[2024-01-24 15:10:41,170] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:10:41,172] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:10:41,172] [INFO] DQC Reference Directory: /var/lib/cwl/stgfa031f02-285c-4299-9040-1db82eceb01f/dqc_reference
[2024-01-24 15:10:42,502] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:10:42,503] [INFO] Task started: Prodigal
[2024-01-24 15:10:42,503] [INFO] Running command: gunzip -c /var/lib/cwl/stg8ae57efb-fccd-4c65-9127-9ad9c5c002af/GCF_002224645.1_ASM222464v1_genomic.fna.gz | prodigal -d GCF_002224645.1_ASM222464v1_genomic.fna/cds.fna -a GCF_002224645.1_ASM222464v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:10:52,487] [INFO] Task succeeded: Prodigal
[2024-01-24 15:10:52,487] [INFO] Task started: HMMsearch
[2024-01-24 15:10:52,488] [INFO] Running command: hmmsearch --tblout GCF_002224645.1_ASM222464v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfa031f02-285c-4299-9040-1db82eceb01f/dqc_reference/reference_markers.hmm GCF_002224645.1_ASM222464v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:10:52,806] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:10:52,807] [INFO] Found 6/6 markers.
[2024-01-24 15:10:52,846] [INFO] Query marker FASTA was written to GCF_002224645.1_ASM222464v1_genomic.fna/markers.fasta
[2024-01-24 15:10:52,847] [INFO] Task started: Blastn
[2024-01-24 15:10:52,847] [INFO] Running command: blastn -query GCF_002224645.1_ASM222464v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfa031f02-285c-4299-9040-1db82eceb01f/dqc_reference/reference_markers.fasta -out GCF_002224645.1_ASM222464v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:10:53,481] [INFO] Task succeeded: Blastn
[2024-01-24 15:10:53,484] [INFO] Selected 15 target genomes.
[2024-01-24 15:10:53,484] [INFO] Target genome list was writen to GCF_002224645.1_ASM222464v1_genomic.fna/target_genomes.txt
[2024-01-24 15:10:53,489] [INFO] Task started: fastANI
[2024-01-24 15:10:53,490] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ae57efb-fccd-4c65-9127-9ad9c5c002af/GCF_002224645.1_ASM222464v1_genomic.fna.gz --refList GCF_002224645.1_ASM222464v1_genomic.fna/target_genomes.txt --output GCF_002224645.1_ASM222464v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:11:01,463] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:01,464] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfa031f02-285c-4299-9040-1db82eceb01f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:11:01,464] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfa031f02-285c-4299-9040-1db82eceb01f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:11:01,468] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:11:01,468] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:11:01,468] [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
Dehalobacterium formicoaceticum	strain=DMC	GCA_002224645.1	51515	51515	type	True	100.0	1253	1255	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 15:11:01,475] [INFO] DFAST Taxonomy check result was written to GCF_002224645.1_ASM222464v1_genomic.fna/tc_result.tsv
[2024-01-24 15:11:01,476] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:11:01,476] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:11:01,476] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfa031f02-285c-4299-9040-1db82eceb01f/dqc_reference/checkm_data
[2024-01-24 15:11:01,478] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:11:01,523] [INFO] Task started: CheckM
[2024-01-24 15:11:01,523] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002224645.1_ASM222464v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002224645.1_ASM222464v1_genomic.fna/checkm_input GCF_002224645.1_ASM222464v1_genomic.fna/checkm_result
[2024-01-24 15:11:36,125] [INFO] Task succeeded: CheckM
[2024-01-24 15:11:36,127] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:11:36,153] [INFO] ===== Completeness check finished =====
[2024-01-24 15:11:36,153] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:11:36,154] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002224645.1_ASM222464v1_genomic.fna/markers.fasta)
[2024-01-24 15:11:36,154] [INFO] Task started: Blastn
[2024-01-24 15:11:36,154] [INFO] Running command: blastn -query GCF_002224645.1_ASM222464v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfa031f02-285c-4299-9040-1db82eceb01f/dqc_reference/reference_markers_gtdb.fasta -out GCF_002224645.1_ASM222464v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:37,003] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:37,009] [INFO] Selected 19 target genomes.
[2024-01-24 15:11:37,010] [INFO] Target genome list was writen to GCF_002224645.1_ASM222464v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:11:37,090] [INFO] Task started: fastANI
[2024-01-24 15:11:37,090] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ae57efb-fccd-4c65-9127-9ad9c5c002af/GCF_002224645.1_ASM222464v1_genomic.fna.gz --refList GCF_002224645.1_ASM222464v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002224645.1_ASM222464v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:11:46,475] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:46,481] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:11:46,481] [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_002224645.1	s__Dehalobacterium formicoaceticum	100.0	1254	1255	d__Bacteria;p__Firmicutes_B;c__Dehalobacteriia;o__Dehalobacteriales;f__Dehalobacteriaceae;g__Dehalobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002777255.1	s__Formimonas warabiya	77.9632	137	1255	d__Bacteria;p__Firmicutes_B;c__Dehalobacteriia;o__Dehalobacteriales;f__Dehalobacteriaceae;g__Formimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012838175.1	s__DUPU01 sp012838175	76.6927	122	1255	d__Bacteria;p__Firmicutes_B;c__Dehalobacteriia;o__Dehalobacteriales;f__Dehalobacteriaceae;g__DUPU01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:11:46,483] [INFO] GTDB search result was written to GCF_002224645.1_ASM222464v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:11:46,484] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:11:46,486] [INFO] DFAST_QC result json was written to GCF_002224645.1_ASM222464v1_genomic.fna/dqc_result.json
[2024-01-24 15:11:46,486] [INFO] DFAST_QC completed!
[2024-01-24 15:11:46,486] [INFO] Total running time: 0h1m5s