[2024-01-24 14:46:34,704] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:46:34,707] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:46:34,707] [INFO] DQC Reference Directory: /var/lib/cwl/stg00edffb8-e398-44f3-be88-ff2d8055bd63/dqc_reference
[2024-01-24 14:46:36,085] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:46:36,086] [INFO] Task started: Prodigal
[2024-01-24 14:46:36,086] [INFO] Running command: gunzip -c /var/lib/cwl/stg5ef34598-b2b5-466a-a6f0-2e4d08a8dab8/GCF_001042475.2_ASM104247v2_genomic.fna.gz | prodigal -d GCF_001042475.2_ASM104247v2_genomic.fna/cds.fna -a GCF_001042475.2_ASM104247v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:46:48,601] [INFO] Task succeeded: Prodigal
[2024-01-24 14:46:48,601] [INFO] Task started: HMMsearch
[2024-01-24 14:46:48,602] [INFO] Running command: hmmsearch --tblout GCF_001042475.2_ASM104247v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg00edffb8-e398-44f3-be88-ff2d8055bd63/dqc_reference/reference_markers.hmm GCF_001042475.2_ASM104247v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:46:48,910] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:46:48,912] [INFO] Found 6/6 markers.
[2024-01-24 14:46:48,956] [INFO] Query marker FASTA was written to GCF_001042475.2_ASM104247v2_genomic.fna/markers.fasta
[2024-01-24 14:46:48,957] [INFO] Task started: Blastn
[2024-01-24 14:46:48,957] [INFO] Running command: blastn -query GCF_001042475.2_ASM104247v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg00edffb8-e398-44f3-be88-ff2d8055bd63/dqc_reference/reference_markers.fasta -out GCF_001042475.2_ASM104247v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:46:49,693] [INFO] Task succeeded: Blastn
[2024-01-24 14:46:49,697] [INFO] Selected 9 target genomes.
[2024-01-24 14:46:49,698] [INFO] Target genome list was writen to GCF_001042475.2_ASM104247v2_genomic.fna/target_genomes.txt
[2024-01-24 14:46:49,703] [INFO] Task started: fastANI
[2024-01-24 14:46:49,703] [INFO] Running command: fastANI --query /var/lib/cwl/stg5ef34598-b2b5-466a-a6f0-2e4d08a8dab8/GCF_001042475.2_ASM104247v2_genomic.fna.gz --refList GCF_001042475.2_ASM104247v2_genomic.fna/target_genomes.txt --output GCF_001042475.2_ASM104247v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:46:57,868] [INFO] Task succeeded: fastANI
[2024-01-24 14:46:57,869] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg00edffb8-e398-44f3-be88-ff2d8055bd63/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:46:57,870] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg00edffb8-e398-44f3-be88-ff2d8055bd63/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:46:57,885] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:46:57,885] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:46:57,886] [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
Bacillus swezeyi	strain=NRRL B-41294	GCA_001969815.1	1925020	1925020	type	True	83.0141	1024	1558	95	below_threshold
Bacillus licheniformis	strain=DSM 13	GCA_000008425.1	1402	1402	type	True	82.4929	992	1558	95	below_threshold
Bacillus licheniformis	strain=ATCC 14580; DSM 13	GCA_000011645.1	1402	1402	type	True	82.4867	994	1558	95	below_threshold
Bacillus licheniformis	strain=ATCC 14580	GCA_006094335.1	1402	1402	type	True	82.4348	993	1558	95	below_threshold
Bacillus licheniformis	strain=DSM 13	GCA_022630555.1	1402	1402	type	True	82.3417	1001	1558	95	below_threshold
Metabacillus flavus	strain=KIGAM252	GCA_018283675.1	2823519	2823519	type	True	77.215	84	1558	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:46:57,888] [INFO] DFAST Taxonomy check result was written to GCF_001042475.2_ASM104247v2_genomic.fna/tc_result.tsv
[2024-01-24 14:46:57,888] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:46:57,889] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:46:57,889] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg00edffb8-e398-44f3-be88-ff2d8055bd63/dqc_reference/checkm_data
[2024-01-24 14:46:57,890] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:46:57,937] [INFO] Task started: CheckM
[2024-01-24 14:46:57,937] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001042475.2_ASM104247v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001042475.2_ASM104247v2_genomic.fna/checkm_input GCF_001042475.2_ASM104247v2_genomic.fna/checkm_result
[2024-01-24 14:47:38,642] [INFO] Task succeeded: CheckM
[2024-01-24 14:47:38,643] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:47:38,670] [INFO] ===== Completeness check finished =====
[2024-01-24 14:47:38,670] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:47:38,670] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001042475.2_ASM104247v2_genomic.fna/markers.fasta)
[2024-01-24 14:47:38,671] [INFO] Task started: Blastn
[2024-01-24 14:47:38,671] [INFO] Running command: blastn -query GCF_001042475.2_ASM104247v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg00edffb8-e398-44f3-be88-ff2d8055bd63/dqc_reference/reference_markers_gtdb.fasta -out GCF_001042475.2_ASM104247v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:39,794] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:39,797] [INFO] Selected 7 target genomes.
[2024-01-24 14:47:39,797] [INFO] Target genome list was writen to GCF_001042475.2_ASM104247v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:47:39,803] [INFO] Task started: fastANI
[2024-01-24 14:47:39,803] [INFO] Running command: fastANI --query /var/lib/cwl/stg5ef34598-b2b5-466a-a6f0-2e4d08a8dab8/GCF_001042475.2_ASM104247v2_genomic.fna.gz --refList GCF_001042475.2_ASM104247v2_genomic.fna/target_genomes_gtdb.txt --output GCF_001042475.2_ASM104247v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:47:46,952] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:46,966] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:47:46,967] [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_001042475.2	s__Bacillus glycinifermentans	100.0	1551	1558	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	97.06	95.94	0.90	0.86	8	conclusive
GCF_001592005.1	s__Bacillus sonorensis	85.9137	1178	1558	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	99.75	99.65	0.97	0.94	11	-
GCF_001969815.1	s__Bacillus swezeyi	83.0081	1025	1558	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	97.68	96.91	0.92	0.90	5	-
GCF_900166645.1	s__Bacillus sonorensis_A	82.5987	1055	1558	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	99.48	99.48	0.95	0.95	2	-
GCF_000011645.1	s__Bacillus licheniformis	82.4679	997	1558	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.4556	99.64	99.26	0.97	0.81	213	-
GCF_001969855.1	s__Bacillus haynesii	82.4571	972	1558	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.4556	97.08	96.53	0.93	0.92	6	-
GCA_001938995.1	s__Bacillus pumilus_G	77.7237	156	1558	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:47:46,970] [INFO] GTDB search result was written to GCF_001042475.2_ASM104247v2_genomic.fna/result_gtdb.tsv
[2024-01-24 14:47:46,971] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:47:46,975] [INFO] DFAST_QC result json was written to GCF_001042475.2_ASM104247v2_genomic.fna/dqc_result.json
[2024-01-24 14:47:46,976] [INFO] DFAST_QC completed!
[2024-01-24 14:47:46,976] [INFO] Total running time: 0h1m12s