[2024-01-24 12:15:19,120] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:15:19,124] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:15:19,125] [INFO] DQC Reference Directory: /var/lib/cwl/stge418e407-d012-4492-93c6-1fa34c9c25c8/dqc_reference
[2024-01-24 12:15:20,443] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:15:20,444] [INFO] Task started: Prodigal
[2024-01-24 12:15:20,445] [INFO] Running command: gunzip -c /var/lib/cwl/stg282382dd-21de-4c29-a519-77bd5a215952/GCF_003367505.1_ASM336750v1_genomic.fna.gz | prodigal -d GCF_003367505.1_ASM336750v1_genomic.fna/cds.fna -a GCF_003367505.1_ASM336750v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:15:30,218] [INFO] Task succeeded: Prodigal
[2024-01-24 12:15:30,219] [INFO] Task started: HMMsearch
[2024-01-24 12:15:30,219] [INFO] Running command: hmmsearch --tblout GCF_003367505.1_ASM336750v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge418e407-d012-4492-93c6-1fa34c9c25c8/dqc_reference/reference_markers.hmm GCF_003367505.1_ASM336750v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:15:30,548] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:15:30,574] [INFO] Found 6/6 markers.
[2024-01-24 12:15:30,619] [INFO] Query marker FASTA was written to GCF_003367505.1_ASM336750v1_genomic.fna/markers.fasta
[2024-01-24 12:15:30,619] [INFO] Task started: Blastn
[2024-01-24 12:15:30,620] [INFO] Running command: blastn -query GCF_003367505.1_ASM336750v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge418e407-d012-4492-93c6-1fa34c9c25c8/dqc_reference/reference_markers.fasta -out GCF_003367505.1_ASM336750v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:31,217] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:31,235] [INFO] Selected 10 target genomes.
[2024-01-24 12:15:31,236] [INFO] Target genome list was writen to GCF_003367505.1_ASM336750v1_genomic.fna/target_genomes.txt
[2024-01-24 12:15:31,240] [INFO] Task started: fastANI
[2024-01-24 12:15:31,240] [INFO] Running command: fastANI --query /var/lib/cwl/stg282382dd-21de-4c29-a519-77bd5a215952/GCF_003367505.1_ASM336750v1_genomic.fna.gz --refList GCF_003367505.1_ASM336750v1_genomic.fna/target_genomes.txt --output GCF_003367505.1_ASM336750v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:41,052] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:41,052] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge418e407-d012-4492-93c6-1fa34c9c25c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:41,052] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge418e407-d012-4492-93c6-1fa34c9c25c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:41,062] [INFO] Found 10 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:15:41,062] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 12:15:41,062] [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 capsici	strain=PB300	GCA_003367505.1	2115968	2115968	type	True	100.0	1500	1502	95	inconclusive
Lysinibacillus boronitolerans	strain=NBRC 103108	GCA_000772935.1	309788	309788	type	True	95.1183	1303	1502	95	inconclusive
Lysinibacillus boronitolerans	strain=NBRC 103108	GCA_002200915.1	309788	309788	type	True	95.1183	1303	1502	95	inconclusive
Lysinibacillus cavernae	strain=SYSU K30005	GCA_009724685.1	2666135	2666135	type	True	87.1093	1219	1502	95	below_threshold
Lysinibacillus fusiformis	strain=NBRC 15717	GCA_006540205.1	28031	28031	type	True	84.9822	1139	1502	95	below_threshold
Lysinibacillus macroides	strain=DSM 54	GCA_001281525.1	33935	33935	type	True	84.515	942	1502	95	below_threshold
Lysinibacillus contaminans	strain=DSM 25560	GCA_001278945.1	1293441	1293441	type	True	79.8021	507	1502	95	below_threshold
Solibacillus merdavium	strain=Sa1YVA6	GCA_014836935.1	2762218	2762218	type	True	78.3931	199	1502	95	below_threshold
Solibacillus faecavium	strain=A46	GCA_014836905.1	2762221	2762221	type	True	78.3558	198	1502	95	below_threshold
Ureibacillus chungkukjangi	strain=2RL32	GCA_003049615.1	1202712	1202712	type	True	78.3016	210	1502	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:41,064] [INFO] DFAST Taxonomy check result was written to GCF_003367505.1_ASM336750v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:41,066] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:41,066] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:41,066] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge418e407-d012-4492-93c6-1fa34c9c25c8/dqc_reference/checkm_data
[2024-01-24 12:15:41,067] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:41,117] [INFO] Task started: CheckM
[2024-01-24 12:15:41,117] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003367505.1_ASM336750v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003367505.1_ASM336750v1_genomic.fna/checkm_input GCF_003367505.1_ASM336750v1_genomic.fna/checkm_result
[2024-01-24 12:16:13,851] [INFO] Task succeeded: CheckM
[2024-01-24 12:16:13,852] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:16:13,882] [INFO] ===== Completeness check finished =====
[2024-01-24 12:16:13,883] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:16:13,883] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003367505.1_ASM336750v1_genomic.fna/markers.fasta)
[2024-01-24 12:16:13,884] [INFO] Task started: Blastn
[2024-01-24 12:16:13,884] [INFO] Running command: blastn -query GCF_003367505.1_ASM336750v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge418e407-d012-4492-93c6-1fa34c9c25c8/dqc_reference/reference_markers_gtdb.fasta -out GCF_003367505.1_ASM336750v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:16:14,643] [INFO] Task succeeded: Blastn
[2024-01-24 12:16:14,649] [INFO] Selected 5 target genomes.
[2024-01-24 12:16:14,650] [INFO] Target genome list was writen to GCF_003367505.1_ASM336750v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:16:14,655] [INFO] Task started: fastANI
[2024-01-24 12:16:14,655] [INFO] Running command: fastANI --query /var/lib/cwl/stg282382dd-21de-4c29-a519-77bd5a215952/GCF_003367505.1_ASM336750v1_genomic.fna.gz --refList GCF_003367505.1_ASM336750v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003367505.1_ASM336750v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:16:20,889] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:20,899] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:16:20,899] [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_003367505.1	s__Lysinibacillus capsici	100.0	1500	1502	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	95.1183	97.93	96.58	0.91	0.87	16	conclusive
GCF_000772935.1	s__Lysinibacillus boronitolerans	95.1183	1303	1502	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	95.1183	99.49	98.68	0.97	0.91	4	conclusive
GCF_016925635.1	s__Lysinibacillus fusiformis_F	93.0097	1318	1502	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_002845985.1	s__Lysinibacillus fusiformis_D	87.7181	1210	1502	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	95.0	99.12	98.25	0.94	0.92	9	-
GCF_009724685.1	s__Lysinibacillus sp009724685	87.1195	1218	1502	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 12:16:20,901] [INFO] GTDB search result was written to GCF_003367505.1_ASM336750v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:16:20,902] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:16:20,909] [INFO] DFAST_QC result json was written to GCF_003367505.1_ASM336750v1_genomic.fna/dqc_result.json
[2024-01-24 12:16:20,909] [INFO] DFAST_QC completed!
[2024-01-24 12:16:20,909] [INFO] Total running time: 0h1m2s