[2024-01-25 20:19:06,321] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:19:06,328] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:19:06,329] [INFO] DQC Reference Directory: /var/lib/cwl/stgf4acf638-afec-4c90-abbb-42ef618c22cf/dqc_reference
[2024-01-25 20:19:07,524] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:19:07,525] [INFO] Task started: Prodigal
[2024-01-25 20:19:07,525] [INFO] Running command: gunzip -c /var/lib/cwl/stgb1ddc19d-e2e3-45d6-a48e-694892127b4d/GCF_014384805.1_ASM1438480v1_genomic.fna.gz | prodigal -d GCF_014384805.1_ASM1438480v1_genomic.fna/cds.fna -a GCF_014384805.1_ASM1438480v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:19:13,223] [INFO] Task succeeded: Prodigal
[2024-01-25 20:19:13,224] [INFO] Task started: HMMsearch
[2024-01-25 20:19:13,224] [INFO] Running command: hmmsearch --tblout GCF_014384805.1_ASM1438480v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf4acf638-afec-4c90-abbb-42ef618c22cf/dqc_reference/reference_markers.hmm GCF_014384805.1_ASM1438480v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:19:13,429] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:19:13,430] [INFO] Found 6/6 markers.
[2024-01-25 20:19:13,451] [INFO] Query marker FASTA was written to GCF_014384805.1_ASM1438480v1_genomic.fna/markers.fasta
[2024-01-25 20:19:13,451] [INFO] Task started: Blastn
[2024-01-25 20:19:13,451] [INFO] Running command: blastn -query GCF_014384805.1_ASM1438480v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf4acf638-afec-4c90-abbb-42ef618c22cf/dqc_reference/reference_markers.fasta -out GCF_014384805.1_ASM1438480v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:19:13,994] [INFO] Task succeeded: Blastn
[2024-01-25 20:19:13,997] [INFO] Selected 22 target genomes.
[2024-01-25 20:19:13,997] [INFO] Target genome list was writen to GCF_014384805.1_ASM1438480v1_genomic.fna/target_genomes.txt
[2024-01-25 20:19:14,010] [INFO] Task started: fastANI
[2024-01-25 20:19:14,010] [INFO] Running command: fastANI --query /var/lib/cwl/stgb1ddc19d-e2e3-45d6-a48e-694892127b4d/GCF_014384805.1_ASM1438480v1_genomic.fna.gz --refList GCF_014384805.1_ASM1438480v1_genomic.fna/target_genomes.txt --output GCF_014384805.1_ASM1438480v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:19:27,021] [INFO] Task succeeded: fastANI
[2024-01-25 20:19:27,021] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf4acf638-afec-4c90-abbb-42ef618c22cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:19:27,022] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf4acf638-afec-4c90-abbb-42ef618c22cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:19:27,025] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:19:27,025] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:19:27,025] [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
Guopingia tenuis	strain=NSJ-63	GCA_014384805.1	2763656	2763656	type	True	100.0	729	730	95	conclusive
--------------------------------------------------------------------------------
[2024-01-25 20:19:27,026] [INFO] DFAST Taxonomy check result was written to GCF_014384805.1_ASM1438480v1_genomic.fna/tc_result.tsv
[2024-01-25 20:19:27,026] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:19:27,027] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:19:27,027] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf4acf638-afec-4c90-abbb-42ef618c22cf/dqc_reference/checkm_data
[2024-01-25 20:19:27,027] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:19:27,051] [INFO] Task started: CheckM
[2024-01-25 20:19:27,051] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014384805.1_ASM1438480v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014384805.1_ASM1438480v1_genomic.fna/checkm_input GCF_014384805.1_ASM1438480v1_genomic.fna/checkm_result
[2024-01-25 20:19:48,304] [INFO] Task succeeded: CheckM
[2024-01-25 20:19:48,308] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:19:48,336] [INFO] ===== Completeness check finished =====
[2024-01-25 20:19:48,336] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:19:48,336] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014384805.1_ASM1438480v1_genomic.fna/markers.fasta)
[2024-01-25 20:19:48,337] [INFO] Task started: Blastn
[2024-01-25 20:19:48,337] [INFO] Running command: blastn -query GCF_014384805.1_ASM1438480v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf4acf638-afec-4c90-abbb-42ef618c22cf/dqc_reference/reference_markers_gtdb.fasta -out GCF_014384805.1_ASM1438480v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:19:49,190] [INFO] Task succeeded: Blastn
[2024-01-25 20:19:49,193] [INFO] Selected 22 target genomes.
[2024-01-25 20:19:49,193] [INFO] Target genome list was writen to GCF_014384805.1_ASM1438480v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:19:49,213] [INFO] Task started: fastANI
[2024-01-25 20:19:49,213] [INFO] Running command: fastANI --query /var/lib/cwl/stgb1ddc19d-e2e3-45d6-a48e-694892127b4d/GCF_014384805.1_ASM1438480v1_genomic.fna.gz --refList GCF_014384805.1_ASM1438480v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014384805.1_ASM1438480v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:19:58,819] [INFO] Task succeeded: fastANI
[2024-01-25 20:19:58,822] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:19:58,822] [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_014384805.1	s__NSJ-63 sp014384805	100.0	729	730	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Christensenellaceae;g__NSJ-63	95.0	98.08	98.04	0.97	0.96	3	conclusive
GCA_910588425.1	s__QANA01 sp910588425	77.3007	85	730	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Christensenellaceae;g__QANA01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:19:58,823] [INFO] GTDB search result was written to GCF_014384805.1_ASM1438480v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:19:58,824] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:19:58,827] [INFO] DFAST_QC result json was written to GCF_014384805.1_ASM1438480v1_genomic.fna/dqc_result.json
[2024-01-25 20:19:58,827] [INFO] DFAST_QC completed!
[2024-01-25 20:19:58,827] [INFO] Total running time: 0h0m53s