[2024-01-24 12:37:24,290] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:37:24,291] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:37:24,292] [INFO] DQC Reference Directory: /var/lib/cwl/stgc1b56ba8-413c-4a9e-8b2e-fa4bf6b0701b/dqc_reference
[2024-01-24 12:37:25,661] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:37:25,661] [INFO] Task started: Prodigal
[2024-01-24 12:37:25,662] [INFO] Running command: gunzip -c /var/lib/cwl/stge3364244-b616-470e-890f-91bd8eb32fdc/GCF_003049575.1_ASM304957v1_genomic.fna.gz | prodigal -d GCF_003049575.1_ASM304957v1_genomic.fna/cds.fna -a GCF_003049575.1_ASM304957v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:35,305] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:35,305] [INFO] Task started: HMMsearch
[2024-01-24 12:37:35,306] [INFO] Running command: hmmsearch --tblout GCF_003049575.1_ASM304957v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc1b56ba8-413c-4a9e-8b2e-fa4bf6b0701b/dqc_reference/reference_markers.hmm GCF_003049575.1_ASM304957v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:37:35,606] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:37:35,608] [INFO] Found 6/6 markers.
[2024-01-24 12:37:35,649] [INFO] Query marker FASTA was written to GCF_003049575.1_ASM304957v1_genomic.fna/markers.fasta
[2024-01-24 12:37:35,650] [INFO] Task started: Blastn
[2024-01-24 12:37:35,650] [INFO] Running command: blastn -query GCF_003049575.1_ASM304957v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc1b56ba8-413c-4a9e-8b2e-fa4bf6b0701b/dqc_reference/reference_markers.fasta -out GCF_003049575.1_ASM304957v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:36,261] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:36,265] [INFO] Selected 19 target genomes.
[2024-01-24 12:37:36,265] [INFO] Target genome list was writen to GCF_003049575.1_ASM304957v1_genomic.fna/target_genomes.txt
[2024-01-24 12:37:36,272] [INFO] Task started: fastANI
[2024-01-24 12:37:36,272] [INFO] Running command: fastANI --query /var/lib/cwl/stge3364244-b616-470e-890f-91bd8eb32fdc/GCF_003049575.1_ASM304957v1_genomic.fna.gz --refList GCF_003049575.1_ASM304957v1_genomic.fna/target_genomes.txt --output GCF_003049575.1_ASM304957v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:37:53,166] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:53,167] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc1b56ba8-413c-4a9e-8b2e-fa4bf6b0701b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:37:53,168] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc1b56ba8-413c-4a9e-8b2e-fa4bf6b0701b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:37:53,186] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:37:53,186] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:37:53,187] [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 parviboronicapiens	strain=BAM-582	GCA_003049575.1	436516	436516	type	True	100.0	1529	1532	95	conclusive
Lysinibacillus sphaericus	strain=KCTC 3346	GCA_000427235.1	1421	1421	suspected-type	True	82.6519	855	1532	95	below_threshold
Lysinibacillus mangiferihumi	strain=M-GX18	GCA_003049665.1	1130819	1130819	type	True	82.6255	868	1532	95	below_threshold
Lysinibacillus tabacifolii	strain=KCTC 33042	GCA_005217585.1	1173107	1173107	suspected-type	True	82.6179	867	1532	95	below_threshold
Lysinibacillus tabacifolii	strain=K3514	GCA_003049565.1	1173107	1173107	suspected-type	True	82.584	872	1532	95	below_threshold
Lysinibacillus sphaericus	strain=NRRL B-23268	GCA_005217555.1	1421	1421	suspected-type	True	82.5684	851	1532	95	below_threshold
Lysinibacillus mangiferihumi	strain=CCTCC AB 2010389	GCA_005217845.1	1130819	1130819	type	True	82.5634	865	1532	95	below_threshold
Lysinibacillus varians	strain=NBRC 109424	GCA_005217815.1	1145276	1145276	suspected-type	True	82.5308	865	1532	95	below_threshold
Lysinibacillus sphaericus	strain=NBRC 15095	GCA_006539805.1	1421	1421	suspected-type	True	82.5256	848	1532	95	below_threshold
Lysinibacillus varians	strain=GY32	GCA_000600105.1	1145276	1145276	suspected-type	True	82.5074	861	1532	95	below_threshold
Lysinibacillus sphaericus	strain=NCTC10338	GCA_900445465.1	1421	1421	suspected-type	True	82.477	876	1532	95	below_threshold
Lysinibacillus agricola	strain=FJAT-51161	GCA_016638705.1	2590012	2590012	type	True	82.3324	885	1532	95	below_threshold
Lysinibacillus xylanilyticus	strain=DSM 23493	GCA_001183605.1	582475	582475	type	True	82.0958	915	1532	95	below_threshold
Lysinibacillus cavernae	strain=SYSU K30005	GCA_009724685.1	2666135	2666135	type	True	81.4622	796	1532	95	below_threshold
Lysinibacillus macroides	strain=DSM 54	GCA_001281525.1	33935	33935	type	True	80.9904	684	1532	95	below_threshold
Lysinibacillus contaminans	strain=DSM 25560	GCA_001278945.1	1293441	1293441	type	True	80.5353	684	1532	95	below_threshold
Solibacillus merdavium	strain=Sa1YVA6	GCA_014836935.1	2762218	2762218	type	True	78.5765	197	1532	95	below_threshold
Solibacillus faecavium	strain=A46	GCA_014836905.1	2762221	2762221	type	True	78.0786	212	1532	95	below_threshold
Ureibacillus chungkukjangi	strain=2RL32	GCA_003049615.1	1202712	1202712	type	True	77.8846	216	1532	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:37:53,189] [INFO] DFAST Taxonomy check result was written to GCF_003049575.1_ASM304957v1_genomic.fna/tc_result.tsv
[2024-01-24 12:37:53,190] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:37:53,190] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:37:53,190] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc1b56ba8-413c-4a9e-8b2e-fa4bf6b0701b/dqc_reference/checkm_data
[2024-01-24 12:37:53,191] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:37:53,236] [INFO] Task started: CheckM
[2024-01-24 12:37:53,236] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003049575.1_ASM304957v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003049575.1_ASM304957v1_genomic.fna/checkm_input GCF_003049575.1_ASM304957v1_genomic.fna/checkm_result
[2024-01-24 12:38:26,804] [INFO] Task succeeded: CheckM
[2024-01-24 12:38:26,805] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:38:26,833] [INFO] ===== Completeness check finished =====
[2024-01-24 12:38:26,834] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:38:26,834] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003049575.1_ASM304957v1_genomic.fna/markers.fasta)
[2024-01-24 12:38:26,835] [INFO] Task started: Blastn
[2024-01-24 12:38:26,835] [INFO] Running command: blastn -query GCF_003049575.1_ASM304957v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc1b56ba8-413c-4a9e-8b2e-fa4bf6b0701b/dqc_reference/reference_markers_gtdb.fasta -out GCF_003049575.1_ASM304957v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:38:27,576] [INFO] Task succeeded: Blastn
[2024-01-24 12:38:27,580] [INFO] Selected 13 target genomes.
[2024-01-24 12:38:27,580] [INFO] Target genome list was writen to GCF_003049575.1_ASM304957v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:38:27,588] [INFO] Task started: fastANI
[2024-01-24 12:38:27,588] [INFO] Running command: fastANI --query /var/lib/cwl/stge3364244-b616-470e-890f-91bd8eb32fdc/GCF_003049575.1_ASM304957v1_genomic.fna.gz --refList GCF_003049575.1_ASM304957v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003049575.1_ASM304957v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:38:41,720] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:41,735] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:38:41,735] [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_003049575.1	s__Lysinibacillus parviboronicapiens	100.0	1529	1532	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	95.0	99.01	98.61	0.95	0.92	4	conclusive
GCF_000392615.1	s__Lysinibacillus sphaericus_B	89.695	1273	1532	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007362955.1	s__Lysinibacillus fusiformis_E	89.1211	1274	1532	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_003049665.1	s__Lysinibacillus mangiferihumi	82.6191	869	1532	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	96.9114	99.98	99.98	0.98	0.98	2	-
GCA_015999545.1	s__Lysinibacillus sp002340205	82.5555	877	1532	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	95.0	98.79	97.71	0.94	0.94	5	-
GCF_002982115.1	s__Lysinibacillus sphaericus	82.5552	877	1532	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_001728805.1	s__Lysinibacillus sphaericus_D	82.5339	856	1532	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	96.1498	99.28	99.28	0.92	0.92	2	-
GCF_016638705.1	s__Lysinibacillus sp001278875	82.3305	885	1532	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_001708185.1	s__Lysinibacillus xylanilyticus_A	82.2345	884	1532	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_001183605.1	s__Lysinibacillus xylanilyticus	82.0872	916	1532	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	95.0	97.05	95.97	0.88	0.83	5	-
GCF_001275675.1	s__Lysinibacillus sp001275675	82.0502	914	1532	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_002237755.1	s__Lysinibacillus sp002237755	82.0474	910	1532	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	95.0	96.32	95.08	0.88	0.84	5	-
GCF_001281525.1	s__Lysinibacillus macroides	80.9965	683	1532	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	95.0	99.95	99.95	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:38:41,737] [INFO] GTDB search result was written to GCF_003049575.1_ASM304957v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:38:41,738] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:38:41,745] [INFO] DFAST_QC result json was written to GCF_003049575.1_ASM304957v1_genomic.fna/dqc_result.json
[2024-01-24 12:38:41,745] [INFO] DFAST_QC completed!
[2024-01-24 12:38:41,745] [INFO] Total running time: 0h1m17s