[2024-01-24 11:20:34,427] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:20:34,429] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:20:34,429] [INFO] DQC Reference Directory: /var/lib/cwl/stg6ef4503a-656f-4f45-b111-51b7fce8f8f6/dqc_reference
[2024-01-24 11:20:35,628] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:20:35,628] [INFO] Task started: Prodigal
[2024-01-24 11:20:35,629] [INFO] Running command: gunzip -c /var/lib/cwl/stg3c503865-643b-41d3-b511-1fb9543ccb3d/GCF_002265435.1_ASM226543v1_genomic.fna.gz | prodigal -d GCF_002265435.1_ASM226543v1_genomic.fna/cds.fna -a GCF_002265435.1_ASM226543v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:20:42,116] [INFO] Task succeeded: Prodigal
[2024-01-24 11:20:42,116] [INFO] Task started: HMMsearch
[2024-01-24 11:20:42,117] [INFO] Running command: hmmsearch --tblout GCF_002265435.1_ASM226543v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6ef4503a-656f-4f45-b111-51b7fce8f8f6/dqc_reference/reference_markers.hmm GCF_002265435.1_ASM226543v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:20:42,374] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:20:42,376] [INFO] Found 6/6 markers.
[2024-01-24 11:20:42,403] [INFO] Query marker FASTA was written to GCF_002265435.1_ASM226543v1_genomic.fna/markers.fasta
[2024-01-24 11:20:42,403] [INFO] Task started: Blastn
[2024-01-24 11:20:42,403] [INFO] Running command: blastn -query GCF_002265435.1_ASM226543v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6ef4503a-656f-4f45-b111-51b7fce8f8f6/dqc_reference/reference_markers.fasta -out GCF_002265435.1_ASM226543v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:20:42,989] [INFO] Task succeeded: Blastn
[2024-01-24 11:20:42,992] [INFO] Selected 26 target genomes.
[2024-01-24 11:20:42,993] [INFO] Target genome list was writen to GCF_002265435.1_ASM226543v1_genomic.fna/target_genomes.txt
[2024-01-24 11:20:43,068] [INFO] Task started: fastANI
[2024-01-24 11:20:43,069] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c503865-643b-41d3-b511-1fb9543ccb3d/GCF_002265435.1_ASM226543v1_genomic.fna.gz --refList GCF_002265435.1_ASM226543v1_genomic.fna/target_genomes.txt --output GCF_002265435.1_ASM226543v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:20:57,265] [INFO] Task succeeded: fastANI
[2024-01-24 11:20:57,266] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6ef4503a-656f-4f45-b111-51b7fce8f8f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:20:57,266] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6ef4503a-656f-4f45-b111-51b7fce8f8f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:20:57,279] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:20:57,279] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:20:57,280] [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
Psychrobacillus faecigallinarum	strain=Sa2BUA9	GCA_014836595.1	2762235	2762235	type	True	78.5953	75	874	95	below_threshold
Lysinibacillus agricola	strain=FJAT-51161	GCA_016638705.1	2590012	2590012	type	True	78.5184	57	874	95	below_threshold
Lysinibacillus xylanilyticus	strain=DSM 23493	GCA_001183605.1	582475	582475	type	True	77.9902	64	874	95	below_threshold
Lysinibacillus boronitolerans	strain=NBRC 103108	GCA_000772935.1	309788	309788	type	True	77.9398	64	874	95	below_threshold
Lysinibacillus boronitolerans	strain=NBRC 103108	GCA_002200915.1	309788	309788	type	True	77.9398	64	874	95	below_threshold
Kurthia sibirica	strain=ATCC 49154	GCA_003143975.1	202750	202750	type	True	77.4199	52	874	95	below_threshold
Kurthia sibirica	strain=NBRC 101530	GCA_007989725.1	202750	202750	type	True	77.3818	51	874	95	below_threshold
Solibacillus cecembensis	strain=DSM 21993	GCA_001439635.1	459347	459347	type	True	77.2744	62	874	95	below_threshold
Kurthia massiliensis	strain=JC30	GCA_000285555.1	1033739	1033739	type	True	76.9627	58	874	95	below_threshold
Kurthia senegalensis	strain=type strain: JC8E	GCA_000285595.1	1033740	1033740	type	True	76.365	51	874	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:20:57,281] [INFO] DFAST Taxonomy check result was written to GCF_002265435.1_ASM226543v1_genomic.fna/tc_result.tsv
[2024-01-24 11:20:57,281] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:20:57,282] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:20:57,282] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6ef4503a-656f-4f45-b111-51b7fce8f8f6/dqc_reference/checkm_data
[2024-01-24 11:20:57,283] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:20:57,309] [INFO] Task started: CheckM
[2024-01-24 11:20:57,309] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002265435.1_ASM226543v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002265435.1_ASM226543v1_genomic.fna/checkm_input GCF_002265435.1_ASM226543v1_genomic.fna/checkm_result
[2024-01-24 11:21:22,953] [INFO] Task succeeded: CheckM
[2024-01-24 11:21:22,955] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 3.99%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:21:22,974] [INFO] ===== Completeness check finished =====
[2024-01-24 11:21:22,974] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:21:22,975] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002265435.1_ASM226543v1_genomic.fna/markers.fasta)
[2024-01-24 11:21:22,975] [INFO] Task started: Blastn
[2024-01-24 11:21:22,975] [INFO] Running command: blastn -query GCF_002265435.1_ASM226543v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6ef4503a-656f-4f45-b111-51b7fce8f8f6/dqc_reference/reference_markers_gtdb.fasta -out GCF_002265435.1_ASM226543v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:21:23,720] [INFO] Task succeeded: Blastn
[2024-01-24 11:21:23,724] [INFO] Selected 20 target genomes.
[2024-01-24 11:21:23,725] [INFO] Target genome list was writen to GCF_002265435.1_ASM226543v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:21:23,773] [INFO] Task started: fastANI
[2024-01-24 11:21:23,773] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c503865-643b-41d3-b511-1fb9543ccb3d/GCF_002265435.1_ASM226543v1_genomic.fna.gz --refList GCF_002265435.1_ASM226543v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002265435.1_ASM226543v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:21:36,606] [INFO] Task succeeded: fastANI
[2024-01-24 11:21:36,619] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:21:36,619] [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_002265435.1	s__Chryseomicrobium hominis	100.0	873	874	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Chryseomicrobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002798305.1	s__Chryseomicrobium excrementi	90.6375	755	874	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Chryseomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016909155.1	s__Chryseomicrobium aureum	81.4692	428	874	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Chryseomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007362955.1	s__Lysinibacillus fusiformis_E	78.1447	67	874	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	78.1161	65	874	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_002833405.1	s__Planococcus sp002833405	78.1111	74	874	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Planococcus	95.0	99.89	99.88	0.99	0.97	4	-
GCF_001275675.1	s__Lysinibacillus sp001275675	77.971	67	874	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_007676755.1	s__Psychrobacillus sp007676755	77.9377	92	874	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Psychrobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003143975.1	s__Kurthia sibirica	77.5318	50	874	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Kurthia	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000285555.1	s__Kurthia massiliensis	76.9984	57	874	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Kurthia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003384035.1	s__Sporosarcina sp003384035	76.9386	55	874	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Sporosarcina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003991225.1	s__Kurthia intestinigallinarum	76.8542	54	874	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Kurthia	95.0	98.65	98.48	0.94	0.89	8	-
--------------------------------------------------------------------------------
[2024-01-24 11:21:36,621] [INFO] GTDB search result was written to GCF_002265435.1_ASM226543v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:21:36,622] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:21:36,625] [INFO] DFAST_QC result json was written to GCF_002265435.1_ASM226543v1_genomic.fna/dqc_result.json
[2024-01-24 11:21:36,625] [INFO] DFAST_QC completed!
[2024-01-24 11:21:36,625] [INFO] Total running time: 0h1m2s