[2024-01-24 13:28:19,229] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:19,232] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:19,232] [INFO] DQC Reference Directory: /var/lib/cwl/stgf94aeec2-98b1-4516-8130-7170ea400f07/dqc_reference
[2024-01-24 13:28:20,598] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:20,603] [INFO] Task started: Prodigal
[2024-01-24 13:28:20,603] [INFO] Running command: gunzip -c /var/lib/cwl/stg7cb0a27a-5d90-4730-9c47-017158442bd7/GCF_022539405.1_ASM2253940v1_genomic.fna.gz | prodigal -d GCF_022539405.1_ASM2253940v1_genomic.fna/cds.fna -a GCF_022539405.1_ASM2253940v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:27,097] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:27,097] [INFO] Task started: HMMsearch
[2024-01-24 13:28:27,097] [INFO] Running command: hmmsearch --tblout GCF_022539405.1_ASM2253940v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf94aeec2-98b1-4516-8130-7170ea400f07/dqc_reference/reference_markers.hmm GCF_022539405.1_ASM2253940v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:27,400] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:27,401] [INFO] Found 6/6 markers.
[2024-01-24 13:28:27,429] [INFO] Query marker FASTA was written to GCF_022539405.1_ASM2253940v1_genomic.fna/markers.fasta
[2024-01-24 13:28:27,430] [INFO] Task started: Blastn
[2024-01-24 13:28:27,430] [INFO] Running command: blastn -query GCF_022539405.1_ASM2253940v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf94aeec2-98b1-4516-8130-7170ea400f07/dqc_reference/reference_markers.fasta -out GCF_022539405.1_ASM2253940v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:28,040] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:28,044] [INFO] Selected 20 target genomes.
[2024-01-24 13:28:28,044] [INFO] Target genome list was writen to GCF_022539405.1_ASM2253940v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:28,054] [INFO] Task started: fastANI
[2024-01-24 13:28:28,054] [INFO] Running command: fastANI --query /var/lib/cwl/stg7cb0a27a-5d90-4730-9c47-017158442bd7/GCF_022539405.1_ASM2253940v1_genomic.fna.gz --refList GCF_022539405.1_ASM2253940v1_genomic.fna/target_genomes.txt --output GCF_022539405.1_ASM2253940v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:41,710] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:41,710] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf94aeec2-98b1-4516-8130-7170ea400f07/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:41,711] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf94aeec2-98b1-4516-8130-7170ea400f07/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:41,714] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:28:41,714] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:41,714] [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
Natranaerofaba carboxydovora	strain=ANCO1	GCA_022539405.1	2742683	2742683	type	True	100.0	1087	1088	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 13:28:41,719] [INFO] DFAST Taxonomy check result was written to GCF_022539405.1_ASM2253940v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:41,720] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:41,720] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:41,721] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf94aeec2-98b1-4516-8130-7170ea400f07/dqc_reference/checkm_data
[2024-01-24 13:28:41,722] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:41,773] [INFO] Task started: CheckM
[2024-01-24 13:28:41,773] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022539405.1_ASM2253940v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022539405.1_ASM2253940v1_genomic.fna/checkm_input GCF_022539405.1_ASM2253940v1_genomic.fna/checkm_result
[2024-01-24 13:29:06,722] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:06,724] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:06,744] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:06,744] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:06,745] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022539405.1_ASM2253940v1_genomic.fna/markers.fasta)
[2024-01-24 13:29:06,745] [INFO] Task started: Blastn
[2024-01-24 13:29:06,745] [INFO] Running command: blastn -query GCF_022539405.1_ASM2253940v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf94aeec2-98b1-4516-8130-7170ea400f07/dqc_reference/reference_markers_gtdb.fasta -out GCF_022539405.1_ASM2253940v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:07,537] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:07,540] [INFO] Selected 30 target genomes.
[2024-01-24 13:29:07,541] [INFO] Target genome list was writen to GCF_022539405.1_ASM2253940v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:07,573] [INFO] Task started: fastANI
[2024-01-24 13:29:07,573] [INFO] Running command: fastANI --query /var/lib/cwl/stg7cb0a27a-5d90-4730-9c47-017158442bd7/GCF_022539405.1_ASM2253940v1_genomic.fna.gz --refList GCF_022539405.1_ASM2253940v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022539405.1_ASM2253940v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:18,475] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:18,476] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:29:18,477] [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
--------------------------------------------------------------------------------
[2024-01-24 13:29:18,478] [INFO] GTDB search result was written to GCF_022539405.1_ASM2253940v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:18,479] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:18,481] [INFO] DFAST_QC result json was written to GCF_022539405.1_ASM2253940v1_genomic.fna/dqc_result.json
[2024-01-24 13:29:18,481] [INFO] DFAST_QC completed!
[2024-01-24 13:29:18,481] [INFO] Total running time: 0h0m59s