[2024-01-24 12:31:34,203] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:34,205] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:34,205] [INFO] DQC Reference Directory: /var/lib/cwl/stg49002313-9a28-4e6c-8d0c-0ab2a0da4b50/dqc_reference
[2024-01-24 12:31:35,405] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:35,406] [INFO] Task started: Prodigal
[2024-01-24 12:31:35,406] [INFO] Running command: gunzip -c /var/lib/cwl/stg57b297ce-0004-417e-b52d-3ead4020e73b/GCF_021496725.1_ASM2149672v1_genomic.fna.gz | prodigal -d GCF_021496725.1_ASM2149672v1_genomic.fna/cds.fna -a GCF_021496725.1_ASM2149672v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:36,630] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:36,630] [INFO] Task started: HMMsearch
[2024-01-24 12:31:36,631] [INFO] Running command: hmmsearch --tblout GCF_021496725.1_ASM2149672v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg49002313-9a28-4e6c-8d0c-0ab2a0da4b50/dqc_reference/reference_markers.hmm GCF_021496725.1_ASM2149672v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:36,805] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:36,806] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg57b297ce-0004-417e-b52d-3ead4020e73b/GCF_021496725.1_ASM2149672v1_genomic.fna.gz]
[2024-01-24 12:31:36,821] [INFO] Query marker FASTA was written to GCF_021496725.1_ASM2149672v1_genomic.fna/markers.fasta
[2024-01-24 12:31:36,821] [INFO] Task started: Blastn
[2024-01-24 12:31:36,821] [INFO] Running command: blastn -query GCF_021496725.1_ASM2149672v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg49002313-9a28-4e6c-8d0c-0ab2a0da4b50/dqc_reference/reference_markers.fasta -out GCF_021496725.1_ASM2149672v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:37,376] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:37,380] [INFO] Selected 16 target genomes.
[2024-01-24 12:31:37,381] [INFO] Target genome list was writen to GCF_021496725.1_ASM2149672v1_genomic.fna/target_genomes.txt
[2024-01-24 12:31:37,428] [INFO] Task started: fastANI
[2024-01-24 12:31:37,429] [INFO] Running command: fastANI --query /var/lib/cwl/stg57b297ce-0004-417e-b52d-3ead4020e73b/GCF_021496725.1_ASM2149672v1_genomic.fna.gz --refList GCF_021496725.1_ASM2149672v1_genomic.fna/target_genomes.txt --output GCF_021496725.1_ASM2149672v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:31:41,982] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:41,983] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg49002313-9a28-4e6c-8d0c-0ab2a0da4b50/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:31:41,983] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg49002313-9a28-4e6c-8d0c-0ab2a0da4b50/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:31:41,990] [INFO] Found 2 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:31:41,990] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:31:41,990] [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
Spiroplasma platyhelix	strain=PALS-1	GCA_021496725.1	301585	301585	type	True	100.0	248	248	95	conclusive
Spiroplasma platyhelix	strain=PALS-1	GCA_012163225.1	301585	301585	type	True	99.9855	245	248	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 12:31:41,992] [INFO] DFAST Taxonomy check result was written to GCF_021496725.1_ASM2149672v1_genomic.fna/tc_result.tsv
[2024-01-24 12:31:41,992] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:31:41,992] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:31:41,992] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg49002313-9a28-4e6c-8d0c-0ab2a0da4b50/dqc_reference/checkm_data
[2024-01-24 12:31:41,993] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:31:42,003] [INFO] Task started: CheckM
[2024-01-24 12:31:42,003] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021496725.1_ASM2149672v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021496725.1_ASM2149672v1_genomic.fna/checkm_input GCF_021496725.1_ASM2149672v1_genomic.fna/checkm_result
[2024-01-24 12:31:54,318] [INFO] Task succeeded: CheckM
[2024-01-24 12:31:54,367] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:31:54,423] [INFO] ===== Completeness check finished =====
[2024-01-24 12:31:54,424] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:31:54,425] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021496725.1_ASM2149672v1_genomic.fna/markers.fasta)
[2024-01-24 12:31:54,425] [INFO] Task started: Blastn
[2024-01-24 12:31:54,425] [INFO] Running command: blastn -query GCF_021496725.1_ASM2149672v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg49002313-9a28-4e6c-8d0c-0ab2a0da4b50/dqc_reference/reference_markers_gtdb.fasta -out GCF_021496725.1_ASM2149672v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:55,174] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:55,179] [INFO] Selected 24 target genomes.
[2024-01-24 12:31:55,179] [INFO] Target genome list was writen to GCF_021496725.1_ASM2149672v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:31:55,209] [INFO] Task started: fastANI
[2024-01-24 12:31:55,209] [INFO] Running command: fastANI --query /var/lib/cwl/stg57b297ce-0004-417e-b52d-3ead4020e73b/GCF_021496725.1_ASM2149672v1_genomic.fna.gz --refList GCF_021496725.1_ASM2149672v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021496725.1_ASM2149672v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:32:00,929] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:00,934] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:32:00,934] [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_012163225.1	s__Spiroplasma_D platyhelix	99.9855	245	248	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__VBWQ01;g__Spiroplasma_D	95.0	N/A	N/A	N/A	N/A	1	conclusive
--------------------------------------------------------------------------------
[2024-01-24 12:32:00,936] [INFO] GTDB search result was written to GCF_021496725.1_ASM2149672v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:32:00,937] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:32:00,940] [INFO] DFAST_QC result json was written to GCF_021496725.1_ASM2149672v1_genomic.fna/dqc_result.json
[2024-01-24 12:32:00,940] [INFO] DFAST_QC completed!
[2024-01-24 12:32:00,940] [INFO] Total running time: 0h0m27s