[2024-01-24 14:22:33,483] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:33,489] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:33,489] [INFO] DQC Reference Directory: /var/lib/cwl/stg52dab385-4fd2-4171-9851-ce1da0e5dea8/dqc_reference
[2024-01-24 14:22:34,777] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:34,778] [INFO] Task started: Prodigal
[2024-01-24 14:22:34,778] [INFO] Running command: gunzip -c /var/lib/cwl/stg3453d78e-1038-4a70-97d0-2165aed26884/GCF_006540265.1_ASM654026v1_genomic.fna.gz | prodigal -d GCF_006540265.1_ASM654026v1_genomic.fna/cds.fna -a GCF_006540265.1_ASM654026v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:38,391] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:38,392] [INFO] Task started: HMMsearch
[2024-01-24 14:22:38,392] [INFO] Running command: hmmsearch --tblout GCF_006540265.1_ASM654026v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg52dab385-4fd2-4171-9851-ce1da0e5dea8/dqc_reference/reference_markers.hmm GCF_006540265.1_ASM654026v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:38,674] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:38,675] [INFO] Found 6/6 markers.
[2024-01-24 14:22:38,699] [INFO] Query marker FASTA was written to GCF_006540265.1_ASM654026v1_genomic.fna/markers.fasta
[2024-01-24 14:22:38,699] [INFO] Task started: Blastn
[2024-01-24 14:22:38,699] [INFO] Running command: blastn -query GCF_006540265.1_ASM654026v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg52dab385-4fd2-4171-9851-ce1da0e5dea8/dqc_reference/reference_markers.fasta -out GCF_006540265.1_ASM654026v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:39,289] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:39,294] [INFO] Selected 9 target genomes.
[2024-01-24 14:22:39,295] [INFO] Target genome list was writen to GCF_006540265.1_ASM654026v1_genomic.fna/target_genomes.txt
[2024-01-24 14:22:39,300] [INFO] Task started: fastANI
[2024-01-24 14:22:39,300] [INFO] Running command: fastANI --query /var/lib/cwl/stg3453d78e-1038-4a70-97d0-2165aed26884/GCF_006540265.1_ASM654026v1_genomic.fna.gz --refList GCF_006540265.1_ASM654026v1_genomic.fna/target_genomes.txt --output GCF_006540265.1_ASM654026v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:22:42,178] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:42,179] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg52dab385-4fd2-4171-9851-ce1da0e5dea8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:22:42,179] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg52dab385-4fd2-4171-9851-ce1da0e5dea8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:22:42,188] [INFO] Found 4 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 14:22:42,189] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:22:42,189] [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
Amylolactobacillus amylophilus	strain=NBRC 15881	GCA_006540265.1	1603	1603	suspected-type	True	100.0	501	502	95	conclusive
Amylolactobacillus amylophilus	strain=DSM 20533	GCA_001936335.1	1603	1603	suspected-type	True	99.9989	502	502	95	conclusive
Amylolactobacillus amylophilus	strain=DSM 20533	GCA_001436185.1	1603	1603	suspected-type	True	99.9982	502	502	95	conclusive
Amylolactobacillus amylophilus	strain=JCM 1125	GCA_001311665.1	1603	1603	suspected-type	True	99.8361	497	502	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 14:22:42,191] [INFO] DFAST Taxonomy check result was written to GCF_006540265.1_ASM654026v1_genomic.fna/tc_result.tsv
[2024-01-24 14:22:42,191] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:22:42,192] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:22:42,192] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg52dab385-4fd2-4171-9851-ce1da0e5dea8/dqc_reference/checkm_data
[2024-01-24 14:22:42,194] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:22:42,212] [INFO] Task started: CheckM
[2024-01-24 14:22:42,212] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006540265.1_ASM654026v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006540265.1_ASM654026v1_genomic.fna/checkm_input GCF_006540265.1_ASM654026v1_genomic.fna/checkm_result
[2024-01-24 14:23:02,014] [INFO] Task succeeded: CheckM
[2024-01-24 14:23:02,015] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:23:02,036] [INFO] ===== Completeness check finished =====
[2024-01-24 14:23:02,036] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:23:02,037] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006540265.1_ASM654026v1_genomic.fna/markers.fasta)
[2024-01-24 14:23:02,037] [INFO] Task started: Blastn
[2024-01-24 14:23:02,037] [INFO] Running command: blastn -query GCF_006540265.1_ASM654026v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg52dab385-4fd2-4171-9851-ce1da0e5dea8/dqc_reference/reference_markers_gtdb.fasta -out GCF_006540265.1_ASM654026v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:02,808] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:02,814] [INFO] Selected 25 target genomes.
[2024-01-24 14:23:02,814] [INFO] Target genome list was writen to GCF_006540265.1_ASM654026v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:23:02,840] [INFO] Task started: fastANI
[2024-01-24 14:23:02,841] [INFO] Running command: fastANI --query /var/lib/cwl/stg3453d78e-1038-4a70-97d0-2165aed26884/GCF_006540265.1_ASM654026v1_genomic.fna.gz --refList GCF_006540265.1_ASM654026v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006540265.1_ASM654026v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:23:12,660] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:12,666] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:23:12,667] [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_001936335.1	s__Amylolactobacillus amylophilus	99.9989	502	502	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Amylolactobacillus	95.0	99.96	99.85	1.00	1.00	5	conclusive
--------------------------------------------------------------------------------
[2024-01-24 14:23:12,669] [INFO] GTDB search result was written to GCF_006540265.1_ASM654026v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:23:12,670] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:23:12,678] [INFO] DFAST_QC result json was written to GCF_006540265.1_ASM654026v1_genomic.fna/dqc_result.json
[2024-01-24 14:23:12,678] [INFO] DFAST_QC completed!
[2024-01-24 14:23:12,678] [INFO] Total running time: 0h0m39s