[2024-01-25 18:50:05,488] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:50:05,489] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:50:05,489] [INFO] DQC Reference Directory: /var/lib/cwl/stgffe5b917-79a3-48cf-b56b-530d26351d3c/dqc_reference
[2024-01-25 18:50:06,622] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:50:06,623] [INFO] Task started: Prodigal
[2024-01-25 18:50:06,623] [INFO] Running command: gunzip -c /var/lib/cwl/stgaa85d7ae-20ed-4489-9065-2212d84fce84/GCF_009724685.1_ASM972468v1_genomic.fna.gz | prodigal -d GCF_009724685.1_ASM972468v1_genomic.fna/cds.fna -a GCF_009724685.1_ASM972468v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:50:15,018] [INFO] Task succeeded: Prodigal
[2024-01-25 18:50:15,019] [INFO] Task started: HMMsearch
[2024-01-25 18:50:15,019] [INFO] Running command: hmmsearch --tblout GCF_009724685.1_ASM972468v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgffe5b917-79a3-48cf-b56b-530d26351d3c/dqc_reference/reference_markers.hmm GCF_009724685.1_ASM972468v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:50:15,246] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:50:15,247] [INFO] Found 6/6 markers.
[2024-01-25 18:50:15,285] [INFO] Query marker FASTA was written to GCF_009724685.1_ASM972468v1_genomic.fna/markers.fasta
[2024-01-25 18:50:15,286] [INFO] Task started: Blastn
[2024-01-25 18:50:15,286] [INFO] Running command: blastn -query GCF_009724685.1_ASM972468v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgffe5b917-79a3-48cf-b56b-530d26351d3c/dqc_reference/reference_markers.fasta -out GCF_009724685.1_ASM972468v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:50:15,838] [INFO] Task succeeded: Blastn
[2024-01-25 18:50:15,841] [INFO] Selected 11 target genomes.
[2024-01-25 18:50:15,841] [INFO] Target genome list was writen to GCF_009724685.1_ASM972468v1_genomic.fna/target_genomes.txt
[2024-01-25 18:50:15,853] [INFO] Task started: fastANI
[2024-01-25 18:50:15,853] [INFO] Running command: fastANI --query /var/lib/cwl/stgaa85d7ae-20ed-4489-9065-2212d84fce84/GCF_009724685.1_ASM972468v1_genomic.fna.gz --refList GCF_009724685.1_ASM972468v1_genomic.fna/target_genomes.txt --output GCF_009724685.1_ASM972468v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:50:25,769] [INFO] Task succeeded: fastANI
[2024-01-25 18:50:25,770] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgffe5b917-79a3-48cf-b56b-530d26351d3c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:50:25,770] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgffe5b917-79a3-48cf-b56b-530d26351d3c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:50:25,778] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:50:25,778] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:50:25,778] [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 cavernae	strain=SYSU K30005	GCA_009724685.1	2666135	2666135	type	True	100.0	1541	1542	95	conclusive
Lysinibacillus boronitolerans	strain=NBRC 103108	GCA_002200915.1	309788	309788	type	True	87.0479	1189	1542	95	below_threshold
Lysinibacillus capsici	strain=PB300	GCA_003367505.1	2115968	2115968	type	True	87.0393	1223	1542	95	below_threshold
Lysinibacillus boronitolerans	strain=NBRC 103108	GCA_000772935.1	309788	309788	type	True	87.0387	1190	1542	95	below_threshold
Lysinibacillus fusiformis	strain=NBRC 15717	GCA_006540205.1	28031	28031	type	True	85.6192	1209	1542	95	below_threshold
Lysinibacillus fusiformis	strain=ATCC 7055	GCA_003049525.1	28031	28031	type	True	85.5453	1211	1542	95	below_threshold
Lysinibacillus contaminans	strain=DSM 25560	GCA_001278945.1	1293441	1293441	type	True	79.8513	510	1542	95	below_threshold
Solibacillus merdavium	strain=Sa1YVA6	GCA_014836935.1	2762218	2762218	type	True	78.3341	204	1542	95	below_threshold
Lysinibacillus composti	strain=DSM 24785	GCA_016908465.1	720633	720633	type	True	78.1611	212	1542	95	below_threshold
Viridibacillus soli	strain=YIM B01967	GCA_016612995.1	2798301	2798301	type	True	78.1364	221	1542	95	below_threshold
Solibacillus faecavium	strain=A46	GCA_014836905.1	2762221	2762221	type	True	78.1108	201	1542	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:50:25,780] [INFO] DFAST Taxonomy check result was written to GCF_009724685.1_ASM972468v1_genomic.fna/tc_result.tsv
[2024-01-25 18:50:25,780] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:50:25,780] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:50:25,781] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgffe5b917-79a3-48cf-b56b-530d26351d3c/dqc_reference/checkm_data
[2024-01-25 18:50:25,781] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:50:25,827] [INFO] Task started: CheckM
[2024-01-25 18:50:25,828] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009724685.1_ASM972468v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009724685.1_ASM972468v1_genomic.fna/checkm_input GCF_009724685.1_ASM972468v1_genomic.fna/checkm_result
[2024-01-25 18:50:54,977] [INFO] Task succeeded: CheckM
[2024-01-25 18:50:54,978] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:50:54,999] [INFO] ===== Completeness check finished =====
[2024-01-25 18:50:54,999] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:50:54,999] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009724685.1_ASM972468v1_genomic.fna/markers.fasta)
[2024-01-25 18:50:55,000] [INFO] Task started: Blastn
[2024-01-25 18:50:55,000] [INFO] Running command: blastn -query GCF_009724685.1_ASM972468v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgffe5b917-79a3-48cf-b56b-530d26351d3c/dqc_reference/reference_markers_gtdb.fasta -out GCF_009724685.1_ASM972468v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:50:55,768] [INFO] Task succeeded: Blastn
[2024-01-25 18:50:55,770] [INFO] Selected 6 target genomes.
[2024-01-25 18:50:55,770] [INFO] Target genome list was writen to GCF_009724685.1_ASM972468v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:50:55,787] [INFO] Task started: fastANI
[2024-01-25 18:50:55,787] [INFO] Running command: fastANI --query /var/lib/cwl/stgaa85d7ae-20ed-4489-9065-2212d84fce84/GCF_009724685.1_ASM972468v1_genomic.fna.gz --refList GCF_009724685.1_ASM972468v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009724685.1_ASM972468v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:51:03,183] [INFO] Task succeeded: fastANI
[2024-01-25 18:51:03,188] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:51:03,188] [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_009724685.1	s__Lysinibacillus sp009724685	100.0	1538	1542	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002845985.1	s__Lysinibacillus fusiformis_D	88.1396	1257	1542	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_016925635.1	s__Lysinibacillus fusiformis_F	87.7982	1263	1542	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_003367505.1	s__Lysinibacillus capsici	87.0393	1223	1542	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	95.1183	97.93	96.58	0.91	0.87	16	-
GCF_000772935.1	s__Lysinibacillus boronitolerans	87.0389	1190	1542	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	95.1183	99.49	98.68	0.97	0.91	4	-
GCF_001308875.1	s__Lysinibacillus sp001308875	86.8078	1245	1542	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 18:51:03,190] [INFO] GTDB search result was written to GCF_009724685.1_ASM972468v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:51:03,190] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:51:03,193] [INFO] DFAST_QC result json was written to GCF_009724685.1_ASM972468v1_genomic.fna/dqc_result.json
[2024-01-25 18:51:03,193] [INFO] DFAST_QC completed!
[2024-01-25 18:51:03,193] [INFO] Total running time: 0h0m58s