[2024-01-24 13:41:40,975] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:41:40,977] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:41:40,977] [INFO] DQC Reference Directory: /var/lib/cwl/stg63b1548a-9f99-45d5-ab1c-34d78519a025/dqc_reference
[2024-01-24 13:41:42,351] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:41:42,356] [INFO] Task started: Prodigal
[2024-01-24 13:41:42,356] [INFO] Running command: gunzip -c /var/lib/cwl/stg8153f711-3416-41ed-9d36-e8d2e0d2a61b/GCF_013385145.1_ASM1338514v1_genomic.fna.gz | prodigal -d GCF_013385145.1_ASM1338514v1_genomic.fna/cds.fna -a GCF_013385145.1_ASM1338514v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:45,922] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:45,922] [INFO] Task started: HMMsearch
[2024-01-24 13:41:45,923] [INFO] Running command: hmmsearch --tblout GCF_013385145.1_ASM1338514v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg63b1548a-9f99-45d5-ab1c-34d78519a025/dqc_reference/reference_markers.hmm GCF_013385145.1_ASM1338514v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:46,162] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:46,164] [INFO] Found 6/6 markers.
[2024-01-24 13:41:46,184] [INFO] Query marker FASTA was written to GCF_013385145.1_ASM1338514v1_genomic.fna/markers.fasta
[2024-01-24 13:41:46,185] [INFO] Task started: Blastn
[2024-01-24 13:41:46,185] [INFO] Running command: blastn -query GCF_013385145.1_ASM1338514v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg63b1548a-9f99-45d5-ab1c-34d78519a025/dqc_reference/reference_markers.fasta -out GCF_013385145.1_ASM1338514v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:46,796] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:46,806] [INFO] Selected 21 target genomes.
[2024-01-24 13:41:46,806] [INFO] Target genome list was writen to GCF_013385145.1_ASM1338514v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:46,814] [INFO] Task started: fastANI
[2024-01-24 13:41:46,815] [INFO] Running command: fastANI --query /var/lib/cwl/stg8153f711-3416-41ed-9d36-e8d2e0d2a61b/GCF_013385145.1_ASM1338514v1_genomic.fna.gz --refList GCF_013385145.1_ASM1338514v1_genomic.fna/target_genomes.txt --output GCF_013385145.1_ASM1338514v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:53,357] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:53,358] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg63b1548a-9f99-45d5-ab1c-34d78519a025/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:53,358] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg63b1548a-9f99-45d5-ab1c-34d78519a025/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:53,367] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:53,367] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:53,368] [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
Bombilactobacillus apium	strain=DCY120	GCA_013385145.1	2675299	2675299	type	True	100.0	563	563	95	conclusive
Bombilactobacillus folatiphilus	strain=SG4_D2	GCA_023380265.1	2923362	2923362	type	True	78.0713	66	563	95	below_threshold
Bombilactobacillus thymidiniphilus	strain=SG4_A1	GCA_023380245.1	2923363	2923363	type	True	77.5528	77	563	95	below_threshold
Bombilactobacillus mellis	strain=Hon2	GCA_000967245.1	1218508	1218508	type	True	77.5489	76	563	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:53,369] [INFO] DFAST Taxonomy check result was written to GCF_013385145.1_ASM1338514v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:53,370] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:53,370] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:53,370] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg63b1548a-9f99-45d5-ab1c-34d78519a025/dqc_reference/checkm_data
[2024-01-24 13:41:53,371] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:53,416] [INFO] Task started: CheckM
[2024-01-24 13:41:53,417] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013385145.1_ASM1338514v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013385145.1_ASM1338514v1_genomic.fna/checkm_input GCF_013385145.1_ASM1338514v1_genomic.fna/checkm_result
[2024-01-24 13:42:11,349] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:11,350] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:11,369] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:11,369] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:11,369] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013385145.1_ASM1338514v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:11,370] [INFO] Task started: Blastn
[2024-01-24 13:42:11,370] [INFO] Running command: blastn -query GCF_013385145.1_ASM1338514v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg63b1548a-9f99-45d5-ab1c-34d78519a025/dqc_reference/reference_markers_gtdb.fasta -out GCF_013385145.1_ASM1338514v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:12,155] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:12,160] [INFO] Selected 27 target genomes.
[2024-01-24 13:42:12,161] [INFO] Target genome list was writen to GCF_013385145.1_ASM1338514v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:12,202] [INFO] Task started: fastANI
[2024-01-24 13:42:12,202] [INFO] Running command: fastANI --query /var/lib/cwl/stg8153f711-3416-41ed-9d36-e8d2e0d2a61b/GCF_013385145.1_ASM1338514v1_genomic.fna.gz --refList GCF_013385145.1_ASM1338514v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013385145.1_ASM1338514v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:20,802] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:20,810] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:20,811] [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_013385145.1	s__Bombilactobacillus apium	100.0	563	563	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Bombilactobacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003522965.1	s__Bombilactobacillus bombi	77.6709	82	563	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Bombilactobacillus	95.0	98.10	98.09	0.88	0.87	3	-
GCF_013346925.1	s__Bombilactobacillus mellis	77.6009	70	563	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Bombilactobacillus	95.0	96.64	95.35	0.94	0.90	11	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:20,812] [INFO] GTDB search result was written to GCF_013385145.1_ASM1338514v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:20,813] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:20,815] [INFO] DFAST_QC result json was written to GCF_013385145.1_ASM1338514v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:20,816] [INFO] DFAST_QC completed!
[2024-01-24 13:42:20,816] [INFO] Total running time: 0h0m40s