[2024-01-25 18:54:35,619] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:54:35,621] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:54:35,621] [INFO] DQC Reference Directory: /var/lib/cwl/stge164543f-abe3-4fcb-a968-3574b8069b29/dqc_reference
[2024-01-25 18:54:36,745] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:54:36,746] [INFO] Task started: Prodigal
[2024-01-25 18:54:36,746] [INFO] Running command: gunzip -c /var/lib/cwl/stg2e25a132-9683-4d99-a2b8-862965ca473a/GCF_003049505.1_ASM304950v1_genomic.fna.gz | prodigal -d GCF_003049505.1_ASM304950v1_genomic.fna/cds.fna -a GCF_003049505.1_ASM304950v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:54:44,271] [INFO] Task succeeded: Prodigal
[2024-01-25 18:54:44,271] [INFO] Task started: HMMsearch
[2024-01-25 18:54:44,271] [INFO] Running command: hmmsearch --tblout GCF_003049505.1_ASM304950v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge164543f-abe3-4fcb-a968-3574b8069b29/dqc_reference/reference_markers.hmm GCF_003049505.1_ASM304950v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:54:44,515] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:54:44,526] [INFO] Found 6/6 markers.
[2024-01-25 18:54:44,565] [INFO] Query marker FASTA was written to GCF_003049505.1_ASM304950v1_genomic.fna/markers.fasta
[2024-01-25 18:54:44,565] [INFO] Task started: Blastn
[2024-01-25 18:54:44,565] [INFO] Running command: blastn -query GCF_003049505.1_ASM304950v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge164543f-abe3-4fcb-a968-3574b8069b29/dqc_reference/reference_markers.fasta -out GCF_003049505.1_ASM304950v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:54:45,137] [INFO] Task succeeded: Blastn
[2024-01-25 18:54:45,140] [INFO] Selected 24 target genomes.
[2024-01-25 18:54:45,140] [INFO] Target genome list was writen to GCF_003049505.1_ASM304950v1_genomic.fna/target_genomes.txt
[2024-01-25 18:54:45,160] [INFO] Task started: fastANI
[2024-01-25 18:54:45,160] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e25a132-9683-4d99-a2b8-862965ca473a/GCF_003049505.1_ASM304950v1_genomic.fna.gz --refList GCF_003049505.1_ASM304950v1_genomic.fna/target_genomes.txt --output GCF_003049505.1_ASM304950v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:55:01,584] [INFO] Task succeeded: fastANI
[2024-01-25 18:55:01,585] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge164543f-abe3-4fcb-a968-3574b8069b29/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:55:01,585] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge164543f-abe3-4fcb-a968-3574b8069b29/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:55:01,598] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:55:01,598] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:55:01,598] [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
Lysinibacillus xylanilyticus	strain=DSM 23493	GCA_001183605.1	582475	582475	type	True	78.3767	235	1315	95	below_threshold
Lysinibacillus varians	strain=GY32	GCA_000600105.1	1145276	1145276	suspected-type	True	78.284	217	1315	95	below_threshold
Lysinibacillus varians	strain=NBRC 109424	GCA_005217815.1	1145276	1145276	suspected-type	True	78.2627	212	1315	95	below_threshold
Solibacillus cecembensis	strain=DSM 21993	GCA_001439635.1	459347	459347	type	True	78.2503	267	1315	95	below_threshold
Lysinibacillus sphaericus	strain=NRRL B-23268	GCA_005217555.1	1421	1421	suspected-type	True	78.2344	217	1315	95	below_threshold
Lysinibacillus sphaericus	strain=NCTC10338	GCA_900445465.1	1421	1421	suspected-type	True	78.1745	221	1315	95	below_threshold
Lysinibacillus agricola	strain=FJAT-51161	GCA_016638705.1	2590012	2590012	type	True	78.171	240	1315	95	below_threshold
Lysinibacillus fusiformis	strain=NRRL NRS-350	GCA_003367495.1	28031	28031	type	True	78.1072	239	1315	95	below_threshold
Lysinibacillus fusiformis	strain=ATCC 7055	GCA_003049525.1	28031	28031	type	True	78.0885	243	1315	95	below_threshold
Lysinibacillus sphaericus	strain=NBRC 15095	GCA_006539805.1	1421	1421	suspected-type	True	78.0671	216	1315	95	below_threshold
Solibacillus merdavium	strain=Sa1YVA6	GCA_014836935.1	2762218	2762218	type	True	78.0403	229	1315	95	below_threshold
Lysinibacillus mangiferihumi	strain=M-GX18	GCA_003049665.1	1130819	1130819	type	True	78.0304	227	1315	95	below_threshold
Lysinibacillus fusiformis	strain=NBRC 15717	GCA_006540205.1	28031	28031	type	True	78.0302	239	1315	95	below_threshold
Lysinibacillus mangiferihumi	strain=CCTCC AB 2010389	GCA_005217845.1	1130819	1130819	type	True	78.0106	227	1315	95	below_threshold
Caryophanon tenue	strain=DSM 14152	GCA_001700315.1	33978	33978	type	True	78.0057	203	1315	95	below_threshold
Lysinibacillus macroides	strain=DSM 54	GCA_001281525.1	33935	33935	type	True	78.0045	279	1315	95	below_threshold
Lysinibacillus parviboronicapiens	strain=BAM-582	GCA_003049575.1	436516	436516	type	True	77.959	239	1315	95	below_threshold
Lysinibacillus cavernae	strain=SYSU K30005	GCA_009724685.1	2666135	2666135	type	True	77.9239	245	1315	95	below_threshold
Lysinibacillus boronitolerans	strain=NBRC 103108	GCA_002200915.1	309788	309788	type	True	77.8276	235	1315	95	below_threshold
Lysinibacillus boronitolerans	strain=NBRC 103108	GCA_000772935.1	309788	309788	type	True	77.8276	235	1315	95	below_threshold
Psychrobacillus faecigallinarum	strain=Sa2BUA9	GCA_014836595.1	2762235	2762235	type	True	77.3765	69	1315	95	below_threshold
Lysinibacillus contaminans	strain=DSM 25560	GCA_001278945.1	1293441	1293441	type	True	77.2308	178	1315	95	below_threshold
Bacillus anthracis	strain=Vollum	GCA_022221345.1	1392	1392	type	True	76.5235	62	1315	95	below_threshold
Metabacillus bambusae	strain=BG109	GCA_017497975.1	2795218	2795218	type	True	75.9118	59	1315	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:55:01,600] [INFO] DFAST Taxonomy check result was written to GCF_003049505.1_ASM304950v1_genomic.fna/tc_result.tsv
[2024-01-25 18:55:01,601] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:55:01,601] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:55:01,601] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge164543f-abe3-4fcb-a968-3574b8069b29/dqc_reference/checkm_data
[2024-01-25 18:55:01,602] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:55:01,645] [INFO] Task started: CheckM
[2024-01-25 18:55:01,646] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003049505.1_ASM304950v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003049505.1_ASM304950v1_genomic.fna/checkm_input GCF_003049505.1_ASM304950v1_genomic.fna/checkm_result
[2024-01-25 18:55:28,240] [INFO] Task succeeded: CheckM
[2024-01-25 18:55:28,240] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:55:28,263] [INFO] ===== Completeness check finished =====
[2024-01-25 18:55:28,263] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:55:28,263] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003049505.1_ASM304950v1_genomic.fna/markers.fasta)
[2024-01-25 18:55:28,263] [INFO] Task started: Blastn
[2024-01-25 18:55:28,263] [INFO] Running command: blastn -query GCF_003049505.1_ASM304950v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge164543f-abe3-4fcb-a968-3574b8069b29/dqc_reference/reference_markers_gtdb.fasta -out GCF_003049505.1_ASM304950v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:55:29,004] [INFO] Task succeeded: Blastn
[2024-01-25 18:55:29,007] [INFO] Selected 15 target genomes.
[2024-01-25 18:55:29,007] [INFO] Target genome list was writen to GCF_003049505.1_ASM304950v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:55:29,013] [INFO] Task started: fastANI
[2024-01-25 18:55:29,014] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e25a132-9683-4d99-a2b8-862965ca473a/GCF_003049505.1_ASM304950v1_genomic.fna.gz --refList GCF_003049505.1_ASM304950v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003049505.1_ASM304950v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:55:40,709] [INFO] Task succeeded: fastANI
[2024-01-25 18:55:40,719] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:55:40,719] [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_003049505.1	s__Metasolibacillus meyeri	100.0	1302	1315	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Metasolibacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000612805.1	s__Metasolibacillus ndiopicus	83.3793	890	1315	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Metasolibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003049645.1	s__Metasolibacillus fluoroglycofenilyticus	83.0069	827	1315	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Metasolibacillus	95.0	98.96	98.96	0.94	0.94	2	-
GCA_002360295.1	s__Metasolibacillus sp002360295	78.5333	263	1315	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Metasolibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002736105.1	s__Solibacillus sp002736105	78.3373	272	1315	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Solibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002982115.1	s__Lysinibacillus sphaericus	78.2666	211	1315	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	96.9114	99.42	98.91	0.95	0.90	10	-
GCF_001708185.1	s__Lysinibacillus xylanilyticus_A	78.2306	239	1315	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001439635.1	s__Solibacillus cecembensis	78.2293	268	1315	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Solibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002973635.1	s__Lysinibacillus sp002973635	78.1682	260	1315	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016638705.1	s__Lysinibacillus sp001278875	78.1557	241	1315	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	95.0	99.95	99.95	0.96	0.96	2	-
GCF_014836935.1	s__Solibacillus sp014836935	78.0249	230	1315	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Solibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003049665.1	s__Lysinibacillus mangiferihumi	78.0145	228	1315	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	96.9114	99.98	99.98	0.98	0.98	2	-
GCF_001281525.1	s__Lysinibacillus macroides	78.0066	280	1315	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	95.0	99.95	99.95	0.98	0.98	2	-
GCF_001700315.1	s__Caryophanon tenue	78.0057	203	1315	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Caryophanon	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001275675.1	s__Lysinibacillus sp001275675	77.8397	246	1315	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:55:40,721] [INFO] GTDB search result was written to GCF_003049505.1_ASM304950v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:55:40,721] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:55:40,724] [INFO] DFAST_QC result json was written to GCF_003049505.1_ASM304950v1_genomic.fna/dqc_result.json
[2024-01-25 18:55:40,725] [INFO] DFAST_QC completed!
[2024-01-25 18:55:40,725] [INFO] Total running time: 0h1m5s