[2024-01-25 20:05:05,593] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:05:05,595] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:05:05,595] [INFO] DQC Reference Directory: /var/lib/cwl/stg84e25eff-b85f-4f5a-9afb-f3c06b893bd1/dqc_reference
[2024-01-25 20:05:06,693] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:05:06,694] [INFO] Task started: Prodigal
[2024-01-25 20:05:06,694] [INFO] Running command: gunzip -c /var/lib/cwl/stg7e4ee380-ae25-477d-b768-9df5d07b6743/GCF_022936085.1_ASM2293608v1_genomic.fna.gz | prodigal -d GCF_022936085.1_ASM2293608v1_genomic.fna/cds.fna -a GCF_022936085.1_ASM2293608v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:05:10,292] [INFO] Task succeeded: Prodigal
[2024-01-25 20:05:10,293] [INFO] Task started: HMMsearch
[2024-01-25 20:05:10,293] [INFO] Running command: hmmsearch --tblout GCF_022936085.1_ASM2293608v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg84e25eff-b85f-4f5a-9afb-f3c06b893bd1/dqc_reference/reference_markers.hmm GCF_022936085.1_ASM2293608v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:05:10,533] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:05:10,535] [INFO] Found 6/6 markers.
[2024-01-25 20:05:10,557] [INFO] Query marker FASTA was written to GCF_022936085.1_ASM2293608v1_genomic.fna/markers.fasta
[2024-01-25 20:05:10,557] [INFO] Task started: Blastn
[2024-01-25 20:05:10,557] [INFO] Running command: blastn -query GCF_022936085.1_ASM2293608v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg84e25eff-b85f-4f5a-9afb-f3c06b893bd1/dqc_reference/reference_markers.fasta -out GCF_022936085.1_ASM2293608v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:05:11,134] [INFO] Task succeeded: Blastn
[2024-01-25 20:05:11,137] [INFO] Selected 8 target genomes.
[2024-01-25 20:05:11,138] [INFO] Target genome list was writen to GCF_022936085.1_ASM2293608v1_genomic.fna/target_genomes.txt
[2024-01-25 20:05:11,146] [INFO] Task started: fastANI
[2024-01-25 20:05:11,146] [INFO] Running command: fastANI --query /var/lib/cwl/stg7e4ee380-ae25-477d-b768-9df5d07b6743/GCF_022936085.1_ASM2293608v1_genomic.fna.gz --refList GCF_022936085.1_ASM2293608v1_genomic.fna/target_genomes.txt --output GCF_022936085.1_ASM2293608v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:05:39,841] [INFO] Task succeeded: fastANI
[2024-01-25 20:05:39,842] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg84e25eff-b85f-4f5a-9afb-f3c06b893bd1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:05:39,842] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg84e25eff-b85f-4f5a-9afb-f3c06b893bd1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:05:39,847] [INFO] Found 4 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 20:05:39,847] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:05:39,847] [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
Orientia tsutsugamushi	strain=Karp	GCA_022936085.1	784	784	suspected-type	True	100.0	815	822	95	conclusive
Orientia tsutsugamushi		GCA_900327275.1	784	784	suspected-type	True	99.9663	814	822	95	conclusive
Orientia tsutsugamushi	strain=Karp	GCA_001654785.2	784	784	suspected-type	True	99.8664	602	822	95	conclusive
Orientia chuto	strain=Dubai	GCA_000964595.1	911112	911112	type	True	81.3781	258	822	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:05:39,848] [INFO] DFAST Taxonomy check result was written to GCF_022936085.1_ASM2293608v1_genomic.fna/tc_result.tsv
[2024-01-25 20:05:39,848] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:05:39,849] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:05:39,849] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg84e25eff-b85f-4f5a-9afb-f3c06b893bd1/dqc_reference/checkm_data
[2024-01-25 20:05:39,849] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:05:39,875] [INFO] Task started: CheckM
[2024-01-25 20:05:39,875] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022936085.1_ASM2293608v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022936085.1_ASM2293608v1_genomic.fna/checkm_input GCF_022936085.1_ASM2293608v1_genomic.fna/checkm_result
[2024-01-25 20:05:56,787] [INFO] Task succeeded: CheckM
[2024-01-25 20:05:56,787] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.45%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:05:56,807] [INFO] ===== Completeness check finished =====
[2024-01-25 20:05:56,807] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:05:56,808] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022936085.1_ASM2293608v1_genomic.fna/markers.fasta)
[2024-01-25 20:05:56,808] [INFO] Task started: Blastn
[2024-01-25 20:05:56,808] [INFO] Running command: blastn -query GCF_022936085.1_ASM2293608v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg84e25eff-b85f-4f5a-9afb-f3c06b893bd1/dqc_reference/reference_markers_gtdb.fasta -out GCF_022936085.1_ASM2293608v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:05:57,623] [INFO] Task succeeded: Blastn
[2024-01-25 20:05:57,626] [INFO] Selected 14 target genomes.
[2024-01-25 20:05:57,626] [INFO] Target genome list was writen to GCF_022936085.1_ASM2293608v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:05:57,642] [INFO] Task started: fastANI
[2024-01-25 20:05:57,642] [INFO] Running command: fastANI --query /var/lib/cwl/stg7e4ee380-ae25-477d-b768-9df5d07b6743/GCF_022936085.1_ASM2293608v1_genomic.fna.gz --refList GCF_022936085.1_ASM2293608v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022936085.1_ASM2293608v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:06:12,118] [INFO] Task succeeded: fastANI
[2024-01-25 20:06:12,122] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:06:12,122] [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_900327275.1	s__Orientia tsutsugamushi	99.9663	814	822	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__Rickettsiaceae;g__Orientia	95.0	97.28	95.31	0.83	0.66	17	conclusive
GCF_000964595.1	s__Orientia chuto	81.3665	258	822	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__Rickettsiaceae;g__Orientia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000309075.1	s__Occidentia massiliensis	77.0369	67	822	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__Rickettsiaceae;g__Occidentia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:06:12,123] [INFO] GTDB search result was written to GCF_022936085.1_ASM2293608v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:06:12,124] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:06:12,126] [INFO] DFAST_QC result json was written to GCF_022936085.1_ASM2293608v1_genomic.fna/dqc_result.json
[2024-01-25 20:06:12,126] [INFO] DFAST_QC completed!
[2024-01-25 20:06:12,126] [INFO] Total running time: 0h1m7s