[2024-01-24 12:46:55,195] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:46:55,197] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:46:55,198] [INFO] DQC Reference Directory: /var/lib/cwl/stgabf35ff8-04ae-493a-ac7d-2da74db3bd1c/dqc_reference
[2024-01-24 12:46:56,475] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:46:56,476] [INFO] Task started: Prodigal
[2024-01-24 12:46:56,477] [INFO] Running command: gunzip -c /var/lib/cwl/stg9fe7cbde-fce9-4e41-8ce1-fe5bb9b1a0b3/GCF_000632845.1_ASM63284v1_genomic.fna.gz | prodigal -d GCF_000632845.1_ASM63284v1_genomic.fna/cds.fna -a GCF_000632845.1_ASM63284v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:46:58,424] [INFO] Task succeeded: Prodigal
[2024-01-24 12:46:58,425] [INFO] Task started: HMMsearch
[2024-01-24 12:46:58,425] [INFO] Running command: hmmsearch --tblout GCF_000632845.1_ASM63284v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgabf35ff8-04ae-493a-ac7d-2da74db3bd1c/dqc_reference/reference_markers.hmm GCF_000632845.1_ASM63284v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:46:58,654] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:46:58,656] [INFO] Found 6/6 markers.
[2024-01-24 12:46:58,692] [INFO] Query marker FASTA was written to GCF_000632845.1_ASM63284v1_genomic.fna/markers.fasta
[2024-01-24 12:46:58,692] [INFO] Task started: Blastn
[2024-01-24 12:46:58,693] [INFO] Running command: blastn -query GCF_000632845.1_ASM63284v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgabf35ff8-04ae-493a-ac7d-2da74db3bd1c/dqc_reference/reference_markers.fasta -out GCF_000632845.1_ASM63284v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:46:59,346] [INFO] Task succeeded: Blastn
[2024-01-24 12:46:59,350] [INFO] Selected 9 target genomes.
[2024-01-24 12:46:59,350] [INFO] Target genome list was writen to GCF_000632845.1_ASM63284v1_genomic.fna/target_genomes.txt
[2024-01-24 12:46:59,357] [INFO] Task started: fastANI
[2024-01-24 12:46:59,357] [INFO] Running command: fastANI --query /var/lib/cwl/stg9fe7cbde-fce9-4e41-8ce1-fe5bb9b1a0b3/GCF_000632845.1_ASM63284v1_genomic.fna.gz --refList GCF_000632845.1_ASM63284v1_genomic.fna/target_genomes.txt --output GCF_000632845.1_ASM63284v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:47:02,840] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:02,840] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgabf35ff8-04ae-493a-ac7d-2da74db3bd1c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:47:02,841] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgabf35ff8-04ae-493a-ac7d-2da74db3bd1c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:47:02,848] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:47:02,849] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:47:02,849] [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
Ehrlichia muris	strain=AS145	GCA_000508225.1	35795	35795	type	True	93.0546	365	382	95	below_threshold
Ehrlichia chaffeensis	strain=Arkansas	GCA_000013145.1	945	945	type	True	85.0299	329	382	95	below_threshold
Ehrlichia ruminantium	strain=Welgevonden	GCA_000026005.1	779	779	type	True	78.8403	227	382	95	below_threshold
Ehrlichia ruminantium	strain=Welgevonden	GCA_000050425.1	779	779	type	True	78.7347	226	382	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:47:02,851] [INFO] DFAST Taxonomy check result was written to GCF_000632845.1_ASM63284v1_genomic.fna/tc_result.tsv
[2024-01-24 12:47:02,852] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:47:02,852] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:47:02,852] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgabf35ff8-04ae-493a-ac7d-2da74db3bd1c/dqc_reference/checkm_data
[2024-01-24 12:47:02,854] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:47:02,870] [INFO] Task started: CheckM
[2024-01-24 12:47:02,871] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000632845.1_ASM63284v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000632845.1_ASM63284v1_genomic.fna/checkm_input GCF_000632845.1_ASM63284v1_genomic.fna/checkm_result
[2024-01-24 12:47:16,705] [INFO] Task succeeded: CheckM
[2024-01-24 12:47:16,706] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:47:16,721] [INFO] ===== Completeness check finished =====
[2024-01-24 12:47:16,721] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:47:16,722] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000632845.1_ASM63284v1_genomic.fna/markers.fasta)
[2024-01-24 12:47:16,722] [INFO] Task started: Blastn
[2024-01-24 12:47:16,722] [INFO] Running command: blastn -query GCF_000632845.1_ASM63284v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgabf35ff8-04ae-493a-ac7d-2da74db3bd1c/dqc_reference/reference_markers_gtdb.fasta -out GCF_000632845.1_ASM63284v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:17,527] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:17,530] [INFO] Selected 5 target genomes.
[2024-01-24 12:47:17,530] [INFO] Target genome list was writen to GCF_000632845.1_ASM63284v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:47:17,534] [INFO] Task started: fastANI
[2024-01-24 12:47:17,534] [INFO] Running command: fastANI --query /var/lib/cwl/stg9fe7cbde-fce9-4e41-8ce1-fe5bb9b1a0b3/GCF_000632845.1_ASM63284v1_genomic.fna.gz --refList GCF_000632845.1_ASM63284v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000632845.1_ASM63284v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:47:19,051] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:19,057] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:47:19,058] [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_000632845.1	s__Ehrlichia sp000632845	100.0	382	382	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__Anaplasmataceae;g__Ehrlichia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000508225.1	s__Ehrlichia muris	93.0546	365	382	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__Anaplasmataceae;g__Ehrlichia	95.0	96.19	96.19	0.98	0.98	3	-
GCF_000013145.1	s__Ehrlichia chaffeensis	85.0299	329	382	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__Anaplasmataceae;g__Ehrlichia	95.0	99.72	99.67	0.99	0.98	9	-
GCF_000012565.1	s__Ehrlichia canis	82.4788	304	382	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__Anaplasmataceae;g__Ehrlichia	95.0	99.82	99.82	0.99	0.99	2	-
GCF_000825765.1	s__Ehrlichia minasensis	82.1608	284	382	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__Anaplasmataceae;g__Ehrlichia	95.0	99.60	99.60	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:47:19,060] [INFO] GTDB search result was written to GCF_000632845.1_ASM63284v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:47:19,061] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:47:19,064] [INFO] DFAST_QC result json was written to GCF_000632845.1_ASM63284v1_genomic.fna/dqc_result.json
[2024-01-24 12:47:19,064] [INFO] DFAST_QC completed!
[2024-01-24 12:47:19,064] [INFO] Total running time: 0h0m24s