[2024-01-24 11:59:12,800] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:59:12,804] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:59:12,804] [INFO] DQC Reference Directory: /var/lib/cwl/stg6332b0af-e4c0-4a89-97e0-e7e32f6b2457/dqc_reference
[2024-01-24 11:59:14,162] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:59:14,163] [INFO] Task started: Prodigal
[2024-01-24 11:59:14,163] [INFO] Running command: gunzip -c /var/lib/cwl/stg3bb213db-fa46-493a-ac9d-e98fd101d565/GCF_003633725.1_ASM363372v1_genomic.fna.gz | prodigal -d GCF_003633725.1_ASM363372v1_genomic.fna/cds.fna -a GCF_003633725.1_ASM363372v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:19,580] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:19,580] [INFO] Task started: HMMsearch
[2024-01-24 11:59:19,581] [INFO] Running command: hmmsearch --tblout GCF_003633725.1_ASM363372v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6332b0af-e4c0-4a89-97e0-e7e32f6b2457/dqc_reference/reference_markers.hmm GCF_003633725.1_ASM363372v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:19,810] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:19,812] [INFO] Found 6/6 markers.
[2024-01-24 11:59:19,844] [INFO] Query marker FASTA was written to GCF_003633725.1_ASM363372v1_genomic.fna/markers.fasta
[2024-01-24 11:59:19,844] [INFO] Task started: Blastn
[2024-01-24 11:59:19,844] [INFO] Running command: blastn -query GCF_003633725.1_ASM363372v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6332b0af-e4c0-4a89-97e0-e7e32f6b2457/dqc_reference/reference_markers.fasta -out GCF_003633725.1_ASM363372v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:20,522] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:20,526] [INFO] Selected 15 target genomes.
[2024-01-24 11:59:20,526] [INFO] Target genome list was writen to GCF_003633725.1_ASM363372v1_genomic.fna/target_genomes.txt
[2024-01-24 11:59:20,551] [INFO] Task started: fastANI
[2024-01-24 11:59:20,551] [INFO] Running command: fastANI --query /var/lib/cwl/stg3bb213db-fa46-493a-ac9d-e98fd101d565/GCF_003633725.1_ASM363372v1_genomic.fna.gz --refList GCF_003633725.1_ASM363372v1_genomic.fna/target_genomes.txt --output GCF_003633725.1_ASM363372v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:59:33,035] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:33,036] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6332b0af-e4c0-4a89-97e0-e7e32f6b2457/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:59:33,036] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6332b0af-e4c0-4a89-97e0-e7e32f6b2457/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:59:33,040] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:59:33,040] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:59:33,040] [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
Brockia lithotrophica	strain=DSM 22653	GCA_003633725.1	933949	933949	type	True	100.0	619	620	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 11:59:33,042] [INFO] DFAST Taxonomy check result was written to GCF_003633725.1_ASM363372v1_genomic.fna/tc_result.tsv
[2024-01-24 11:59:33,043] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:59:33,043] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:59:33,043] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6332b0af-e4c0-4a89-97e0-e7e32f6b2457/dqc_reference/checkm_data
[2024-01-24 11:59:33,044] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:59:33,070] [INFO] Task started: CheckM
[2024-01-24 11:59:33,071] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003633725.1_ASM363372v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003633725.1_ASM363372v1_genomic.fna/checkm_input GCF_003633725.1_ASM363372v1_genomic.fna/checkm_result
[2024-01-24 11:59:54,872] [INFO] Task succeeded: CheckM
[2024-01-24 11:59:54,873] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:59:54,892] [INFO] ===== Completeness check finished =====
[2024-01-24 11:59:54,893] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:59:54,893] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003633725.1_ASM363372v1_genomic.fna/markers.fasta)
[2024-01-24 11:59:54,894] [INFO] Task started: Blastn
[2024-01-24 11:59:54,894] [INFO] Running command: blastn -query GCF_003633725.1_ASM363372v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6332b0af-e4c0-4a89-97e0-e7e32f6b2457/dqc_reference/reference_markers_gtdb.fasta -out GCF_003633725.1_ASM363372v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:55,833] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:55,837] [INFO] Selected 17 target genomes.
[2024-01-24 11:59:55,837] [INFO] Target genome list was writen to GCF_003633725.1_ASM363372v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:59:55,854] [INFO] Task started: fastANI
[2024-01-24 11:59:55,855] [INFO] Running command: fastANI --query /var/lib/cwl/stg3bb213db-fa46-493a-ac9d-e98fd101d565/GCF_003633725.1_ASM363372v1_genomic.fna.gz --refList GCF_003633725.1_ASM363372v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003633725.1_ASM363372v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:00:06,417] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:06,421] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:00:06,421] [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_003633725.1	s__Brockia lithotrophica	100.0	619	620	d__Bacteria;p__Firmicutes;c__Bacilli;o__DSM-22653;f__DSM-22653;g__Brockia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003050565.1	s__Brockia lithotrophica_A	87.4482	503	620	d__Bacteria;p__Firmicutes;c__Bacilli;o__DSM-22653;f__DSM-22653;g__Brockia	95.0	98.87	98.28	0.95	0.89	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:00:06,439] [INFO] GTDB search result was written to GCF_003633725.1_ASM363372v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:00:06,439] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:00:06,442] [INFO] DFAST_QC result json was written to GCF_003633725.1_ASM363372v1_genomic.fna/dqc_result.json
[2024-01-24 12:00:06,443] [INFO] DFAST_QC completed!
[2024-01-24 12:00:06,443] [INFO] Total running time: 0h0m54s