[2023-06-29 14:06:23,338] [INFO] DFAST_QC pipeline started.
[2023-06-29 14:06:23,340] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 14:06:23,340] [INFO] DQC Reference Directory: /var/lib/cwl/stgd6e3eeae-4752-481b-87ae-5e87cb74f317/dqc_reference
[2023-06-29 14:06:24,555] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 14:06:24,556] [INFO] Task started: Prodigal
[2023-06-29 14:06:24,556] [INFO] Running command: gunzip -c /var/lib/cwl/stgc5bd3418-dad7-4949-8e54-fb24c1720ae7/GCA_021847875.1_ASM2184787v1_genomic.fna.gz | prodigal -d GCA_021847875.1_ASM2184787v1_genomic.fna/cds.fna -a GCA_021847875.1_ASM2184787v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 14:06:32,953] [INFO] Task succeeded: Prodigal
[2023-06-29 14:06:32,954] [INFO] Task started: HMMsearch
[2023-06-29 14:06:32,954] [INFO] Running command: hmmsearch --tblout GCA_021847875.1_ASM2184787v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd6e3eeae-4752-481b-87ae-5e87cb74f317/dqc_reference/reference_markers.hmm GCA_021847875.1_ASM2184787v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 14:06:33,177] [INFO] Task succeeded: HMMsearch
[2023-06-29 14:06:33,178] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgc5bd3418-dad7-4949-8e54-fb24c1720ae7/GCA_021847875.1_ASM2184787v1_genomic.fna.gz]
[2023-06-29 14:06:33,213] [INFO] Query marker FASTA was written to GCA_021847875.1_ASM2184787v1_genomic.fna/markers.fasta
[2023-06-29 14:06:33,214] [INFO] Task started: Blastn
[2023-06-29 14:06:33,214] [INFO] Running command: blastn -query GCA_021847875.1_ASM2184787v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd6e3eeae-4752-481b-87ae-5e87cb74f317/dqc_reference/reference_markers.fasta -out GCA_021847875.1_ASM2184787v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 14:06:33,768] [INFO] Task succeeded: Blastn
[2023-06-29 14:06:33,772] [INFO] Selected 11 target genomes.
[2023-06-29 14:06:33,773] [INFO] Target genome list was writen to GCA_021847875.1_ASM2184787v1_genomic.fna/target_genomes.txt
[2023-06-29 14:06:33,775] [INFO] Task started: fastANI
[2023-06-29 14:06:33,775] [INFO] Running command: fastANI --query /var/lib/cwl/stgc5bd3418-dad7-4949-8e54-fb24c1720ae7/GCA_021847875.1_ASM2184787v1_genomic.fna.gz --refList GCA_021847875.1_ASM2184787v1_genomic.fna/target_genomes.txt --output GCA_021847875.1_ASM2184787v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 14:06:42,163] [INFO] Task succeeded: fastANI
[2023-06-29 14:06:42,163] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd6e3eeae-4752-481b-87ae-5e87cb74f317/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 14:06:42,164] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd6e3eeae-4752-481b-87ae-5e87cb74f317/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 14:06:42,171] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 14:06:42,171] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 14:06:42,171] [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
Acidobacterium capsulatum	strain=ATCC 51196	GCA_000022565.1	33075	33075	type	True	77.275	52	575	95	below_threshold
Paracidobacterium acidisoli	strain=4G-K13	GCA_003428625.2	2303751	2303751	type	True	76.428	50	575	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 14:06:42,174] [INFO] DFAST Taxonomy check result was written to GCA_021847875.1_ASM2184787v1_genomic.fna/tc_result.tsv
[2023-06-29 14:06:42,175] [INFO] ===== Taxonomy check completed =====
[2023-06-29 14:06:42,175] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 14:06:42,175] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd6e3eeae-4752-481b-87ae-5e87cb74f317/dqc_reference/checkm_data
[2023-06-29 14:06:42,176] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 14:06:42,212] [INFO] Task started: CheckM
[2023-06-29 14:06:42,212] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021847875.1_ASM2184787v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021847875.1_ASM2184787v1_genomic.fna/checkm_input GCA_021847875.1_ASM2184787v1_genomic.fna/checkm_result
[2023-06-29 14:07:11,686] [INFO] Task succeeded: CheckM
[2023-06-29 14:07:11,688] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 41.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 14:07:11,725] [INFO] ===== Completeness check finished =====
[2023-06-29 14:07:11,726] [INFO] ===== Start GTDB Search =====
[2023-06-29 14:07:11,726] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021847875.1_ASM2184787v1_genomic.fna/markers.fasta)
[2023-06-29 14:07:11,727] [INFO] Task started: Blastn
[2023-06-29 14:07:11,727] [INFO] Running command: blastn -query GCA_021847875.1_ASM2184787v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd6e3eeae-4752-481b-87ae-5e87cb74f317/dqc_reference/reference_markers_gtdb.fasta -out GCA_021847875.1_ASM2184787v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 14:07:12,433] [INFO] Task succeeded: Blastn
[2023-06-29 14:07:12,438] [INFO] Selected 14 target genomes.
[2023-06-29 14:07:12,438] [INFO] Target genome list was writen to GCA_021847875.1_ASM2184787v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 14:07:12,464] [INFO] Task started: fastANI
[2023-06-29 14:07:12,465] [INFO] Running command: fastANI --query /var/lib/cwl/stgc5bd3418-dad7-4949-8e54-fb24c1720ae7/GCA_021847875.1_ASM2184787v1_genomic.fna.gz --refList GCA_021847875.1_ASM2184787v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021847875.1_ASM2184787v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 14:07:22,063] [INFO] Task succeeded: fastANI
[2023-06-29 14:07:22,070] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 14:07:22,071] [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_000022565.1	s__Acidobacterium capsulatum	77.275	52	575	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Acidobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003428625.2	s__Palsa-343 sp003428625	76.428	50	575	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Palsa-343	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 14:07:22,074] [INFO] GTDB search result was written to GCA_021847875.1_ASM2184787v1_genomic.fna/result_gtdb.tsv
[2023-06-29 14:07:22,075] [INFO] ===== GTDB Search completed =====
[2023-06-29 14:07:22,078] [INFO] DFAST_QC result json was written to GCA_021847875.1_ASM2184787v1_genomic.fna/dqc_result.json
[2023-06-29 14:07:22,078] [INFO] DFAST_QC completed!
[2023-06-29 14:07:22,078] [INFO] Total running time: 0h0m59s