[2024-01-25 17:41:50,598] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:41:50,601] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:41:50,601] [INFO] DQC Reference Directory: /var/lib/cwl/stg3e0b953b-6e7d-40fd-a382-6b7a48ef159a/dqc_reference
[2024-01-25 17:41:51,726] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:41:51,726] [INFO] Task started: Prodigal
[2024-01-25 17:41:51,726] [INFO] Running command: gunzip -c /var/lib/cwl/stgceb0349c-a070-418b-8539-f38fb20319f6/GCF_000964595.1_ASM96459v1_genomic.fna.gz | prodigal -d GCF_000964595.1_ASM96459v1_genomic.fna/cds.fna -a GCF_000964595.1_ASM96459v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:41:53,085] [INFO] Task succeeded: Prodigal
[2024-01-25 17:41:53,085] [INFO] Task started: HMMsearch
[2024-01-25 17:41:53,085] [INFO] Running command: hmmsearch --tblout GCF_000964595.1_ASM96459v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3e0b953b-6e7d-40fd-a382-6b7a48ef159a/dqc_reference/reference_markers.hmm GCF_000964595.1_ASM96459v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:41:53,261] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:41:53,262] [INFO] Found 6/6 markers.
[2024-01-25 17:41:53,279] [INFO] Query marker FASTA was written to GCF_000964595.1_ASM96459v1_genomic.fna/markers.fasta
[2024-01-25 17:41:53,279] [INFO] Task started: Blastn
[2024-01-25 17:41:53,280] [INFO] Running command: blastn -query GCF_000964595.1_ASM96459v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3e0b953b-6e7d-40fd-a382-6b7a48ef159a/dqc_reference/reference_markers.fasta -out GCF_000964595.1_ASM96459v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:41:53,802] [INFO] Task succeeded: Blastn
[2024-01-25 17:41:53,805] [INFO] Selected 6 target genomes.
[2024-01-25 17:41:53,805] [INFO] Target genome list was writen to GCF_000964595.1_ASM96459v1_genomic.fna/target_genomes.txt
[2024-01-25 17:41:53,810] [INFO] Task started: fastANI
[2024-01-25 17:41:53,810] [INFO] Running command: fastANI --query /var/lib/cwl/stgceb0349c-a070-418b-8539-f38fb20319f6/GCF_000964595.1_ASM96459v1_genomic.fna.gz --refList GCF_000964595.1_ASM96459v1_genomic.fna/target_genomes.txt --output GCF_000964595.1_ASM96459v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:41:56,507] [INFO] Task succeeded: fastANI
[2024-01-25 17:41:56,507] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3e0b953b-6e7d-40fd-a382-6b7a48ef159a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:41:56,507] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3e0b953b-6e7d-40fd-a382-6b7a48ef159a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:41:56,513] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:41:56,513] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:41:56,513] [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 chuto	strain=Dubai	GCA_000964595.1	911112	911112	type	True	100.0	337	341	95	conclusive
Orientia tsutsugamushi	strain=Karp	GCA_001654785.2	784	784	suspected-type	True	81.4275	255	341	95	below_threshold
Orientia tsutsugamushi		GCA_900327275.1	784	784	suspected-type	True	81.3653	257	341	95	below_threshold
Orientia tsutsugamushi	strain=Karp	GCA_022936085.1	784	784	suspected-type	True	81.3615	260	341	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:41:56,515] [INFO] DFAST Taxonomy check result was written to GCF_000964595.1_ASM96459v1_genomic.fna/tc_result.tsv
[2024-01-25 17:41:56,515] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:41:56,516] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:41:56,516] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3e0b953b-6e7d-40fd-a382-6b7a48ef159a/dqc_reference/checkm_data
[2024-01-25 17:41:56,517] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:41:56,532] [INFO] Task started: CheckM
[2024-01-25 17:41:56,532] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000964595.1_ASM96459v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000964595.1_ASM96459v1_genomic.fna/checkm_input GCF_000964595.1_ASM96459v1_genomic.fna/checkm_result
[2024-01-25 17:42:08,015] [INFO] Task succeeded: CheckM
[2024-01-25 17:42:08,016] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:42:08,032] [INFO] ===== Completeness check finished =====
[2024-01-25 17:42:08,033] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:42:08,033] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000964595.1_ASM96459v1_genomic.fna/markers.fasta)
[2024-01-25 17:42:08,033] [INFO] Task started: Blastn
[2024-01-25 17:42:08,033] [INFO] Running command: blastn -query GCF_000964595.1_ASM96459v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3e0b953b-6e7d-40fd-a382-6b7a48ef159a/dqc_reference/reference_markers_gtdb.fasta -out GCF_000964595.1_ASM96459v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:42:08,831] [INFO] Task succeeded: Blastn
[2024-01-25 17:42:08,834] [INFO] Selected 13 target genomes.
[2024-01-25 17:42:08,834] [INFO] Target genome list was writen to GCF_000964595.1_ASM96459v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:42:08,856] [INFO] Task started: fastANI
[2024-01-25 17:42:08,856] [INFO] Running command: fastANI --query /var/lib/cwl/stgceb0349c-a070-418b-8539-f38fb20319f6/GCF_000964595.1_ASM96459v1_genomic.fna.gz --refList GCF_000964595.1_ASM96459v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000964595.1_ASM96459v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:42:12,495] [INFO] Task succeeded: fastANI
[2024-01-25 17:42:12,498] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:42:12,499] [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_000964595.1	s__Orientia chuto	100.0	337	341	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__Rickettsiaceae;g__Orientia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900327275.1	s__Orientia tsutsugamushi	81.4124	254	341	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__Rickettsiaceae;g__Orientia	95.0	97.28	95.31	0.83	0.66	17	-
--------------------------------------------------------------------------------
[2024-01-25 17:42:12,500] [INFO] GTDB search result was written to GCF_000964595.1_ASM96459v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:42:12,501] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:42:12,503] [INFO] DFAST_QC result json was written to GCF_000964595.1_ASM96459v1_genomic.fna/dqc_result.json
[2024-01-25 17:42:12,503] [INFO] DFAST_QC completed!
[2024-01-25 17:42:12,504] [INFO] Total running time: 0h0m22s