[2024-01-24 11:12:57,839] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:57,841] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:57,841] [INFO] DQC Reference Directory: /var/lib/cwl/stg622bfd22-57df-43a7-8e50-d34159bf1d38/dqc_reference
[2024-01-24 11:12:59,174] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:59,175] [INFO] Task started: Prodigal
[2024-01-24 11:12:59,176] [INFO] Running command: gunzip -c /var/lib/cwl/stg003dafa1-54cc-4a21-8475-59221b64d44e/GCF_009877435.1_ASM987743v1_genomic.fna.gz | prodigal -d GCF_009877435.1_ASM987743v1_genomic.fna/cds.fna -a GCF_009877435.1_ASM987743v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:13:10,016] [INFO] Task succeeded: Prodigal
[2024-01-24 11:13:10,017] [INFO] Task started: HMMsearch
[2024-01-24 11:13:10,017] [INFO] Running command: hmmsearch --tblout GCF_009877435.1_ASM987743v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg622bfd22-57df-43a7-8e50-d34159bf1d38/dqc_reference/reference_markers.hmm GCF_009877435.1_ASM987743v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:13:10,303] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:13:10,304] [INFO] Found 6/6 markers.
[2024-01-24 11:13:10,339] [INFO] Query marker FASTA was written to GCF_009877435.1_ASM987743v1_genomic.fna/markers.fasta
[2024-01-24 11:13:10,339] [INFO] Task started: Blastn
[2024-01-24 11:13:10,339] [INFO] Running command: blastn -query GCF_009877435.1_ASM987743v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg622bfd22-57df-43a7-8e50-d34159bf1d38/dqc_reference/reference_markers.fasta -out GCF_009877435.1_ASM987743v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:10,975] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:10,978] [INFO] Selected 9 target genomes.
[2024-01-24 11:13:10,979] [INFO] Target genome list was writen to GCF_009877435.1_ASM987743v1_genomic.fna/target_genomes.txt
[2024-01-24 11:13:10,982] [INFO] Task started: fastANI
[2024-01-24 11:13:10,983] [INFO] Running command: fastANI --query /var/lib/cwl/stg003dafa1-54cc-4a21-8475-59221b64d44e/GCF_009877435.1_ASM987743v1_genomic.fna.gz --refList GCF_009877435.1_ASM987743v1_genomic.fna/target_genomes.txt --output GCF_009877435.1_ASM987743v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:18,185] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:18,185] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg622bfd22-57df-43a7-8e50-d34159bf1d38/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:18,186] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg622bfd22-57df-43a7-8e50-d34159bf1d38/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:18,192] [INFO] Found 6 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:13:18,192] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:13:18,192] [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
Heliomicrobium gestii	strain=DSM 11169	GCA_009877435.1	2699	2699	type	True	100.0	1206	1208	95	conclusive
Heliomicrobium gestii	strain=DSM 11169	GCA_016908025.1	2699	2699	type	True	99.9993	1206	1208	95	conclusive
Heliomicrobium undosum	strain=DSM 13378	GCA_009877425.1	121734	121734	type	True	84.717	868	1208	95	below_threshold
Heliomicrobium modesticaldum	strain=Ice1; ATCC 51547	GCA_000019165.1	35701	35701	type	True	83.4965	688	1208	95	below_threshold
Heliobacterium chlorum	strain=DSM 3682	GCA_014502795.1	2698	2698	type	True	77.9054	212	1208	95	below_threshold
Heliobacterium mobile	strain=DSM 6151	GCA_009720735.1	28064	28064	type	True	77.8265	209	1208	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:18,194] [INFO] DFAST Taxonomy check result was written to GCF_009877435.1_ASM987743v1_genomic.fna/tc_result.tsv
[2024-01-24 11:13:18,195] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:18,195] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:18,195] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg622bfd22-57df-43a7-8e50-d34159bf1d38/dqc_reference/checkm_data
[2024-01-24 11:13:18,196] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:18,236] [INFO] Task started: CheckM
[2024-01-24 11:13:18,237] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009877435.1_ASM987743v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009877435.1_ASM987743v1_genomic.fna/checkm_input GCF_009877435.1_ASM987743v1_genomic.fna/checkm_result
[2024-01-24 11:13:54,691] [INFO] Task succeeded: CheckM
[2024-01-24 11:13:54,693] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:13:54,714] [INFO] ===== Completeness check finished =====
[2024-01-24 11:13:54,714] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:13:54,715] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009877435.1_ASM987743v1_genomic.fna/markers.fasta)
[2024-01-24 11:13:54,715] [INFO] Task started: Blastn
[2024-01-24 11:13:54,715] [INFO] Running command: blastn -query GCF_009877435.1_ASM987743v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg622bfd22-57df-43a7-8e50-d34159bf1d38/dqc_reference/reference_markers_gtdb.fasta -out GCF_009877435.1_ASM987743v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:55,715] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:55,721] [INFO] Selected 11 target genomes.
[2024-01-24 11:13:55,722] [INFO] Target genome list was writen to GCF_009877435.1_ASM987743v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:13:55,732] [INFO] Task started: fastANI
[2024-01-24 11:13:55,733] [INFO] Running command: fastANI --query /var/lib/cwl/stg003dafa1-54cc-4a21-8475-59221b64d44e/GCF_009877435.1_ASM987743v1_genomic.fna.gz --refList GCF_009877435.1_ASM987743v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009877435.1_ASM987743v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:14:02,573] [INFO] Task succeeded: fastANI
[2024-01-24 11:14:02,581] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:14:02,582] [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_009877435.1	s__Heliomicrobium gestii	100.0	1206	1208	d__Bacteria;p__Firmicutes_B;c__Desulfitobacteriia;o__Heliobacteriales;f__Heliobacteriaceae;g__Heliomicrobium	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_009877425.1	s__Heliomicrobium undosum	84.7201	868	1208	d__Bacteria;p__Firmicutes_B;c__Desulfitobacteriia;o__Heliobacteriales;f__Heliobacteriaceae;g__Heliomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000019165.1	s__Heliomicrobium modesticaldum	83.5065	687	1208	d__Bacteria;p__Firmicutes_B;c__Desulfitobacteriia;o__Heliobacteriales;f__Heliobacteriaceae;g__Heliomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014502795.1	s__Heliobacterium chlorum	77.9054	212	1208	d__Bacteria;p__Firmicutes_B;c__Desulfitobacteriia;o__Heliobacteriales;f__Heliobacteriaceae;g__Heliobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009720735.1	s__Heliobacillus mobilis	77.83	210	1208	d__Bacteria;p__Firmicutes_B;c__Desulfitobacteriia;o__Heliobacteriales;f__Heliobacteriaceae;g__Heliobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:14:02,583] [INFO] GTDB search result was written to GCF_009877435.1_ASM987743v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:14:02,583] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:14:02,586] [INFO] DFAST_QC result json was written to GCF_009877435.1_ASM987743v1_genomic.fna/dqc_result.json
[2024-01-24 11:14:02,586] [INFO] DFAST_QC completed!
[2024-01-24 11:14:02,586] [INFO] Total running time: 0h1m5s