[2024-01-24 13:01:26,531] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:26,534] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:26,534] [INFO] DQC Reference Directory: /var/lib/cwl/stga1654c3c-ff42-4201-bdd5-66161c1d01c9/dqc_reference
[2024-01-24 13:01:27,900] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:27,901] [INFO] Task started: Prodigal
[2024-01-24 13:01:27,901] [INFO] Running command: gunzip -c /var/lib/cwl/stgf4c1073d-8d78-4f3c-bb51-06b6d0d65e6e/GCF_009649955.1_ASM964995v1_genomic.fna.gz | prodigal -d GCF_009649955.1_ASM964995v1_genomic.fna/cds.fna -a GCF_009649955.1_ASM964995v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:35,536] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:35,536] [INFO] Task started: HMMsearch
[2024-01-24 13:01:35,537] [INFO] Running command: hmmsearch --tblout GCF_009649955.1_ASM964995v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga1654c3c-ff42-4201-bdd5-66161c1d01c9/dqc_reference/reference_markers.hmm GCF_009649955.1_ASM964995v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:35,824] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:35,825] [INFO] Found 6/6 markers.
[2024-01-24 13:01:35,852] [INFO] Query marker FASTA was written to GCF_009649955.1_ASM964995v1_genomic.fna/markers.fasta
[2024-01-24 13:01:35,853] [INFO] Task started: Blastn
[2024-01-24 13:01:35,853] [INFO] Running command: blastn -query GCF_009649955.1_ASM964995v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga1654c3c-ff42-4201-bdd5-66161c1d01c9/dqc_reference/reference_markers.fasta -out GCF_009649955.1_ASM964995v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:36,419] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:36,423] [INFO] Selected 17 target genomes.
[2024-01-24 13:01:36,423] [INFO] Target genome list was writen to GCF_009649955.1_ASM964995v1_genomic.fna/target_genomes.txt
[2024-01-24 13:01:36,444] [INFO] Task started: fastANI
[2024-01-24 13:01:36,445] [INFO] Running command: fastANI --query /var/lib/cwl/stgf4c1073d-8d78-4f3c-bb51-06b6d0d65e6e/GCF_009649955.1_ASM964995v1_genomic.fna.gz --refList GCF_009649955.1_ASM964995v1_genomic.fna/target_genomes.txt --output GCF_009649955.1_ASM964995v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:01:51,188] [INFO] Task succeeded: fastANI
[2024-01-24 13:01:51,189] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga1654c3c-ff42-4201-bdd5-66161c1d01c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:01:51,189] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga1654c3c-ff42-4201-bdd5-66161c1d01c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:01:51,194] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:01:51,194] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:01:51,195] [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
Heliorestis convoluta	strain=HH	GCA_009649955.1	356322	356322	type	True	100.0	1072	1072	95	conclusive
Heliorestis acidaminivorans	strain=DSM 24790	GCA_008933955.1	553427	553427	type	True	80.5476	407	1072	95	below_threshold
Heliobacterium mobile	strain=DSM 6151	GCA_009720735.1	28064	28064	type	True	77.1405	53	1072	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:01:51,196] [INFO] DFAST Taxonomy check result was written to GCF_009649955.1_ASM964995v1_genomic.fna/tc_result.tsv
[2024-01-24 13:01:51,198] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:01:51,198] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:01:51,199] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga1654c3c-ff42-4201-bdd5-66161c1d01c9/dqc_reference/checkm_data
[2024-01-24 13:01:51,201] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:01:51,246] [INFO] Task started: CheckM
[2024-01-24 13:01:51,247] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009649955.1_ASM964995v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009649955.1_ASM964995v1_genomic.fna/checkm_input GCF_009649955.1_ASM964995v1_genomic.fna/checkm_result
[2024-01-24 13:02:20,076] [INFO] Task succeeded: CheckM
[2024-01-24 13:02:20,078] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:02:20,104] [INFO] ===== Completeness check finished =====
[2024-01-24 13:02:20,105] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:02:20,106] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009649955.1_ASM964995v1_genomic.fna/markers.fasta)
[2024-01-24 13:02:20,106] [INFO] Task started: Blastn
[2024-01-24 13:02:20,107] [INFO] Running command: blastn -query GCF_009649955.1_ASM964995v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga1654c3c-ff42-4201-bdd5-66161c1d01c9/dqc_reference/reference_markers_gtdb.fasta -out GCF_009649955.1_ASM964995v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:20,830] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:20,835] [INFO] Selected 23 target genomes.
[2024-01-24 13:02:20,836] [INFO] Target genome list was writen to GCF_009649955.1_ASM964995v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:02:20,855] [INFO] Task started: fastANI
[2024-01-24 13:02:20,855] [INFO] Running command: fastANI --query /var/lib/cwl/stgf4c1073d-8d78-4f3c-bb51-06b6d0d65e6e/GCF_009649955.1_ASM964995v1_genomic.fna.gz --refList GCF_009649955.1_ASM964995v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009649955.1_ASM964995v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:02:33,796] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:33,800] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:02:33,800] [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_009649955.1	s__Heliorestis convoluta	100.0	1072	1072	d__Bacteria;p__Firmicutes_B;c__Desulfitobacteriia;o__Heliobacteriales;f__Heliobacteriaceae;g__Heliorestis	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_008933955.1	s__Heliorestis acidaminivorans	80.5345	409	1072	d__Bacteria;p__Firmicutes_B;c__Desulfitobacteriia;o__Heliobacteriales;f__Heliobacteriaceae;g__Heliorestis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009720735.1	s__Heliobacillus mobilis	77.5238	54	1072	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 13:02:33,801] [INFO] GTDB search result was written to GCF_009649955.1_ASM964995v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:02:33,802] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:02:33,812] [INFO] DFAST_QC result json was written to GCF_009649955.1_ASM964995v1_genomic.fna/dqc_result.json
[2024-01-24 13:02:33,813] [INFO] DFAST_QC completed!
[2024-01-24 13:02:33,813] [INFO] Total running time: 0h1m7s