[2023-06-13 08:07:26,149] [INFO] DFAST_QC pipeline started.
[2023-06-13 08:07:26,159] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 08:07:26,159] [INFO] DQC Reference Directory: /var/lib/cwl/stg6fc32640-e9c8-4e3e-af45-ed584c8bc8bd/dqc_reference
[2023-06-13 08:07:27,432] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 08:07:27,432] [INFO] Task started: Prodigal
[2023-06-13 08:07:27,433] [INFO] Running command: gunzip -c /var/lib/cwl/stga467e99a-0c92-4533-8ec0-6f789619c6ad/GCA_022690815.1_ASM2269081v1_genomic.fna.gz | prodigal -d GCA_022690815.1_ASM2269081v1_genomic.fna/cds.fna -a GCA_022690815.1_ASM2269081v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 08:07:34,991] [INFO] Task succeeded: Prodigal
[2023-06-13 08:07:34,992] [INFO] Task started: HMMsearch
[2023-06-13 08:07:34,992] [INFO] Running command: hmmsearch --tblout GCA_022690815.1_ASM2269081v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6fc32640-e9c8-4e3e-af45-ed584c8bc8bd/dqc_reference/reference_markers.hmm GCA_022690815.1_ASM2269081v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 08:07:35,222] [INFO] Task succeeded: HMMsearch
[2023-06-13 08:07:35,224] [INFO] Found 6/6 markers.
[2023-06-13 08:07:35,254] [INFO] Query marker FASTA was written to GCA_022690815.1_ASM2269081v1_genomic.fna/markers.fasta
[2023-06-13 08:07:35,255] [INFO] Task started: Blastn
[2023-06-13 08:07:35,255] [INFO] Running command: blastn -query GCA_022690815.1_ASM2269081v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6fc32640-e9c8-4e3e-af45-ed584c8bc8bd/dqc_reference/reference_markers.fasta -out GCA_022690815.1_ASM2269081v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 08:07:35,856] [INFO] Task succeeded: Blastn
[2023-06-13 08:07:35,861] [INFO] Selected 15 target genomes.
[2023-06-13 08:07:35,862] [INFO] Target genome list was writen to GCA_022690815.1_ASM2269081v1_genomic.fna/target_genomes.txt
[2023-06-13 08:07:35,867] [INFO] Task started: fastANI
[2023-06-13 08:07:35,867] [INFO] Running command: fastANI --query /var/lib/cwl/stga467e99a-0c92-4533-8ec0-6f789619c6ad/GCA_022690815.1_ASM2269081v1_genomic.fna.gz --refList GCA_022690815.1_ASM2269081v1_genomic.fna/target_genomes.txt --output GCA_022690815.1_ASM2269081v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 08:07:45,565] [INFO] Task succeeded: fastANI
[2023-06-13 08:07:45,566] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6fc32640-e9c8-4e3e-af45-ed584c8bc8bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 08:07:45,567] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6fc32640-e9c8-4e3e-af45-ed584c8bc8bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 08:07:45,572] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 08:07:45,573] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 08:07:45,573] [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
Ferrimicrobium acidiphilum	strain=T23	GCA_000949255.1	121039	121039	type	True	78.7032	175	819	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 08:07:45,575] [INFO] DFAST Taxonomy check result was written to GCA_022690815.1_ASM2269081v1_genomic.fna/tc_result.tsv
[2023-06-13 08:07:45,576] [INFO] ===== Taxonomy check completed =====
[2023-06-13 08:07:45,576] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 08:07:45,577] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6fc32640-e9c8-4e3e-af45-ed584c8bc8bd/dqc_reference/checkm_data
[2023-06-13 08:07:45,578] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 08:07:45,606] [INFO] Task started: CheckM
[2023-06-13 08:07:45,606] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022690815.1_ASM2269081v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022690815.1_ASM2269081v1_genomic.fna/checkm_input GCA_022690815.1_ASM2269081v1_genomic.fna/checkm_result
[2023-06-13 08:08:13,485] [INFO] Task succeeded: CheckM
[2023-06-13 08:08:13,487] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 08:08:13,507] [INFO] ===== Completeness check finished =====
[2023-06-13 08:08:13,507] [INFO] ===== Start GTDB Search =====
[2023-06-13 08:08:13,508] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022690815.1_ASM2269081v1_genomic.fna/markers.fasta)
[2023-06-13 08:08:13,508] [INFO] Task started: Blastn
[2023-06-13 08:08:13,508] [INFO] Running command: blastn -query GCA_022690815.1_ASM2269081v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6fc32640-e9c8-4e3e-af45-ed584c8bc8bd/dqc_reference/reference_markers_gtdb.fasta -out GCA_022690815.1_ASM2269081v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 08:08:14,375] [INFO] Task succeeded: Blastn
[2023-06-13 08:08:14,380] [INFO] Selected 23 target genomes.
[2023-06-13 08:08:14,380] [INFO] Target genome list was writen to GCA_022690815.1_ASM2269081v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 08:08:14,395] [INFO] Task started: fastANI
[2023-06-13 08:08:14,395] [INFO] Running command: fastANI --query /var/lib/cwl/stga467e99a-0c92-4533-8ec0-6f789619c6ad/GCA_022690815.1_ASM2269081v1_genomic.fna.gz --refList GCA_022690815.1_ASM2269081v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022690815.1_ASM2269081v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 08:08:25,143] [INFO] Task succeeded: fastANI
[2023-06-13 08:08:25,148] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 08:08:25,148] [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_000745905.1	s__Ferrimicrobium acidiphilum	78.573	168	819	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Acidimicrobiaceae;g__Ferrimicrobium	95.0	99.97	99.97	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2023-06-13 08:08:25,150] [INFO] GTDB search result was written to GCA_022690815.1_ASM2269081v1_genomic.fna/result_gtdb.tsv
[2023-06-13 08:08:25,151] [INFO] ===== GTDB Search completed =====
[2023-06-13 08:08:25,153] [INFO] DFAST_QC result json was written to GCA_022690815.1_ASM2269081v1_genomic.fna/dqc_result.json
[2023-06-13 08:08:25,154] [INFO] DFAST_QC completed!
[2023-06-13 08:08:25,154] [INFO] Total running time: 0h0m59s