fna/checkm_input GCF_024169475.1_ASM2416947v1_genomic.fna/checkm_result
[2024-01-24 11:45:51,119] [INFO] Task succeeded: CheckM
[2024-01-24 11:45:51,121] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:45:51,140] [INFO] ===== Completeness check finished =====
[2024-01-24 11:45:51,140] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:45:51,140] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024169475.1_ASM2416947v1_genomic.fna/markers.fasta)
[2024-01-24 11:45:51,141] [INFO] Task started: Blastn
[2024-01-24 11:45:51,141] [INFO] Running command: blastn -query GCF_024169475.1_ASM2416947v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg360bcdd2-7c55-4f2e-96f8-f9f5d4441af7/dqc_reference/reference_markers_gtdb.fasta -out GCF_024169475.1_ASM2416947v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:45:51,899] [INFO] Task succeeded: Blastn
[2024-01-24 11:45:51,902] [INFO] Selected 7 target genomes.
[2024-01-24 11:45:51,902] [INFO] Target genome list was writen to GCF_024169475.1_ASM2416947v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:45:51,924] [INFO] Task started: fastANI
[2024-01-24 11:45:51,924] [INFO] Running command: fastANI --query /var/lib/cwl/stg73d9d496-c07e-47df-9b15-e828e23bec24/GCF_024169475.1_ASM2416947v1_genomic.fna.gz --refList GCF_024169475.1_ASM2416947v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024169475.1_ASM2416947v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:46:05,272] [INFO] Task succeeded: fastANI
[2024-01-24 11:46:05,280] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:46:05,280] [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_001636405.1	s__Peribacillus frigoritolerans	96.9086	1616	1832	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	conclusive
GCF_002835675.1	s__Peribacillus sp002835675	93.3744	1509	1832	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_002243645.1	s__Peribacillus simplex	93.2694	1541	1832	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	-
GCF_018613325.1	s__Peribacillus sp018613325	93.1004	1488	1832	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_900156045.1	s__Peribacillus simplex_D	92.7325	1570	1832	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_017355165.1	s__Peribacillus sp017355165	91.9998	1393	1832	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_001578185.1	s__Peribacillus simplex_A	90.0237	1434	1832	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 11:46:05,282] [INFO] GTDB search result was written to GCF_024169475.1_ASM2416947v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:46:05,283] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:46:05,286] [INFO] DFAST_QC result json was written to GCF_024169475.1_ASM2416947v1_genomic.fna/dqc_result.json
[2024-01-24 11:46:05,286] [INFO] DFAST_QC completed!
[2024-01-24 11:46:05,286] [INFO] Total running time: 0h1m27s