[2024-01-24 13:03:20,577] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:03:20,579] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:03:20,580] [INFO] DQC Reference Directory: /var/lib/cwl/stg5025c8d1-79f5-41cc-91c6-2f1241c5f64d/dqc_reference
[2024-01-24 13:03:21,842] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:03:21,843] [INFO] Task started: Prodigal
[2024-01-24 13:03:21,843] [INFO] Running command: gunzip -c /var/lib/cwl/stgfdfeb90b-703d-4534-bbef-2d973685b624/GCF_004341035.1_ASM434103v1_genomic.fna.gz | prodigal -d GCF_004341035.1_ASM434103v1_genomic.fna/cds.fna -a GCF_004341035.1_ASM434103v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:03:32,500] [INFO] Task succeeded: Prodigal
[2024-01-24 13:03:32,500] [INFO] Task started: HMMsearch
[2024-01-24 13:03:32,500] [INFO] Running command: hmmsearch --tblout GCF_004341035.1_ASM434103v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5025c8d1-79f5-41cc-91c6-2f1241c5f64d/dqc_reference/reference_markers.hmm GCF_004341035.1_ASM434103v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:03:32,792] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:03:32,794] [INFO] Found 6/6 markers.
[2024-01-24 13:03:32,837] [INFO] Query marker FASTA was written to GCF_004341035.1_ASM434103v1_genomic.fna/markers.fasta
[2024-01-24 13:03:32,838] [INFO] Task started: Blastn
[2024-01-24 13:03:32,838] [INFO] Running command: blastn -query GCF_004341035.1_ASM434103v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5025c8d1-79f5-41cc-91c6-2f1241c5f64d/dqc_reference/reference_markers.fasta -out GCF_004341035.1_ASM434103v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:03:33,407] [INFO] Task succeeded: Blastn
[2024-01-24 13:03:33,410] [INFO] Selected 26 target genomes.
[2024-01-24 13:03:33,410] [INFO] Target genome list was writen to GCF_004341035.1_ASM434103v1_genomic.fna/target_genomes.txt
[2024-01-24 13:03:33,421] [INFO] Task started: fastANI
[2024-01-24 13:03:33,421] [INFO] Running command: fastANI --query /var/lib/cwl/stgfdfeb90b-703d-4534-bbef-2d973685b624/GCF_004341035.1_ASM434103v1_genomic.fna.gz --refList GCF_004341035.1_ASM434103v1_genomic.fna/target_genomes.txt --output GCF_004341035.1_ASM434103v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:03:50,961] [INFO] Task succeeded: fastANI
[2024-01-24 13:03:50,962] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5025c8d1-79f5-41cc-91c6-2f1241c5f64d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:03:50,963] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5025c8d1-79f5-41cc-91c6-2f1241c5f64d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:03:50,970] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:03:50,970] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:03:50,971] [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
Scopulibacillus darangshiensis	strain=DSM 19377	GCA_004341035.1	442528	442528	type	True	100.0	1498	1503	95	conclusive
Scopulibacillus daqui	strain=DSM 28236	GCA_016908855.1	1469162	1469162	type	True	76.642	125	1503	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:03:50,973] [INFO] DFAST Taxonomy check result was written to GCF_004341035.1_ASM434103v1_genomic.fna/tc_result.tsv
[2024-01-24 13:03:50,973] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:03:50,974] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:03:50,974] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5025c8d1-79f5-41cc-91c6-2f1241c5f64d/dqc_reference/checkm_data
[2024-01-24 13:03:50,976] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:03:51,020] [INFO] Task started: CheckM
[2024-01-24 13:03:51,021] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004341035.1_ASM434103v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004341035.1_ASM434103v1_genomic.fna/checkm_input GCF_004341035.1_ASM434103v1_genomic.fna/checkm_result
[2024-01-24 13:04:28,135] [INFO] Task succeeded: CheckM
[2024-01-24 13:04:28,137] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:04:28,165] [INFO] ===== Completeness check finished =====
[2024-01-24 13:04:28,166] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:04:28,166] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004341035.1_ASM434103v1_genomic.fna/markers.fasta)
[2024-01-24 13:04:28,167] [INFO] Task started: Blastn
[2024-01-24 13:04:28,167] [INFO] Running command: blastn -query GCF_004341035.1_ASM434103v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5025c8d1-79f5-41cc-91c6-2f1241c5f64d/dqc_reference/reference_markers_gtdb.fasta -out GCF_004341035.1_ASM434103v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:04:29,313] [INFO] Task succeeded: Blastn
[2024-01-24 13:04:29,319] [INFO] Selected 29 target genomes.
[2024-01-24 13:04:29,319] [INFO] Target genome list was writen to GCF_004341035.1_ASM434103v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:04:29,340] [INFO] Task started: fastANI
[2024-01-24 13:04:29,340] [INFO] Running command: fastANI --query /var/lib/cwl/stgfdfeb90b-703d-4534-bbef-2d973685b624/GCF_004341035.1_ASM434103v1_genomic.fna.gz --refList GCF_004341035.1_ASM434103v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004341035.1_ASM434103v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:04:53,246] [INFO] Task succeeded: fastANI
[2024-01-24 13:04:53,250] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:04:53,250] [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_004341035.1	s__Scopulibacillus darangshiensis	100.0	1498	1503	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Sporolactobacillaceae;g__Scopulibacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_006517395.1	s__Terrilactibacillus laevilacticus	76.9512	76	1503	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Sporolactobacillaceae;g__Terrilactibacillus	95.0	99.19	99.19	0.93	0.93	2	-
GCF_016908855.1	s__Scopulibacillus daqui	76.642	125	1503	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Sporolactobacillaceae;g__Scopulibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:04:53,252] [INFO] GTDB search result was written to GCF_004341035.1_ASM434103v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:04:53,252] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:04:53,255] [INFO] DFAST_QC result json was written to GCF_004341035.1_ASM434103v1_genomic.fna/dqc_result.json
[2024-01-24 13:04:53,255] [INFO] DFAST_QC completed!
[2024-01-24 13:04:53,255] [INFO] Total running time: 0h1m33s