[2024-01-24 12:14:35,739] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:35,741] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:35,741] [INFO] DQC Reference Directory: /var/lib/cwl/stg3152de43-8971-4ca1-8c00-24ae6e65eff1/dqc_reference
[2024-01-24 12:14:36,999] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:37,000] [INFO] Task started: Prodigal
[2024-01-24 12:14:37,001] [INFO] Running command: gunzip -c /var/lib/cwl/stgf4833b6d-40b3-4170-94fd-30960b08135e/GCF_005217555.1_ASM521755v1_genomic.fna.gz | prodigal -d GCF_005217555.1_ASM521755v1_genomic.fna/cds.fna -a GCF_005217555.1_ASM521755v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:46,096] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:46,096] [INFO] Task started: HMMsearch
[2024-01-24 12:14:46,096] [INFO] Running command: hmmsearch --tblout GCF_005217555.1_ASM521755v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3152de43-8971-4ca1-8c00-24ae6e65eff1/dqc_reference/reference_markers.hmm GCF_005217555.1_ASM521755v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:46,365] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:46,366] [INFO] Found 6/6 markers.
[2024-01-24 12:14:46,409] [INFO] Query marker FASTA was written to GCF_005217555.1_ASM521755v1_genomic.fna/markers.fasta
[2024-01-24 12:14:46,411] [INFO] Task started: Blastn
[2024-01-24 12:14:46,411] [INFO] Running command: blastn -query GCF_005217555.1_ASM521755v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3152de43-8971-4ca1-8c00-24ae6e65eff1/dqc_reference/reference_markers.fasta -out GCF_005217555.1_ASM521755v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:47,014] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:47,018] [INFO] Selected 10 target genomes.
[2024-01-24 12:14:47,019] [INFO] Target genome list was writen to GCF_005217555.1_ASM521755v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:47,023] [INFO] Task started: fastANI
[2024-01-24 12:14:47,024] [INFO] Running command: fastANI --query /var/lib/cwl/stgf4833b6d-40b3-4170-94fd-30960b08135e/GCF_005217555.1_ASM521755v1_genomic.fna.gz --refList GCF_005217555.1_ASM521755v1_genomic.fna/target_genomes.txt --output GCF_005217555.1_ASM521755v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:56,178] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:56,178] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3152de43-8971-4ca1-8c00-24ae6e65eff1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:56,178] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3152de43-8971-4ca1-8c00-24ae6e65eff1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:56,188] [INFO] Found 9 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 12:14:56,188] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:14:56,188] [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 sphaericus	strain=NRRL B-23268	GCA_005217555.1	1421	1421	suspected-type	True	100.0	1471	1474	95	conclusive
Lysinibacillus sphaericus	strain=DSM 28	GCA_002982115.1	1421	1421	suspected-type	True	99.9988	1471	1474	95	conclusive
Lysinibacillus sphaericus	strain=NCTC10338	GCA_900445465.1	1421	1421	suspected-type	True	99.9987	1472	1474	95	conclusive
Lysinibacillus sphaericus	strain=KCTC 3346	GCA_000427235.1	1421	1421	suspected-type	True	99.9969	1460	1474	95	conclusive
Lysinibacillus sphaericus	strain=NBRC 15095	GCA_006539805.1	1421	1421	suspected-type	True	99.9698	1410	1474	95	conclusive
Lysinibacillus cavernae	strain=SYSU K30005	GCA_009724685.1	2666135	2666135	type	True	81.5595	737	1474	95	below_threshold
Lysinibacillus contaminans	strain=DSM 25560	GCA_001278945.1	1293441	1293441	type	True	80.4281	579	1474	95	below_threshold
Paenisporosarcina cavernae	strain=K2R23-3	GCA_003595195.1	2320858	2320858	type	True	77.9696	84	1474	95	below_threshold
Cytobacillus solani	strain=FJAT-18043	GCA_001420595.1	1637975	1637975	type	True	77.8455	55	1474	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:56,192] [INFO] DFAST Taxonomy check result was written to GCF_005217555.1_ASM521755v1_genomic.fna/tc_result.tsv
[2024-01-24 12:14:56,192] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:56,193] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:56,193] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3152de43-8971-4ca1-8c00-24ae6e65eff1/dqc_reference/checkm_data
[2024-01-24 12:14:56,194] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:56,237] [INFO] Task started: CheckM
[2024-01-24 12:14:56,237] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005217555.1_ASM521755v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005217555.1_ASM521755v1_genomic.fna/checkm_input GCF_005217555.1_ASM521755v1_genomic.fna/checkm_result
[2024-01-24 12:15:28,874] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:28,875] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:28,905] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:28,906] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:28,906] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005217555.1_ASM521755v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:28,906] [INFO] Task started: Blastn
[2024-01-24 12:15:28,906] [INFO] Running command: blastn -query GCF_005217555.1_ASM521755v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3152de43-8971-4ca1-8c00-24ae6e65eff1/dqc_reference/reference_markers_gtdb.fasta -out GCF_005217555.1_ASM521755v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:29,728] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:29,731] [INFO] Selected 8 target genomes.
[2024-01-24 12:15:29,732] [INFO] Target genome list was writen to GCF_005217555.1_ASM521755v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:29,737] [INFO] Task started: fastANI
[2024-01-24 12:15:29,737] [INFO] Running command: fastANI --query /var/lib/cwl/stgf4833b6d-40b3-4170-94fd-30960b08135e/GCF_005217555.1_ASM521755v1_genomic.fna.gz --refList GCF_005217555.1_ASM521755v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005217555.1_ASM521755v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:39,260] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:39,268] [INFO] Found 8 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-24 12:15:39,268] [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_002982115.1	s__Lysinibacillus sphaericus	99.9988	1471	1474	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	96.9114	99.42	98.91	0.95	0.90	10	inconclusive
GCF_003049665.1	s__Lysinibacillus mangiferihumi	96.8986	1294	1474	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_001728805.1	s__Lysinibacillus sphaericus_D	96.1719	1287	1474	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	96.1498	99.28	99.28	0.92	0.92	2	inconclusive
GCA_015999545.1	s__Lysinibacillus sp002340205	86.2745	1147	1474	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_000392615.1	s__Lysinibacillus sphaericus_B	82.5664	841	1474	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	82.5222	886	1474	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	82.2228	773	1474	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_001275675.1	s__Lysinibacillus sp001275675	81.8702	807	1474	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:15:39,271] [INFO] GTDB search result was written to GCF_005217555.1_ASM521755v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:39,272] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:39,274] [INFO] DFAST_QC result json was written to GCF_005217555.1_ASM521755v1_genomic.fna/dqc_result.json
[2024-01-24 12:15:39,275] [INFO] DFAST_QC completed!
[2024-01-24 12:15:39,275] [INFO] Total running time: 0h1m4s