[2024-01-24 12:06:33,582] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:33,584] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:33,584] [INFO] DQC Reference Directory: /var/lib/cwl/stge38b23b9-8aba-450f-8a94-e7574f956ad0/dqc_reference
[2024-01-24 12:06:34,816] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:34,817] [INFO] Task started: Prodigal
[2024-01-24 12:06:34,817] [INFO] Running command: gunzip -c /var/lib/cwl/stg593c35e5-6dfd-4c6e-90ae-245a86d7c219/GCF_014384895.1_ASM1438489v1_genomic.fna.gz | prodigal -d GCF_014384895.1_ASM1438489v1_genomic.fna/cds.fna -a GCF_014384895.1_ASM1438489v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:45,502] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:45,502] [INFO] Task started: HMMsearch
[2024-01-24 12:06:45,503] [INFO] Running command: hmmsearch --tblout GCF_014384895.1_ASM1438489v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge38b23b9-8aba-450f-8a94-e7574f956ad0/dqc_reference/reference_markers.hmm GCF_014384895.1_ASM1438489v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:45,772] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:45,773] [INFO] Found 6/6 markers.
[2024-01-24 12:06:45,814] [INFO] Query marker FASTA was written to GCF_014384895.1_ASM1438489v1_genomic.fna/markers.fasta
[2024-01-24 12:06:45,815] [INFO] Task started: Blastn
[2024-01-24 12:06:45,815] [INFO] Running command: blastn -query GCF_014384895.1_ASM1438489v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge38b23b9-8aba-450f-8a94-e7574f956ad0/dqc_reference/reference_markers.fasta -out GCF_014384895.1_ASM1438489v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:46,389] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:46,393] [INFO] Selected 14 target genomes.
[2024-01-24 12:06:46,393] [INFO] Target genome list was writen to GCF_014384895.1_ASM1438489v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:46,399] [INFO] Task started: fastANI
[2024-01-24 12:06:46,400] [INFO] Running command: fastANI --query /var/lib/cwl/stg593c35e5-6dfd-4c6e-90ae-245a86d7c219/GCF_014384895.1_ASM1438489v1_genomic.fna.gz --refList GCF_014384895.1_ASM1438489v1_genomic.fna/target_genomes.txt --output GCF_014384895.1_ASM1438489v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:54,924] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:54,924] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge38b23b9-8aba-450f-8a94-e7574f956ad0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:54,924] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge38b23b9-8aba-450f-8a94-e7574f956ad0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:54,928] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:06:54,928] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:06:54,928] [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
Bianquea renquensis	strain=NSJ-32	GCA_014384895.1	2763661	2763661	type	True	100.0	1255	1262	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 12:06:54,930] [INFO] DFAST Taxonomy check result was written to GCF_014384895.1_ASM1438489v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:54,930] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:54,930] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:54,931] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge38b23b9-8aba-450f-8a94-e7574f956ad0/dqc_reference/checkm_data
[2024-01-24 12:06:54,932] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:54,974] [INFO] Task started: CheckM
[2024-01-24 12:06:54,974] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014384895.1_ASM1438489v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014384895.1_ASM1438489v1_genomic.fna/checkm_input GCF_014384895.1_ASM1438489v1_genomic.fna/checkm_result
[2024-01-24 12:07:30,489] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:30,490] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:30,511] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:30,511] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:30,511] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014384895.1_ASM1438489v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:30,512] [INFO] Task started: Blastn
[2024-01-24 12:07:30,512] [INFO] Running command: blastn -query GCF_014384895.1_ASM1438489v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge38b23b9-8aba-450f-8a94-e7574f956ad0/dqc_reference/reference_markers_gtdb.fasta -out GCF_014384895.1_ASM1438489v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:31,245] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:31,249] [INFO] Selected 21 target genomes.
[2024-01-24 12:07:31,249] [INFO] Target genome list was writen to GCF_014384895.1_ASM1438489v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:31,288] [INFO] Task started: fastANI
[2024-01-24 12:07:31,289] [INFO] Running command: fastANI --query /var/lib/cwl/stg593c35e5-6dfd-4c6e-90ae-245a86d7c219/GCF_014384895.1_ASM1438489v1_genomic.fna.gz --refList GCF_014384895.1_ASM1438489v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014384895.1_ASM1438489v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:43,129] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:43,133] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:07:43,134] [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
GCA_014384895.1	s__NSJ-32 sp014384895	100.0	1255	1262	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__UBA1390;g__NSJ-32	95.0	99.82	99.82	0.83	0.83	2	conclusive
--------------------------------------------------------------------------------
[2024-01-24 12:07:43,136] [INFO] GTDB search result was written to GCF_014384895.1_ASM1438489v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:43,136] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:43,140] [INFO] DFAST_QC result json was written to GCF_014384895.1_ASM1438489v1_genomic.fna/dqc_result.json
[2024-01-24 12:07:43,140] [INFO] DFAST_QC completed!
[2024-01-24 12:07:43,140] [INFO] Total running time: 0h1m10s