[2024-01-25 19:13:05,626] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:13:05,634] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:13:05,635] [INFO] DQC Reference Directory: /var/lib/cwl/stg2248ad7c-bf63-444b-a700-c3610d4142c5/dqc_reference
[2024-01-25 19:13:06,832] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:13:06,832] [INFO] Task started: Prodigal
[2024-01-25 19:13:06,833] [INFO] Running command: gunzip -c /var/lib/cwl/stga7d2b1ef-f400-4b26-a169-b1dc722e1644/GCF_003515775.1_ASM351577v1_genomic.fna.gz | prodigal -d GCF_003515775.1_ASM351577v1_genomic.fna/cds.fna -a GCF_003515775.1_ASM351577v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:13:14,845] [INFO] Task succeeded: Prodigal
[2024-01-25 19:13:14,846] [INFO] Task started: HMMsearch
[2024-01-25 19:13:14,846] [INFO] Running command: hmmsearch --tblout GCF_003515775.1_ASM351577v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2248ad7c-bf63-444b-a700-c3610d4142c5/dqc_reference/reference_markers.hmm GCF_003515775.1_ASM351577v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:13:15,076] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:13:15,078] [INFO] Found 6/6 markers.
[2024-01-25 19:13:15,109] [INFO] Query marker FASTA was written to GCF_003515775.1_ASM351577v1_genomic.fna/markers.fasta
[2024-01-25 19:13:15,109] [INFO] Task started: Blastn
[2024-01-25 19:13:15,109] [INFO] Running command: blastn -query GCF_003515775.1_ASM351577v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2248ad7c-bf63-444b-a700-c3610d4142c5/dqc_reference/reference_markers.fasta -out GCF_003515775.1_ASM351577v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:13:15,713] [INFO] Task succeeded: Blastn
[2024-01-25 19:13:15,715] [INFO] Selected 18 target genomes.
[2024-01-25 19:13:15,715] [INFO] Target genome list was writen to GCF_003515775.1_ASM351577v1_genomic.fna/target_genomes.txt
[2024-01-25 19:13:15,733] [INFO] Task started: fastANI
[2024-01-25 19:13:15,733] [INFO] Running command: fastANI --query /var/lib/cwl/stga7d2b1ef-f400-4b26-a169-b1dc722e1644/GCF_003515775.1_ASM351577v1_genomic.fna.gz --refList GCF_003515775.1_ASM351577v1_genomic.fna/target_genomes.txt --output GCF_003515775.1_ASM351577v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:13:26,691] [INFO] Task succeeded: fastANI
[2024-01-25 19:13:26,691] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2248ad7c-bf63-444b-a700-c3610d4142c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:13:26,692] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2248ad7c-bf63-444b-a700-c3610d4142c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:13:26,699] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:13:26,699] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:13:26,699] [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
Ureibacillus chungkukjangi	strain=KACC 16626	GCA_003217295.1	1202712	1202712	type	True	79.5915	426	1244	95	below_threshold
Ureibacillus chungkukjangi	strain=2RL32	GCA_003049615.1	1202712	1202712	type	True	79.5414	433	1244	95	below_threshold
Ureibacillus sinduriensis	strain=JCM 15800	GCA_002200845.1	561440	561440	type	True	79.1325	439	1244	95	below_threshold
Ureibacillus sinduriensis	strain=JCM 15800	GCA_000772955.1	561440	561440	type	True	79.1325	439	1244	95	below_threshold
Ureibacillus massiliensis	strain=4400831	GCA_002200855.1	292806	292806	type	True	78.4275	219	1244	95	below_threshold
Lysinibacillus composti	strain=DSM 24785	GCA_016908465.1	720633	720633	type	True	78.3274	292	1244	95	below_threshold
Lysinibacillus macroides	strain=DSM 54	GCA_001281525.1	33935	33935	type	True	77.7665	150	1244	95	below_threshold
Solibacillus isronensis	strain=B3W22	GCA_000298255.1	412383	412383	type	True	77.5966	176	1244	95	below_threshold
Solibacillus kalamii	strain=DSM 101595	GCA_016909025.1	1748298	1748298	type	True	77.3723	184	1244	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:13:26,700] [INFO] DFAST Taxonomy check result was written to GCF_003515775.1_ASM351577v1_genomic.fna/tc_result.tsv
[2024-01-25 19:13:26,701] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:13:26,701] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:13:26,701] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2248ad7c-bf63-444b-a700-c3610d4142c5/dqc_reference/checkm_data
[2024-01-25 19:13:26,702] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:13:26,743] [INFO] Task started: CheckM
[2024-01-25 19:13:26,743] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003515775.1_ASM351577v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003515775.1_ASM351577v1_genomic.fna/checkm_input GCF_003515775.1_ASM351577v1_genomic.fna/checkm_result
[2024-01-25 19:13:54,619] [INFO] Task succeeded: CheckM
[2024-01-25 19:13:54,620] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:13:54,641] [INFO] ===== Completeness check finished =====
[2024-01-25 19:13:54,641] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:13:54,641] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003515775.1_ASM351577v1_genomic.fna/markers.fasta)
[2024-01-25 19:13:54,642] [INFO] Task started: Blastn
[2024-01-25 19:13:54,642] [INFO] Running command: blastn -query GCF_003515775.1_ASM351577v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2248ad7c-bf63-444b-a700-c3610d4142c5/dqc_reference/reference_markers_gtdb.fasta -out GCF_003515775.1_ASM351577v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:13:55,388] [INFO] Task succeeded: Blastn
[2024-01-25 19:13:55,390] [INFO] Selected 11 target genomes.
[2024-01-25 19:13:55,390] [INFO] Target genome list was writen to GCF_003515775.1_ASM351577v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:13:55,412] [INFO] Task started: fastANI
[2024-01-25 19:13:55,412] [INFO] Running command: fastANI --query /var/lib/cwl/stga7d2b1ef-f400-4b26-a169-b1dc722e1644/GCF_003515775.1_ASM351577v1_genomic.fna.gz --refList GCF_003515775.1_ASM351577v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003515775.1_ASM351577v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:14:03,484] [INFO] Task succeeded: fastANI
[2024-01-25 19:14:03,494] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:14:03,494] [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_003515775.1	s__Ureibacillus yapensis	100.0	1244	1244	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_005491425.1	s__Ureibacillus sp005491425	79.9219	447	1244	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003217295.1	s__Ureibacillus chungkukjangi	79.5915	426	1244	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_014836845.1	s__Ureibacillus sp014836845	79.5091	363	1244	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003711845.1	s__Ureibacillus halotolerans	79.4409	363	1244	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000772955.1	s__Ureibacillus sinduriensis	79.1325	439	1244	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003966145.1	s__Ureibacillus telephonicus	78.8406	345	1244	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900217795.1	s__Ureibacillus xyleni	78.7506	295	1244	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003628435.1	s__Ureibacillus endophyticus	78.5935	294	1244	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003977595.1	s__Ureibacillus antri	78.4148	355	1244	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	98.58	98.58	0.91	0.91	2	-
GCF_003991225.1	s__Kurthia intestinigallinarum	77.5609	70	1244	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Kurthia	95.0	98.65	98.48	0.94	0.89	8	-
--------------------------------------------------------------------------------
[2024-01-25 19:14:03,499] [INFO] GTDB search result was written to GCF_003515775.1_ASM351577v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:14:03,501] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:14:03,503] [INFO] DFAST_QC result json was written to GCF_003515775.1_ASM351577v1_genomic.fna/dqc_result.json
[2024-01-25 19:14:03,504] [INFO] DFAST_QC completed!
[2024-01-25 19:14:03,504] [INFO] Total running time: 0h0m58s