[2024-01-24 12:21:59,416] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:21:59,420] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:21:59,420] [INFO] DQC Reference Directory: /var/lib/cwl/stg3e607e78-abde-491c-956d-92f75135cf0d/dqc_reference
[2024-01-24 12:22:00,948] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:00,949] [INFO] Task started: Prodigal
[2024-01-24 12:22:00,949] [INFO] Running command: gunzip -c /var/lib/cwl/stgc8c0bec4-c166-4d69-8896-1020ebd0bbb0/GCF_000285595.1_ASM28559v1_genomic.fna.gz | prodigal -d GCF_000285595.1_ASM28559v1_genomic.fna/cds.fna -a GCF_000285595.1_ASM28559v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:07,651] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:07,651] [INFO] Task started: HMMsearch
[2024-01-24 12:22:07,651] [INFO] Running command: hmmsearch --tblout GCF_000285595.1_ASM28559v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3e607e78-abde-491c-956d-92f75135cf0d/dqc_reference/reference_markers.hmm GCF_000285595.1_ASM28559v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:07,973] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:07,975] [INFO] Found 6/6 markers.
[2024-01-24 12:22:08,019] [INFO] Query marker FASTA was written to GCF_000285595.1_ASM28559v1_genomic.fna/markers.fasta
[2024-01-24 12:22:08,019] [INFO] Task started: Blastn
[2024-01-24 12:22:08,019] [INFO] Running command: blastn -query GCF_000285595.1_ASM28559v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3e607e78-abde-491c-956d-92f75135cf0d/dqc_reference/reference_markers.fasta -out GCF_000285595.1_ASM28559v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:08,682] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:08,685] [INFO] Selected 17 target genomes.
[2024-01-24 12:22:08,685] [INFO] Target genome list was writen to GCF_000285595.1_ASM28559v1_genomic.fna/target_genomes.txt
[2024-01-24 12:22:08,691] [INFO] Task started: fastANI
[2024-01-24 12:22:08,691] [INFO] Running command: fastANI --query /var/lib/cwl/stgc8c0bec4-c166-4d69-8896-1020ebd0bbb0/GCF_000285595.1_ASM28559v1_genomic.fna.gz --refList GCF_000285595.1_ASM28559v1_genomic.fna/target_genomes.txt --output GCF_000285595.1_ASM28559v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:19,889] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:19,889] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3e607e78-abde-491c-956d-92f75135cf0d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:19,889] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3e607e78-abde-491c-956d-92f75135cf0d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:19,901] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:22:19,902] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:22:19,902] [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
Kurthia senegalensis	strain=type strain: JC8E	GCA_000285595.1	1033740	1033740	type	True	100.0	982	984	95	conclusive
Kurthia massiliensis	strain=JC30	GCA_000285555.1	1033739	1033739	type	True	80.7913	497	984	95	below_threshold
Kurthia huakuii	strain=LAM0618	GCA_000505545.1	1421019	1421019	type	True	80.7693	437	984	95	below_threshold
Kurthia gibsonii	strain=NBRC 15534	GCA_006539985.1	33946	33946	type	True	78.8636	227	984	95	below_threshold
Kurthia zopfii	strain=NCTC10597	GCA_900452285.1	1650	1650	type	True	78.7578	233	984	95	below_threshold
Kurthia zopfii	strain=DSM 20580	GCA_004363595.1	1650	1650	type	True	78.6686	235	984	95	below_threshold
Kurthia zopfii	strain=ATCC 33403	GCA_003143955.1	1650	1650	type	True	78.6535	233	984	95	below_threshold
Rummeliibacillus suwonensis	strain=G20	GCA_007896435.1	1306154	1306154	type	True	77.9271	167	984	95	below_threshold
Viridibacillus soli	strain=YIM B01967	GCA_016612995.1	2798301	2798301	type	True	77.7611	180	984	95	below_threshold
Psychrobacillus vulpis	strain=Z8	GCA_006861825.1	2325572	2325572	type	True	77.1844	74	984	95	below_threshold
Lysinibacillus composti	strain=MCCC 1A13240	GCA_003856865.1	720633	720633	type	True	77.0924	125	984	95	below_threshold
Bacillus anthracis	strain=Vollum	GCA_022221345.1	1392	1392	type	True	76.8489	62	984	95	below_threshold
Bacillus sanguinis	strain=BML-BC004	GCA_018332475.1	2817476	2817476	type	True	76.6718	69	984	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:22:19,906] [INFO] DFAST Taxonomy check result was written to GCF_000285595.1_ASM28559v1_genomic.fna/tc_result.tsv
[2024-01-24 12:22:19,906] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:19,907] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:19,907] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3e607e78-abde-491c-956d-92f75135cf0d/dqc_reference/checkm_data
[2024-01-24 12:22:19,908] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:19,939] [INFO] Task started: CheckM
[2024-01-24 12:22:19,940] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000285595.1_ASM28559v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000285595.1_ASM28559v1_genomic.fna/checkm_input GCF_000285595.1_ASM28559v1_genomic.fna/checkm_result
[2024-01-24 12:22:46,825] [INFO] Task succeeded: CheckM
[2024-01-24 12:22:46,826] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:22:46,845] [INFO] ===== Completeness check finished =====
[2024-01-24 12:22:46,845] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:22:46,846] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000285595.1_ASM28559v1_genomic.fna/markers.fasta)
[2024-01-24 12:22:46,846] [INFO] Task started: Blastn
[2024-01-24 12:22:46,846] [INFO] Running command: blastn -query GCF_000285595.1_ASM28559v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3e607e78-abde-491c-956d-92f75135cf0d/dqc_reference/reference_markers_gtdb.fasta -out GCF_000285595.1_ASM28559v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:47,717] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:47,721] [INFO] Selected 10 target genomes.
[2024-01-24 12:22:47,721] [INFO] Target genome list was writen to GCF_000285595.1_ASM28559v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:22:47,737] [INFO] Task started: fastANI
[2024-01-24 12:22:47,737] [INFO] Running command: fastANI --query /var/lib/cwl/stgc8c0bec4-c166-4d69-8896-1020ebd0bbb0/GCF_000285595.1_ASM28559v1_genomic.fna.gz --refList GCF_000285595.1_ASM28559v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000285595.1_ASM28559v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:22:54,493] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:54,506] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:22:54,506] [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_000285595.1	s__Kurthia senegalensis	100.0	982	984	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Kurthia	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_000285555.1	s__Kurthia massiliensis	80.8046	496	984	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_000505545.1	s__Kurthia huakuii	80.7549	437	984	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Kurthia	95.0	99.98	99.98	0.99	0.99	2	-
GCF_003991225.1	s__Kurthia intestinigallinarum	80.6933	486	984	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Kurthia	95.0	98.65	98.48	0.94	0.89	8	-
GCF_006539985.1	s__Kurthia gibsonii	78.8636	227	984	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Kurthia	95.0	97.46	97.18	0.93	0.90	4	-
GCF_003143955.1	s__Kurthia zopfii	78.6535	233	984	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Kurthia	95.0	99.54	98.21	0.97	0.90	5	-
GCA_018065935.1	s__Kurthia sp018065935	78.5705	198	984	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Kurthia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007896435.1	s__Rummeliibacillus suwonensis	77.901	167	984	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Rummeliibacillus	95.0	98.15	97.53	0.89	0.86	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:22:54,629] [INFO] GTDB search result was written to GCF_000285595.1_ASM28559v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:22:54,630] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:22:54,635] [INFO] DFAST_QC result json was written to GCF_000285595.1_ASM28559v1_genomic.fna/dqc_result.json
[2024-01-24 12:22:54,635] [INFO] DFAST_QC completed!
[2024-01-24 12:22:54,635] [INFO] Total running time: 0h0m55s