[2024-01-24 15:01:14,954] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:01:14,955] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:01:14,955] [INFO] DQC Reference Directory: /var/lib/cwl/stg2f9e7e0c-5cc1-4785-ba11-91771f441c3c/dqc_reference
[2024-01-24 15:01:16,152] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:01:16,153] [INFO] Task started: Prodigal
[2024-01-24 15:01:16,153] [INFO] Running command: gunzip -c /var/lib/cwl/stgac832110-17bd-4bbd-8817-1cf633dea112/GCF_009877425.1_ASM987742v1_genomic.fna.gz | prodigal -d GCF_009877425.1_ASM987742v1_genomic.fna/cds.fna -a GCF_009877425.1_ASM987742v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:01:26,825] [INFO] Task succeeded: Prodigal
[2024-01-24 15:01:26,826] [INFO] Task started: HMMsearch
[2024-01-24 15:01:26,826] [INFO] Running command: hmmsearch --tblout GCF_009877425.1_ASM987742v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2f9e7e0c-5cc1-4785-ba11-91771f441c3c/dqc_reference/reference_markers.hmm GCF_009877425.1_ASM987742v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:01:27,082] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:01:27,084] [INFO] Found 6/6 markers.
[2024-01-24 15:01:27,115] [INFO] Query marker FASTA was written to GCF_009877425.1_ASM987742v1_genomic.fna/markers.fasta
[2024-01-24 15:01:27,116] [INFO] Task started: Blastn
[2024-01-24 15:01:27,116] [INFO] Running command: blastn -query GCF_009877425.1_ASM987742v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2f9e7e0c-5cc1-4785-ba11-91771f441c3c/dqc_reference/reference_markers.fasta -out GCF_009877425.1_ASM987742v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:01:27,738] [INFO] Task succeeded: Blastn
[2024-01-24 15:01:27,741] [INFO] Selected 7 target genomes.
[2024-01-24 15:01:27,742] [INFO] Target genome list was writen to GCF_009877425.1_ASM987742v1_genomic.fna/target_genomes.txt
[2024-01-24 15:01:27,768] [INFO] Task started: fastANI
[2024-01-24 15:01:27,768] [INFO] Running command: fastANI --query /var/lib/cwl/stgac832110-17bd-4bbd-8817-1cf633dea112/GCF_009877425.1_ASM987742v1_genomic.fna.gz --refList GCF_009877425.1_ASM987742v1_genomic.fna/target_genomes.txt --output GCF_009877425.1_ASM987742v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:01:32,895] [INFO] Task succeeded: fastANI
[2024-01-24 15:01:32,896] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2f9e7e0c-5cc1-4785-ba11-91771f441c3c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:01:32,897] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2f9e7e0c-5cc1-4785-ba11-91771f441c3c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:01:32,907] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:01:32,907] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:01:32,907] [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 undosum	strain=DSM 13378	GCA_009877425.1	121734	121734	type	True	100.0	1235	1237	95	conclusive
Heliomicrobium modesticaldum	strain=Ice1; ATCC 51547	GCA_000019165.1	35701	35701	type	True	89.9528	765	1237	95	below_threshold
Heliomicrobium gestii	strain=DSM 11169	GCA_016908025.1	2699	2699	type	True	84.5555	872	1237	95	below_threshold
Heliomicrobium gestii	strain=DSM 11169	GCA_009877435.1	2699	2699	type	True	84.5522	872	1237	95	below_threshold
Heliobacterium mobile	strain=DSM 6151	GCA_009720735.1	28064	28064	type	True	77.8426	239	1237	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:01:32,909] [INFO] DFAST Taxonomy check result was written to GCF_009877425.1_ASM987742v1_genomic.fna/tc_result.tsv
[2024-01-24 15:01:32,910] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:01:32,910] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:01:32,910] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2f9e7e0c-5cc1-4785-ba11-91771f441c3c/dqc_reference/checkm_data
[2024-01-24 15:01:32,912] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:01:32,955] [INFO] Task started: CheckM
[2024-01-24 15:01:32,955] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009877425.1_ASM987742v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009877425.1_ASM987742v1_genomic.fna/checkm_input GCF_009877425.1_ASM987742v1_genomic.fna/checkm_result
[2024-01-24 15:02:07,720] [INFO] Task succeeded: CheckM
[2024-01-24 15:02:07,721] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:02:07,745] [INFO] ===== Completeness check finished =====
[2024-01-24 15:02:07,745] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:02:07,746] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009877425.1_ASM987742v1_genomic.fna/markers.fasta)
[2024-01-24 15:02:07,746] [INFO] Task started: Blastn
[2024-01-24 15:02:07,746] [INFO] Running command: blastn -query GCF_009877425.1_ASM987742v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2f9e7e0c-5cc1-4785-ba11-91771f441c3c/dqc_reference/reference_markers_gtdb.fasta -out GCF_009877425.1_ASM987742v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:08,678] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:08,682] [INFO] Selected 10 target genomes.
[2024-01-24 15:02:08,682] [INFO] Target genome list was writen to GCF_009877425.1_ASM987742v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:02:08,691] [INFO] Task started: fastANI
[2024-01-24 15:02:08,692] [INFO] Running command: fastANI --query /var/lib/cwl/stgac832110-17bd-4bbd-8817-1cf633dea112/GCF_009877425.1_ASM987742v1_genomic.fna.gz --refList GCF_009877425.1_ASM987742v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009877425.1_ASM987742v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:02:15,244] [INFO] Task succeeded: fastANI
[2024-01-24 15:02:15,256] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:02:15,257] [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_009877425.1	s__Heliomicrobium undosum	100.0	1235	1237	d__Bacteria;p__Firmicutes_B;c__Desulfitobacteriia;o__Heliobacteriales;f__Heliobacteriaceae;g__Heliomicrobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000019165.1	s__Heliomicrobium modesticaldum	89.9764	763	1237	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_009877435.1	s__Heliomicrobium gestii	84.5609	871	1237	d__Bacteria;p__Firmicutes_B;c__Desulfitobacteriia;o__Heliobacteriales;f__Heliobacteriaceae;g__Heliomicrobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014502795.1	s__Heliobacterium chlorum	78.0499	225	1237	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	77.8262	239	1237	d__Bacteria;p__Firmicutes_B;c__Desulfitobacteriia;o__Heliobacteriales;f__Heliobacteriaceae;g__Heliobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004341395.1	s__Heliophilum fasciatum	76.7206	73	1237	d__Bacteria;p__Firmicutes_B;c__Desulfitobacteriia;o__Heliobacteriales;f__Heliobacteriaceae;g__Heliophilum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:02:15,262] [INFO] GTDB search result was written to GCF_009877425.1_ASM987742v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:02:15,263] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:02:15,265] [INFO] DFAST_QC result json was written to GCF_009877425.1_ASM987742v1_genomic.fna/dqc_result.json
[2024-01-24 15:02:15,266] [INFO] DFAST_QC completed!
[2024-01-24 15:02:15,266] [INFO] Total running time: 0h1m0s