[2024-01-24 13:22:10,725] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:10,729] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:10,729] [INFO] DQC Reference Directory: /var/lib/cwl/stgf4613a7a-53ce-4462-86f4-8ca0513fbac4/dqc_reference
[2024-01-24 13:22:12,138] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:12,139] [INFO] Task started: Prodigal
[2024-01-24 13:22:12,139] [INFO] Running command: gunzip -c /var/lib/cwl/stg75122084-9eb9-45a7-aa84-3cad5f18d9ea/GCF_011812965.1_ASM1181296v1_genomic.fna.gz | prodigal -d GCF_011812965.1_ASM1181296v1_genomic.fna/cds.fna -a GCF_011812965.1_ASM1181296v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:16,583] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:16,583] [INFO] Task started: HMMsearch
[2024-01-24 13:22:16,583] [INFO] Running command: hmmsearch --tblout GCF_011812965.1_ASM1181296v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf4613a7a-53ce-4462-86f4-8ca0513fbac4/dqc_reference/reference_markers.hmm GCF_011812965.1_ASM1181296v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:16,799] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:16,800] [INFO] Found 6/6 markers.
[2024-01-24 13:22:16,826] [INFO] Query marker FASTA was written to GCF_011812965.1_ASM1181296v1_genomic.fna/markers.fasta
[2024-01-24 13:22:16,827] [INFO] Task started: Blastn
[2024-01-24 13:22:16,827] [INFO] Running command: blastn -query GCF_011812965.1_ASM1181296v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf4613a7a-53ce-4462-86f4-8ca0513fbac4/dqc_reference/reference_markers.fasta -out GCF_011812965.1_ASM1181296v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:17,524] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:17,527] [INFO] Selected 15 target genomes.
[2024-01-24 13:22:17,528] [INFO] Target genome list was writen to GCF_011812965.1_ASM1181296v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:17,533] [INFO] Task started: fastANI
[2024-01-24 13:22:17,533] [INFO] Running command: fastANI --query /var/lib/cwl/stg75122084-9eb9-45a7-aa84-3cad5f18d9ea/GCF_011812965.1_ASM1181296v1_genomic.fna.gz --refList GCF_011812965.1_ASM1181296v1_genomic.fna/target_genomes.txt --output GCF_011812965.1_ASM1181296v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:23,328] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:23,329] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf4613a7a-53ce-4462-86f4-8ca0513fbac4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:23,329] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf4613a7a-53ce-4462-86f4-8ca0513fbac4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:23,334] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:22:23,334] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:22:23,334] [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
Entomospira entomophilus	strain=BR193	GCA_011812965.1	2719988	2719988	type	True	100.0	591	591	95	conclusive
Entomospira nematocera	strain=BR208	GCA_011812995.1	2719987	2719987	type	True	82.3906	394	591	95	below_threshold
Entomospira culicis	strain=BR151	GCA_011812985.1	2719989	2719989	type	True	77.8069	68	591	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:23,341] [INFO] DFAST Taxonomy check result was written to GCF_011812965.1_ASM1181296v1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:23,342] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:23,342] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:23,342] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf4613a7a-53ce-4462-86f4-8ca0513fbac4/dqc_reference/checkm_data
[2024-01-24 13:22:23,343] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:23,371] [INFO] Task started: CheckM
[2024-01-24 13:22:23,372] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011812965.1_ASM1181296v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011812965.1_ASM1181296v1_genomic.fna/checkm_input GCF_011812965.1_ASM1181296v1_genomic.fna/checkm_result
[2024-01-24 13:22:44,320] [INFO] Task succeeded: CheckM
[2024-01-24 13:22:44,321] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:22:44,336] [INFO] ===== Completeness check finished =====
[2024-01-24 13:22:44,336] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:22:44,337] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011812965.1_ASM1181296v1_genomic.fna/markers.fasta)
[2024-01-24 13:22:44,337] [INFO] Task started: Blastn
[2024-01-24 13:22:44,337] [INFO] Running command: blastn -query GCF_011812965.1_ASM1181296v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf4613a7a-53ce-4462-86f4-8ca0513fbac4/dqc_reference/reference_markers_gtdb.fasta -out GCF_011812965.1_ASM1181296v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:45,338] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:45,342] [INFO] Selected 19 target genomes.
[2024-01-24 13:22:45,342] [INFO] Target genome list was writen to GCF_011812965.1_ASM1181296v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:22:45,399] [INFO] Task started: fastANI
[2024-01-24 13:22:45,399] [INFO] Running command: fastANI --query /var/lib/cwl/stg75122084-9eb9-45a7-aa84-3cad5f18d9ea/GCF_011812965.1_ASM1181296v1_genomic.fna.gz --refList GCF_011812965.1_ASM1181296v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011812965.1_ASM1181296v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:22:53,837] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:53,842] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:22:53,843] [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_011812965.1	s__Entomospira entomophilus	100.0	591	591	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__WRBN01;f__WRBN01;g__Entomospira	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_011812995.1	s__Entomospira nematocera	82.3765	395	591	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__WRBN01;f__WRBN01;g__Entomospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011812985.1	s__Entomospira culicis	77.5761	68	591	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__WRBN01;f__WRBN01;g__Entomospira	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:22:53,854] [INFO] GTDB search result was written to GCF_011812965.1_ASM1181296v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:22:53,856] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:22:53,860] [INFO] DFAST_QC result json was written to GCF_011812965.1_ASM1181296v1_genomic.fna/dqc_result.json
[2024-01-24 13:22:53,860] [INFO] DFAST_QC completed!
[2024-01-24 13:22:53,860] [INFO] Total running time: 0h0m43s