[2024-01-24 12:31:34,168] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:34,170] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:34,171] [INFO] DQC Reference Directory: /var/lib/cwl/stga3c0fdcf-e732-4400-865f-701712a025f2/dqc_reference
[2024-01-24 12:31:35,416] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:35,417] [INFO] Task started: Prodigal
[2024-01-24 12:31:35,417] [INFO] Running command: gunzip -c /var/lib/cwl/stg66703bca-7b96-48f0-8e0c-120440e2c66f/GCF_001484965.1_ASM148496v1_genomic.fna.gz | prodigal -d GCF_001484965.1_ASM148496v1_genomic.fna/cds.fna -a GCF_001484965.1_ASM148496v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:45,614] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:45,614] [INFO] Task started: HMMsearch
[2024-01-24 12:31:45,614] [INFO] Running command: hmmsearch --tblout GCF_001484965.1_ASM148496v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga3c0fdcf-e732-4400-865f-701712a025f2/dqc_reference/reference_markers.hmm GCF_001484965.1_ASM148496v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:45,878] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:45,879] [INFO] Found 6/6 markers.
[2024-01-24 12:31:45,915] [INFO] Query marker FASTA was written to GCF_001484965.1_ASM148496v1_genomic.fna/markers.fasta
[2024-01-24 12:31:45,915] [INFO] Task started: Blastn
[2024-01-24 12:31:45,916] [INFO] Running command: blastn -query GCF_001484965.1_ASM148496v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga3c0fdcf-e732-4400-865f-701712a025f2/dqc_reference/reference_markers.fasta -out GCF_001484965.1_ASM148496v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:46,493] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:46,497] [INFO] Selected 23 target genomes.
[2024-01-24 12:31:46,498] [INFO] Target genome list was writen to GCF_001484965.1_ASM148496v1_genomic.fna/target_genomes.txt
[2024-01-24 12:31:46,538] [INFO] Task started: fastANI
[2024-01-24 12:31:46,538] [INFO] Running command: fastANI --query /var/lib/cwl/stg66703bca-7b96-48f0-8e0c-120440e2c66f/GCF_001484965.1_ASM148496v1_genomic.fna.gz --refList GCF_001484965.1_ASM148496v1_genomic.fna/target_genomes.txt --output GCF_001484965.1_ASM148496v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:32:01,217] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:01,218] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga3c0fdcf-e732-4400-865f-701712a025f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:32:01,218] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga3c0fdcf-e732-4400-865f-701712a025f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:32:01,225] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:32:01,225] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:32:01,225] [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
Alkalihalobacillus shacheensis	strain=HNA-14	GCA_001484965.1	1649580	1649580	type	True	100.0	1283	1287	95	conclusive
Alkalihalobacillus krulwichiae	strain=NBRC 102362	GCA_001591945.1	199441	199441	type	True	76.7451	54	1287	95	below_threshold
Alkalihalobacillus krulwichiae	strain=AM31D	GCA_002109385.1	199441	199441	type	True	76.6528	54	1287	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:32:01,227] [INFO] DFAST Taxonomy check result was written to GCF_001484965.1_ASM148496v1_genomic.fna/tc_result.tsv
[2024-01-24 12:32:01,228] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:32:01,228] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:32:01,228] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga3c0fdcf-e732-4400-865f-701712a025f2/dqc_reference/checkm_data
[2024-01-24 12:32:01,229] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:32:01,267] [INFO] Task started: CheckM
[2024-01-24 12:32:01,267] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001484965.1_ASM148496v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001484965.1_ASM148496v1_genomic.fna/checkm_input GCF_001484965.1_ASM148496v1_genomic.fna/checkm_result
[2024-01-24 12:32:36,255] [INFO] Task succeeded: CheckM
[2024-01-24 12:32:36,257] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:32:36,281] [INFO] ===== Completeness check finished =====
[2024-01-24 12:32:36,281] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:32:36,282] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001484965.1_ASM148496v1_genomic.fna/markers.fasta)
[2024-01-24 12:32:36,282] [INFO] Task started: Blastn
[2024-01-24 12:32:36,282] [INFO] Running command: blastn -query GCF_001484965.1_ASM148496v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga3c0fdcf-e732-4400-865f-701712a025f2/dqc_reference/reference_markers_gtdb.fasta -out GCF_001484965.1_ASM148496v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:37,026] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:37,031] [INFO] Selected 23 target genomes.
[2024-01-24 12:32:37,031] [INFO] Target genome list was writen to GCF_001484965.1_ASM148496v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:32:37,079] [INFO] Task started: fastANI
[2024-01-24 12:32:37,080] [INFO] Running command: fastANI --query /var/lib/cwl/stg66703bca-7b96-48f0-8e0c-120440e2c66f/GCF_001484965.1_ASM148496v1_genomic.fna.gz --refList GCF_001484965.1_ASM148496v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001484965.1_ASM148496v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:32:53,798] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:53,805] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:32:53,806] [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_001484965.1	s__Bacillus_H shacheensis	100.0	1283	1287	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_H	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001598215.1	s__Bacillus_H clausii_B	77.1317	95	1287	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_H	95.0	99.35	99.35	0.94	0.94	2	-
GCF_002109385.1	s__Bacillus_L krulwichiae	76.6528	54	1287	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_L	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:32:53,808] [INFO] GTDB search result was written to GCF_001484965.1_ASM148496v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:32:53,808] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:32:53,811] [INFO] DFAST_QC result json was written to GCF_001484965.1_ASM148496v1_genomic.fna/dqc_result.json
[2024-01-24 12:32:53,812] [INFO] DFAST_QC completed!
[2024-01-24 12:32:53,812] [INFO] Total running time: 0h1m20s