[2024-01-24 12:44:43,806] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:43,808] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:43,808] [INFO] DQC Reference Directory: /var/lib/cwl/stg30497c88-afc0-498c-bea0-5fac247c8fd4/dqc_reference
[2024-01-24 12:44:45,233] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:45,234] [INFO] Task started: Prodigal
[2024-01-24 12:44:45,235] [INFO] Running command: gunzip -c /var/lib/cwl/stg4b13f92d-12a8-4add-a7a5-7f9b5fd868e0/GCF_014639255.1_ASM1463925v1_genomic.fna.gz | prodigal -d GCF_014639255.1_ASM1463925v1_genomic.fna/cds.fna -a GCF_014639255.1_ASM1463925v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:44:54,909] [INFO] Task succeeded: Prodigal
[2024-01-24 12:44:54,910] [INFO] Task started: HMMsearch
[2024-01-24 12:44:54,910] [INFO] Running command: hmmsearch --tblout GCF_014639255.1_ASM1463925v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg30497c88-afc0-498c-bea0-5fac247c8fd4/dqc_reference/reference_markers.hmm GCF_014639255.1_ASM1463925v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:44:55,268] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:44:55,270] [INFO] Found 6/6 markers.
[2024-01-24 12:44:55,313] [INFO] Query marker FASTA was written to GCF_014639255.1_ASM1463925v1_genomic.fna/markers.fasta
[2024-01-24 12:44:55,314] [INFO] Task started: Blastn
[2024-01-24 12:44:55,314] [INFO] Running command: blastn -query GCF_014639255.1_ASM1463925v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg30497c88-afc0-498c-bea0-5fac247c8fd4/dqc_reference/reference_markers.fasta -out GCF_014639255.1_ASM1463925v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:44:55,918] [INFO] Task succeeded: Blastn
[2024-01-24 12:44:55,921] [INFO] Selected 22 target genomes.
[2024-01-24 12:44:55,922] [INFO] Target genome list was writen to GCF_014639255.1_ASM1463925v1_genomic.fna/target_genomes.txt
[2024-01-24 12:44:55,933] [INFO] Task started: fastANI
[2024-01-24 12:44:55,933] [INFO] Running command: fastANI --query /var/lib/cwl/stg4b13f92d-12a8-4add-a7a5-7f9b5fd868e0/GCF_014639255.1_ASM1463925v1_genomic.fna.gz --refList GCF_014639255.1_ASM1463925v1_genomic.fna/target_genomes.txt --output GCF_014639255.1_ASM1463925v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:11,546] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:11,547] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg30497c88-afc0-498c-bea0-5fac247c8fd4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:11,547] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg30497c88-afc0-498c-bea0-5fac247c8fd4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:11,552] [INFO] Found 3 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:45:11,552] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:45:11,552] [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
Pullulanibacillus pueri	strain=CGMCC 1.12777	GCA_014639255.1	1437324	1437324	type	True	100.0	1478	1480	95	conclusive
Pullulanibacillus pueri	strain=DSM 100927	GCA_016908895.1	1437324	1437324	type	True	99.996	1472	1480	95	conclusive
Pullulanibacillus camelliae	strain=CGMCC 1.15371	GCA_014642655.1	1707096	1707096	type	True	78.4693	267	1480	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:11,554] [INFO] DFAST Taxonomy check result was written to GCF_014639255.1_ASM1463925v1_genomic.fna/tc_result.tsv
[2024-01-24 12:45:11,554] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:11,555] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:11,555] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg30497c88-afc0-498c-bea0-5fac247c8fd4/dqc_reference/checkm_data
[2024-01-24 12:45:11,556] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:11,624] [INFO] Task started: CheckM
[2024-01-24 12:45:11,624] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014639255.1_ASM1463925v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014639255.1_ASM1463925v1_genomic.fna/checkm_input GCF_014639255.1_ASM1463925v1_genomic.fna/checkm_result
[2024-01-24 12:45:46,725] [INFO] Task succeeded: CheckM
[2024-01-24 12:45:46,726] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:45:46,750] [INFO] ===== Completeness check finished =====
[2024-01-24 12:45:46,751] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:45:46,751] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014639255.1_ASM1463925v1_genomic.fna/markers.fasta)
[2024-01-24 12:45:46,751] [INFO] Task started: Blastn
[2024-01-24 12:45:46,752] [INFO] Running command: blastn -query GCF_014639255.1_ASM1463925v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg30497c88-afc0-498c-bea0-5fac247c8fd4/dqc_reference/reference_markers_gtdb.fasta -out GCF_014639255.1_ASM1463925v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:47,521] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:47,526] [INFO] Selected 27 target genomes.
[2024-01-24 12:45:47,526] [INFO] Target genome list was writen to GCF_014639255.1_ASM1463925v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:45:47,565] [INFO] Task started: fastANI
[2024-01-24 12:45:47,565] [INFO] Running command: fastANI --query /var/lib/cwl/stg4b13f92d-12a8-4add-a7a5-7f9b5fd868e0/GCF_014639255.1_ASM1463925v1_genomic.fna.gz --refList GCF_014639255.1_ASM1463925v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014639255.1_ASM1463925v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:46:06,105] [INFO] Task succeeded: fastANI
[2024-01-24 12:46:06,111] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:46:06,111] [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_014639255.1	s__Pullulanibacillus pueri	100.0	1478	1480	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Sporolactobacillaceae;g__Pullulanibacillus	95.0	100.00	100.00	0.99	0.99	2	conclusive
GCF_014642655.1	s__Pullulanibacillus camelliae	78.4018	273	1480	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Sporolactobacillaceae;g__Pullulanibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:46:06,113] [INFO] GTDB search result was written to GCF_014639255.1_ASM1463925v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:46:06,114] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:46:06,117] [INFO] DFAST_QC result json was written to GCF_014639255.1_ASM1463925v1_genomic.fna/dqc_result.json
[2024-01-24 12:46:06,117] [INFO] DFAST_QC completed!
[2024-01-24 12:46:06,117] [INFO] Total running time: 0h1m22s