[2024-01-25 17:50:50,900] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:50:50,903] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:50:50,903] [INFO] DQC Reference Directory: /var/lib/cwl/stg98f4ddb0-e573-49ec-8fe3-7c843ae56f84/dqc_reference
[2024-01-25 17:50:52,009] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:50:52,010] [INFO] Task started: Prodigal
[2024-01-25 17:50:52,010] [INFO] Running command: gunzip -c /var/lib/cwl/stga5bcf682-bf9c-4640-9911-db0e3b1ffc83/GCF_028748145.1_ASM2874814v1_genomic.fna.gz | prodigal -d GCF_028748145.1_ASM2874814v1_genomic.fna/cds.fna -a GCF_028748145.1_ASM2874814v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:50:56,035] [INFO] Task succeeded: Prodigal
[2024-01-25 17:50:56,035] [INFO] Task started: HMMsearch
[2024-01-25 17:50:56,035] [INFO] Running command: hmmsearch --tblout GCF_028748145.1_ASM2874814v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg98f4ddb0-e573-49ec-8fe3-7c843ae56f84/dqc_reference/reference_markers.hmm GCF_028748145.1_ASM2874814v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:50:56,220] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:50:56,221] [INFO] Found 6/6 markers.
[2024-01-25 17:50:56,239] [INFO] Query marker FASTA was written to GCF_028748145.1_ASM2874814v1_genomic.fna/markers.fasta
[2024-01-25 17:50:56,239] [INFO] Task started: Blastn
[2024-01-25 17:50:56,239] [INFO] Running command: blastn -query GCF_028748145.1_ASM2874814v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg98f4ddb0-e573-49ec-8fe3-7c843ae56f84/dqc_reference/reference_markers.fasta -out GCF_028748145.1_ASM2874814v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:50:56,805] [INFO] Task succeeded: Blastn
[2024-01-25 17:50:56,808] [INFO] Selected 9 target genomes.
[2024-01-25 17:50:56,808] [INFO] Target genome list was writen to GCF_028748145.1_ASM2874814v1_genomic.fna/target_genomes.txt
[2024-01-25 17:50:56,815] [INFO] Task started: fastANI
[2024-01-25 17:50:56,815] [INFO] Running command: fastANI --query /var/lib/cwl/stga5bcf682-bf9c-4640-9911-db0e3b1ffc83/GCF_028748145.1_ASM2874814v1_genomic.fna.gz --refList GCF_028748145.1_ASM2874814v1_genomic.fna/target_genomes.txt --output GCF_028748145.1_ASM2874814v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:51:00,224] [INFO] Task succeeded: fastANI
[2024-01-25 17:51:00,224] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg98f4ddb0-e573-49ec-8fe3-7c843ae56f84/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:51:00,224] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg98f4ddb0-e573-49ec-8fe3-7c843ae56f84/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:51:00,228] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:51:00,229] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:51:00,229] [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 culicis	strain=BR151	GCA_011812985.1	2719989	2719989	type	True	99.9996	584	588	95	conclusive
Entomospira entomophilus	strain=BR193	GCA_011812965.1	2719988	2719988	type	True	77.9496	75	588	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:51:00,230] [INFO] DFAST Taxonomy check result was written to GCF_028748145.1_ASM2874814v1_genomic.fna/tc_result.tsv
[2024-01-25 17:51:00,230] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:51:00,230] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:51:00,231] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg98f4ddb0-e573-49ec-8fe3-7c843ae56f84/dqc_reference/checkm_data
[2024-01-25 17:51:00,231] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:51:00,251] [INFO] Task started: CheckM
[2024-01-25 17:51:00,252] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_028748145.1_ASM2874814v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_028748145.1_ASM2874814v1_genomic.fna/checkm_input GCF_028748145.1_ASM2874814v1_genomic.fna/checkm_result
[2024-01-25 17:51:17,386] [INFO] Task succeeded: CheckM
[2024-01-25 17:51:17,387] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:51:17,400] [INFO] ===== Completeness check finished =====
[2024-01-25 17:51:17,400] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:51:17,400] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_028748145.1_ASM2874814v1_genomic.fna/markers.fasta)
[2024-01-25 17:51:17,401] [INFO] Task started: Blastn
[2024-01-25 17:51:17,401] [INFO] Running command: blastn -query GCF_028748145.1_ASM2874814v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg98f4ddb0-e573-49ec-8fe3-7c843ae56f84/dqc_reference/reference_markers_gtdb.fasta -out GCF_028748145.1_ASM2874814v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:51:18,341] [INFO] Task succeeded: Blastn
[2024-01-25 17:51:18,344] [INFO] Selected 19 target genomes.
[2024-01-25 17:51:18,345] [INFO] Target genome list was writen to GCF_028748145.1_ASM2874814v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:51:18,375] [INFO] Task started: fastANI
[2024-01-25 17:51:18,375] [INFO] Running command: fastANI --query /var/lib/cwl/stga5bcf682-bf9c-4640-9911-db0e3b1ffc83/GCF_028748145.1_ASM2874814v1_genomic.fna.gz --refList GCF_028748145.1_ASM2874814v1_genomic.fna/target_genomes_gtdb.txt --output GCF_028748145.1_ASM2874814v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:51:28,528] [INFO] Task succeeded: fastANI
[2024-01-25 17:51:28,531] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:51:28,531] [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_011812985.1	s__Entomospira culicis	99.9996	584	588	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__WRBN01;f__WRBN01;g__Entomospira	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_011812965.1	s__Entomospira entomophilus	77.9496	75	588	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__WRBN01;f__WRBN01;g__Entomospira	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:51:28,532] [INFO] GTDB search result was written to GCF_028748145.1_ASM2874814v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:51:28,533] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:51:28,535] [INFO] DFAST_QC result json was written to GCF_028748145.1_ASM2874814v1_genomic.fna/dqc_result.json
[2024-01-25 17:51:28,535] [INFO] DFAST_QC completed!
[2024-01-25 17:51:28,535] [INFO] Total running time: 0h0m38s