[2024-01-24 12:31:04,059] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:04,061] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:04,061] [INFO] DQC Reference Directory: /var/lib/cwl/stg998f00e5-a978-45b5-87a0-4279194e301e/dqc_reference
[2024-01-24 12:31:05,252] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:05,253] [INFO] Task started: Prodigal
[2024-01-24 12:31:05,253] [INFO] Running command: gunzip -c /var/lib/cwl/stgb848d586-1583-4f83-aa24-1c32c97eba9b/GCF_000299035.1_ASM29903v1_genomic.fna.gz | prodigal -d GCF_000299035.1_ASM29903v1_genomic.fna/cds.fna -a GCF_000299035.1_ASM29903v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:16,049] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:16,050] [INFO] Task started: HMMsearch
[2024-01-24 12:31:16,050] [INFO] Running command: hmmsearch --tblout GCF_000299035.1_ASM29903v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg998f00e5-a978-45b5-87a0-4279194e301e/dqc_reference/reference_markers.hmm GCF_000299035.1_ASM29903v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:16,372] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:16,374] [INFO] Found 6/6 markers.
[2024-01-24 12:31:16,433] [INFO] Query marker FASTA was written to GCF_000299035.1_ASM29903v1_genomic.fna/markers.fasta
[2024-01-24 12:31:16,433] [INFO] Task started: Blastn
[2024-01-24 12:31:16,433] [INFO] Running command: blastn -query GCF_000299035.1_ASM29903v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg998f00e5-a978-45b5-87a0-4279194e301e/dqc_reference/reference_markers.fasta -out GCF_000299035.1_ASM29903v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:17,053] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:17,058] [INFO] Selected 16 target genomes.
[2024-01-24 12:31:17,058] [INFO] Target genome list was writen to GCF_000299035.1_ASM29903v1_genomic.fna/target_genomes.txt
[2024-01-24 12:31:17,085] [INFO] Task started: fastANI
[2024-01-24 12:31:17,085] [INFO] Running command: fastANI --query /var/lib/cwl/stgb848d586-1583-4f83-aa24-1c32c97eba9b/GCF_000299035.1_ASM29903v1_genomic.fna.gz --refList GCF_000299035.1_ASM29903v1_genomic.fna/target_genomes.txt --output GCF_000299035.1_ASM29903v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:31:33,931] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:33,932] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg998f00e5-a978-45b5-87a0-4279194e301e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:31:33,932] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg998f00e5-a978-45b5-87a0-4279194e301e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:31:33,948] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:31:33,948] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:31:33,948] [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
Bacillus gaemokensis	strain=KCTC 13318	GCA_001590835.1	574375	574375	type	True	87.516	1354	1794	95	below_threshold
Bacillus gaemokensis	strain=JCM 15801	GCA_000712615.1	574375	574375	type	True	87.5074	1320	1794	95	below_threshold
Bacillus clarus	strain=BHP	GCA_000746925.1	2338372	2338372	type	True	84.7237	1240	1794	95	below_threshold
Bacillus clarus	strain=PS00077A	GCA_003428195.1	2338372	2338372	type	True	84.6746	1199	1794	95	below_threshold
Bacillus mycoides	strain=DSM 2048	GCA_022630575.1	1405	1405	type	True	83.6703	1156	1794	95	below_threshold
Bacillus cereus	strain=FSL M8-0473	GCA_002014665.1	1396	1396	suspected-type	True	83.6619	1044	1794	95	below_threshold
Bacillus cereus	strain=ATCC 14579	GCA_006094295.1	1396	1396	suspected-type	True	83.6082	1083	1794	95	below_threshold
Bacillus cereus	strain=ATCC 14579	GCA_000007825.1	1396	1396	suspected-type	True	83.5615	1071	1794	95	below_threshold
Bacillus cytotoxicus	strain=NVH 391-98	GCA_000017425.1	580165	580165	type	True	83.4567	934	1794	95	below_threshold
Bacillus anthracis	strain=Vollum	GCA_022221345.1	1392	1392	type	True	83.4138	1076	1794	95	below_threshold
Bacillus anthracis	strain=Vollum	GCA_000742895.1	1392	1392	type	True	83.3416	1100	1794	95	below_threshold
Bacillus sanguinis	strain=BML-BC004	GCA_018332475.1	2817476	2817476	type	True	83.2705	979	1794	95	below_threshold
Bacillus anthracis	strain=Vollum	GCA_000167275.1	1392	1392	type	True	83.2522	1081	1794	95	below_threshold
Gottfriedia endophyticus	strain=RG28	GCA_017814275.1	2820819	2820819	type	True	77.5981	166	1794	95	below_threshold
Anoxybacillus kestanbolensis	strain=NCIMB 13971	GCA_023653015.1	227476	227476	type	True	76.9021	72	1794	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:31:33,950] [INFO] DFAST Taxonomy check result was written to GCF_000299035.1_ASM29903v1_genomic.fna/tc_result.tsv
[2024-01-24 12:31:33,951] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:31:33,951] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:31:33,951] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg998f00e5-a978-45b5-87a0-4279194e301e/dqc_reference/checkm_data
[2024-01-24 12:31:33,952] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:31:34,004] [INFO] Task started: CheckM
[2024-01-24 12:31:34,004] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000299035.1_ASM29903v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000299035.1_ASM29903v1_genomic.fna/checkm_input GCF_000299035.1_ASM29903v1_genomic.fna/checkm_result
[2024-01-24 12:32:10,318] [INFO] Task succeeded: CheckM
[2024-01-24 12:32:10,320] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:32:10,349] [INFO] ===== Completeness check finished =====
[2024-01-24 12:32:10,349] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:32:10,349] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000299035.1_ASM29903v1_genomic.fna/markers.fasta)
[2024-01-24 12:32:10,350] [INFO] Task started: Blastn
[2024-01-24 12:32:10,350] [INFO] Running command: blastn -query GCF_000299035.1_ASM29903v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg998f00e5-a978-45b5-87a0-4279194e301e/dqc_reference/reference_markers_gtdb.fasta -out GCF_000299035.1_ASM29903v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:11,110] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:11,114] [INFO] Selected 7 target genomes.
[2024-01-24 12:32:11,114] [INFO] Target genome list was writen to GCF_000299035.1_ASM29903v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:32:11,121] [INFO] Task started: fastANI
[2024-01-24 12:32:11,121] [INFO] Running command: fastANI --query /var/lib/cwl/stgb848d586-1583-4f83-aa24-1c32c97eba9b/GCF_000299035.1_ASM29903v1_genomic.fna.gz --refList GCF_000299035.1_ASM29903v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000299035.1_ASM29903v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:32:21,777] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:21,791] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:32:21,791] [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_000299035.1	s__Bacillus_A bingmayongensis	100.0	1792	1794	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	97.40	97.40	0.86	0.86	2	conclusive
GCF_013314535.1	s__Bacillus_A sp013314535	90.4266	1380	1794	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	99.95	99.95	0.99	0.99	2	-
GCF_000161455.1	s__Bacillus_A pseudomycoides	90.2189	1377	1794	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	97.62	95.81	0.91	0.85	116	-
GCF_002559665.1	s__Bacillus_A cereus_AV	90.0213	1349	1794	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002584535.1	s__Bacillus_A cereus_AW	89.3143	1296	1794	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	99.12	98.24	0.93	0.90	5	-
GCF_002561295.1	s__Bacillus_A cereus_S	88.7125	1242	1794	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	99.16	96.34	0.94	0.87	9	-
GCF_002551815.1	s__Bacillus_A sp002551815	86.967	1127	1794	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	99.80	99.69	0.94	0.92	5	-
--------------------------------------------------------------------------------
[2024-01-24 12:32:21,793] [INFO] GTDB search result was written to GCF_000299035.1_ASM29903v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:32:21,794] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:32:21,797] [INFO] DFAST_QC result json was written to GCF_000299035.1_ASM29903v1_genomic.fna/dqc_result.json
[2024-01-24 12:32:21,797] [INFO] DFAST_QC completed!
[2024-01-24 12:32:21,797] [INFO] Total running time: 0h1m18s