[2023-06-27 06:42:40,538] [INFO] DFAST_QC pipeline started.
[2023-06-27 06:42:40,540] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 06:42:40,540] [INFO] DQC Reference Directory: /var/lib/cwl/stg226371f7-f166-4781-8033-70ecf76093f6/dqc_reference
[2023-06-27 06:42:41,914] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 06:42:41,915] [INFO] Task started: Prodigal
[2023-06-27 06:42:41,915] [INFO] Running command: gunzip -c /var/lib/cwl/stg61dbd705-6084-4aa8-9b77-edf92cc88129/GCA_002407765.1_ASM240776v1_genomic.fna.gz | prodigal -d GCA_002407765.1_ASM240776v1_genomic.fna/cds.fna -a GCA_002407765.1_ASM240776v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 06:42:46,284] [INFO] Task succeeded: Prodigal
[2023-06-27 06:42:46,285] [INFO] Task started: HMMsearch
[2023-06-27 06:42:46,285] [INFO] Running command: hmmsearch --tblout GCA_002407765.1_ASM240776v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg226371f7-f166-4781-8033-70ecf76093f6/dqc_reference/reference_markers.hmm GCA_002407765.1_ASM240776v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 06:42:46,499] [INFO] Task succeeded: HMMsearch
[2023-06-27 06:42:46,500] [INFO] Found 6/6 markers.
[2023-06-27 06:42:46,522] [INFO] Query marker FASTA was written to GCA_002407765.1_ASM240776v1_genomic.fna/markers.fasta
[2023-06-27 06:42:46,523] [INFO] Task started: Blastn
[2023-06-27 06:42:46,523] [INFO] Running command: blastn -query GCA_002407765.1_ASM240776v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg226371f7-f166-4781-8033-70ecf76093f6/dqc_reference/reference_markers.fasta -out GCA_002407765.1_ASM240776v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 06:42:47,147] [INFO] Task succeeded: Blastn
[2023-06-27 06:42:47,186] [INFO] Selected 11 target genomes.
[2023-06-27 06:42:47,186] [INFO] Target genome list was writen to GCA_002407765.1_ASM240776v1_genomic.fna/target_genomes.txt
[2023-06-27 06:42:47,187] [INFO] Task started: fastANI
[2023-06-27 06:42:47,188] [INFO] Running command: fastANI --query /var/lib/cwl/stg61dbd705-6084-4aa8-9b77-edf92cc88129/GCA_002407765.1_ASM240776v1_genomic.fna.gz --refList GCA_002407765.1_ASM240776v1_genomic.fna/target_genomes.txt --output GCA_002407765.1_ASM240776v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 06:42:53,618] [INFO] Task succeeded: fastANI
[2023-06-27 06:42:53,619] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg226371f7-f166-4781-8033-70ecf76093f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 06:42:53,619] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg226371f7-f166-4781-8033-70ecf76093f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 06:42:53,624] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2023-06-27 06:42:53,624] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-27 06:42:53,624] [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
Aminobacterium mobile	strain=DSM 12262	GCA_000526395.1	81467	81467	type	True	98.8982	608	638	95	conclusive
--------------------------------------------------------------------------------
[2023-06-27 06:42:53,627] [INFO] DFAST Taxonomy check result was written to GCA_002407765.1_ASM240776v1_genomic.fna/tc_result.tsv
[2023-06-27 06:42:53,628] [INFO] ===== Taxonomy check completed =====
[2023-06-27 06:42:53,628] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 06:42:53,628] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg226371f7-f166-4781-8033-70ecf76093f6/dqc_reference/checkm_data
[2023-06-27 06:42:53,630] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 06:42:53,655] [INFO] Task started: CheckM
[2023-06-27 06:42:53,655] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002407765.1_ASM240776v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002407765.1_ASM240776v1_genomic.fna/checkm_input GCA_002407765.1_ASM240776v1_genomic.fna/checkm_result
[2023-06-27 06:43:14,575] [INFO] Task succeeded: CheckM
[2023-06-27 06:43:14,577] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.74%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 06:43:14,599] [INFO] ===== Completeness check finished =====
[2023-06-27 06:43:14,599] [INFO] ===== Start GTDB Search =====
[2023-06-27 06:43:14,600] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002407765.1_ASM240776v1_genomic.fna/markers.fasta)
[2023-06-27 06:43:14,600] [INFO] Task started: Blastn
[2023-06-27 06:43:14,600] [INFO] Running command: blastn -query GCA_002407765.1_ASM240776v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg226371f7-f166-4781-8033-70ecf76093f6/dqc_reference/reference_markers_gtdb.fasta -out GCA_002407765.1_ASM240776v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 06:43:15,396] [INFO] Task succeeded: Blastn
[2023-06-27 06:43:15,400] [INFO] Selected 17 target genomes.
[2023-06-27 06:43:15,401] [INFO] Target genome list was writen to GCA_002407765.1_ASM240776v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 06:43:15,401] [INFO] Task started: fastANI
[2023-06-27 06:43:15,402] [INFO] Running command: fastANI --query /var/lib/cwl/stg61dbd705-6084-4aa8-9b77-edf92cc88129/GCA_002407765.1_ASM240776v1_genomic.fna.gz --refList GCA_002407765.1_ASM240776v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002407765.1_ASM240776v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 06:43:22,180] [INFO] Task succeeded: fastANI
[2023-06-27 06:43:22,184] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 06:43:22,184] [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_000526395.1	s__Aminobacterium mobile	98.8982	608	638	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Aminobacteriaceae;g__Aminobacterium	95.0	98.90	98.59	0.97	0.94	16	conclusive
GCA_002432275.1	s__Aminobacterium sp002432275	78.3503	123	638	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Aminobacteriaceae;g__Aminobacterium	95.0	99.52	99.48	0.90	0.84	5	-
--------------------------------------------------------------------------------
[2023-06-27 06:43:22,186] [INFO] GTDB search result was written to GCA_002407765.1_ASM240776v1_genomic.fna/result_gtdb.tsv
[2023-06-27 06:43:22,187] [INFO] ===== GTDB Search completed =====
[2023-06-27 06:43:22,190] [INFO] DFAST_QC result json was written to GCA_002407765.1_ASM240776v1_genomic.fna/dqc_result.json
[2023-06-27 06:43:22,190] [INFO] DFAST_QC completed!
[2023-06-27 06:43:22,190] [INFO] Total running time: 0h0m42s