[2023-06-27 17:41:20,646] [INFO] DFAST_QC pipeline started.
[2023-06-27 17:41:20,649] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 17:41:20,650] [INFO] DQC Reference Directory: /var/lib/cwl/stge4035e28-2af9-45eb-a3f3-02932e3e0fb3/dqc_reference
[2023-06-27 17:41:21,986] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 17:41:21,987] [INFO] Task started: Prodigal
[2023-06-27 17:41:21,988] [INFO] Running command: gunzip -c /var/lib/cwl/stg75f929b1-0fc0-47cf-a3cf-4e871ab15623/GCA_002376495.1_ASM237649v1_genomic.fna.gz | prodigal -d GCA_002376495.1_ASM237649v1_genomic.fna/cds.fna -a GCA_002376495.1_ASM237649v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 17:41:30,279] [INFO] Task succeeded: Prodigal
[2023-06-27 17:41:30,280] [INFO] Task started: HMMsearch
[2023-06-27 17:41:30,280] [INFO] Running command: hmmsearch --tblout GCA_002376495.1_ASM237649v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge4035e28-2af9-45eb-a3f3-02932e3e0fb3/dqc_reference/reference_markers.hmm GCA_002376495.1_ASM237649v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 17:41:30,684] [INFO] Task succeeded: HMMsearch
[2023-06-27 17:41:30,685] [INFO] Found 6/6 markers.
[2023-06-27 17:41:30,723] [INFO] Query marker FASTA was written to GCA_002376495.1_ASM237649v1_genomic.fna/markers.fasta
[2023-06-27 17:41:30,723] [INFO] Task started: Blastn
[2023-06-27 17:41:30,724] [INFO] Running command: blastn -query GCA_002376495.1_ASM237649v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge4035e28-2af9-45eb-a3f3-02932e3e0fb3/dqc_reference/reference_markers.fasta -out GCA_002376495.1_ASM237649v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 17:41:31,455] [INFO] Task succeeded: Blastn
[2023-06-27 17:41:31,458] [INFO] Selected 21 target genomes.
[2023-06-27 17:41:31,459] [INFO] Target genome list was writen to GCA_002376495.1_ASM237649v1_genomic.fna/target_genomes.txt
[2023-06-27 17:41:31,465] [INFO] Task started: fastANI
[2023-06-27 17:41:31,465] [INFO] Running command: fastANI --query /var/lib/cwl/stg75f929b1-0fc0-47cf-a3cf-4e871ab15623/GCA_002376495.1_ASM237649v1_genomic.fna.gz --refList GCA_002376495.1_ASM237649v1_genomic.fna/target_genomes.txt --output GCA_002376495.1_ASM237649v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 17:41:51,341] [INFO] Task succeeded: fastANI
[2023-06-27 17:41:51,342] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge4035e28-2af9-45eb-a3f3-02932e3e0fb3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 17:41:51,343] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge4035e28-2af9-45eb-a3f3-02932e3e0fb3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 17:41:51,362] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2023-06-27 17:41:51,362] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-27 17:41:51,363] [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	95.9722	1295	1449	95	conclusive
Lysinibacillus agricola	strain=FJAT-51161	GCA_016638705.1	2590012	2590012	type	True	89.6073	1092	1449	95	below_threshold
Lysinibacillus cavernae	strain=SYSU K30005	GCA_009724685.1	2666135	2666135	type	True	82.1964	827	1449	95	below_threshold
Lysinibacillus parviboronicapiens	strain=BAM-582	GCA_003049575.1	436516	436516	type	True	81.9128	837	1449	95	below_threshold
Lysinibacillus capsici	strain=PB300	GCA_003367505.1	2115968	2115968	type	True	81.8631	788	1449	95	below_threshold
Lysinibacillus fusiformis	strain=ATCC 7055	GCA_003049525.1	28031	28031	type	True	81.7751	807	1449	95	below_threshold
Lysinibacillus mangiferihumi	strain=CCTCC AB 2010389	GCA_005217845.1	1130819	1130819	type	True	81.7543	729	1449	95	below_threshold
Lysinibacillus mangiferihumi	strain=M-GX18	GCA_003049665.1	1130819	1130819	type	True	81.7141	737	1449	95	below_threshold
Lysinibacillus fusiformis	strain=NBRC 15717	GCA_006540205.1	28031	28031	type	True	81.6808	797	1449	95	below_threshold
Lysinibacillus tabacifolii	strain=KCTC 33042	GCA_005217585.1	1173107	1173107	suspected-type	True	81.5752	727	1449	95	below_threshold
Lysinibacillus sphaericus	strain=NBRC 15095	GCA_006539805.1	1421	1421	suspected-type	True	81.5658	739	1449	95	below_threshold
Lysinibacillus varians	strain=NBRC 109424	GCA_005217815.1	1145276	1145276	suspected-type	True	81.5584	722	1449	95	below_threshold
Lysinibacillus varians	strain=GY32	GCA_000600105.1	1145276	1145276	suspected-type	True	81.51	730	1449	95	below_threshold
Lysinibacillus contaminans	strain=DSM 25560	GCA_001278945.1	1293441	1293441	type	True	80.1554	521	1449	95	below_threshold
Solibacillus faecavium	strain=A46	GCA_014836905.1	2762221	2762221	type	True	77.7475	193	1449	95	below_threshold
Solibacillus merdavium	strain=Sa1YVA6	GCA_014836935.1	2762218	2762218	type	True	77.6061	198	1449	95	below_threshold
Bacillus gaemokensis	strain=JCM 15801	GCA_000712615.1	574375	574375	type	True	76.7915	92	1449	95	below_threshold
Bacillus gaemokensis	strain=KCTC 13318	GCA_001590835.1	574375	574375	type	True	76.6954	98	1449	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 17:41:51,365] [INFO] DFAST Taxonomy check result was written to GCA_002376495.1_ASM237649v1_genomic.fna/tc_result.tsv
[2023-06-27 17:41:51,366] [INFO] ===== Taxonomy check completed =====
[2023-06-27 17:41:51,366] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 17:41:51,366] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge4035e28-2af9-45eb-a3f3-02932e3e0fb3/dqc_reference/checkm_data
[2023-06-27 17:41:51,368] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 17:41:51,418] [INFO] Task started: CheckM
[2023-06-27 17:41:51,418] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002376495.1_ASM237649v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002376495.1_ASM237649v1_genomic.fna/checkm_input GCA_002376495.1_ASM237649v1_genomic.fna/checkm_result
[2023-06-27 17:42:21,494] [INFO] Task succeeded: CheckM
[2023-06-27 17:42:21,496] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.74%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 17:42:21,520] [INFO] ===== Completeness check finished =====
[2023-06-27 17:42:21,521] [INFO] ===== Start GTDB Search =====
[2023-06-27 17:42:21,521] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002376495.1_ASM237649v1_genomic.fna/markers.fasta)
[2023-06-27 17:42:21,521] [INFO] Task started: Blastn
[2023-06-27 17:42:21,522] [INFO] Running command: blastn -query GCA_002376495.1_ASM237649v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge4035e28-2af9-45eb-a3f3-02932e3e0fb3/dqc_reference/reference_markers_gtdb.fasta -out GCA_002376495.1_ASM237649v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 17:42:22,249] [INFO] Task succeeded: Blastn
[2023-06-27 17:42:22,254] [INFO] Selected 7 target genomes.
[2023-06-27 17:42:22,254] [INFO] Target genome list was writen to GCA_002376495.1_ASM237649v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 17:42:22,263] [INFO] Task started: fastANI
[2023-06-27 17:42:22,263] [INFO] Running command: fastANI --query /var/lib/cwl/stg75f929b1-0fc0-47cf-a3cf-4e871ab15623/GCA_002376495.1_ASM237649v1_genomic.fna.gz --refList GCA_002376495.1_ASM237649v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002376495.1_ASM237649v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 17:42:33,096] [INFO] Task succeeded: fastANI
[2023-06-27 17:42:33,106] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 17:42:33,106] [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_001183605.1	s__Lysinibacillus xylanilyticus	95.9722	1295	1449	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	95.0	97.05	95.97	0.88	0.83	5	conclusive
GCF_006864135.1	s__Lysinibacillus sp006864135	91.2365	1183	1449	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	95.0	95.97	95.97	0.86	0.86	2	-
GCF_001275675.1	s__Lysinibacillus sp001275675	91.2261	1179	1449	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	89.6044	1200	1449	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_016638705.1	s__Lysinibacillus sp001278875	89.5834	1094	1449	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	88.0746	1109	1449	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_002973635.1	s__Lysinibacillus sp002973635	83.2328	940	1449	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 17:42:33,108] [INFO] GTDB search result was written to GCA_002376495.1_ASM237649v1_genomic.fna/result_gtdb.tsv
[2023-06-27 17:42:33,108] [INFO] ===== GTDB Search completed =====
[2023-06-27 17:42:33,112] [INFO] DFAST_QC result json was written to GCA_002376495.1_ASM237649v1_genomic.fna/dqc_result.json
[2023-06-27 17:42:33,112] [INFO] DFAST_QC completed!
[2023-06-27 17:42:33,112] [INFO] Total running time: 0h1m12s