[2024-01-25 18:43:20,414] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:43:20,416] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:43:20,416] [INFO] DQC Reference Directory: /var/lib/cwl/stg6d175915-f564-4661-b677-ce4fad67e5dc/dqc_reference
[2024-01-25 18:43:21,545] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:43:21,546] [INFO] Task started: Prodigal
[2024-01-25 18:43:21,546] [INFO] Running command: gunzip -c /var/lib/cwl/stg3f3983b5-03a6-4714-bf2b-93ee01d0259b/GCF_000013145.1_ASM1314v1_genomic.fna.gz | prodigal -d GCF_000013145.1_ASM1314v1_genomic.fna/cds.fna -a GCF_000013145.1_ASM1314v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:43:23,316] [INFO] Task succeeded: Prodigal
[2024-01-25 18:43:23,316] [INFO] Task started: HMMsearch
[2024-01-25 18:43:23,316] [INFO] Running command: hmmsearch --tblout GCF_000013145.1_ASM1314v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6d175915-f564-4661-b677-ce4fad67e5dc/dqc_reference/reference_markers.hmm GCF_000013145.1_ASM1314v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:43:23,474] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:43:23,475] [INFO] Found 6/6 markers.
[2024-01-25 18:43:23,488] [INFO] Query marker FASTA was written to GCF_000013145.1_ASM1314v1_genomic.fna/markers.fasta
[2024-01-25 18:43:23,489] [INFO] Task started: Blastn
[2024-01-25 18:43:23,489] [INFO] Running command: blastn -query GCF_000013145.1_ASM1314v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6d175915-f564-4661-b677-ce4fad67e5dc/dqc_reference/reference_markers.fasta -out GCF_000013145.1_ASM1314v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:43:24,006] [INFO] Task succeeded: Blastn
[2024-01-25 18:43:24,009] [INFO] Selected 7 target genomes.
[2024-01-25 18:43:24,009] [INFO] Target genome list was writen to GCF_000013145.1_ASM1314v1_genomic.fna/target_genomes.txt
[2024-01-25 18:43:24,014] [INFO] Task started: fastANI
[2024-01-25 18:43:24,014] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f3983b5-03a6-4714-bf2b-93ee01d0259b/GCF_000013145.1_ASM1314v1_genomic.fna.gz --refList GCF_000013145.1_ASM1314v1_genomic.fna/target_genomes.txt --output GCF_000013145.1_ASM1314v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:43:26,361] [INFO] Task succeeded: fastANI
[2024-01-25 18:43:26,362] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6d175915-f564-4661-b677-ce4fad67e5dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:43:26,362] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6d175915-f564-4661-b677-ce4fad67e5dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:43:26,367] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:43:26,367] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:43:26,367] [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 chaffeensis	strain=Arkansas	GCA_000013145.1	945	945	type	True	100.0	392	392	95	conclusive
Ehrlichia muris	strain=AS145	GCA_000508225.1	35795	35795	type	True	84.9845	332	392	95	below_threshold
Ehrlichia ruminantium	strain=Welgevonden	GCA_000026005.1	779	779	type	True	78.8881	224	392	95	below_threshold
Ehrlichia ruminantium	strain=Welgevonden	GCA_000050425.1	779	779	type	True	78.8616	221	392	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:43:26,369] [INFO] DFAST Taxonomy check result was written to GCF_000013145.1_ASM1314v1_genomic.fna/tc_result.tsv
[2024-01-25 18:43:26,369] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:43:26,369] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:43:26,369] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6d175915-f564-4661-b677-ce4fad67e5dc/dqc_reference/checkm_data
[2024-01-25 18:43:26,370] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:43:26,385] [INFO] Task started: CheckM
[2024-01-25 18:43:26,386] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000013145.1_ASM1314v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000013145.1_ASM1314v1_genomic.fna/checkm_input GCF_000013145.1_ASM1314v1_genomic.fna/checkm_result
[2024-01-25 18:43:38,279] [INFO] Task succeeded: CheckM
[2024-01-25 18:43:38,280] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:43:38,293] [INFO] ===== Completeness check finished =====
[2024-01-25 18:43:38,294] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:43:38,294] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000013145.1_ASM1314v1_genomic.fna/markers.fasta)
[2024-01-25 18:43:38,294] [INFO] Task started: Blastn
[2024-01-25 18:43:38,294] [INFO] Running command: blastn -query GCF_000013145.1_ASM1314v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6d175915-f564-4661-b677-ce4fad67e5dc/dqc_reference/reference_markers_gtdb.fasta -out GCF_000013145.1_ASM1314v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:43:39,027] [INFO] Task succeeded: Blastn
[2024-01-25 18:43:39,030] [INFO] Selected 6 target genomes.
[2024-01-25 18:43:39,030] [INFO] Target genome list was writen to GCF_000013145.1_ASM1314v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:43:39,054] [INFO] Task started: fastANI
[2024-01-25 18:43:39,055] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f3983b5-03a6-4714-bf2b-93ee01d0259b/GCF_000013145.1_ASM1314v1_genomic.fna.gz --refList GCF_000013145.1_ASM1314v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000013145.1_ASM1314v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:43:40,895] [INFO] Task succeeded: fastANI
[2024-01-25 18:43:40,900] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:43:40,900] [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_000013145.1	s__Ehrlichia chaffeensis	100.0	392	392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__Anaplasmataceae;g__Ehrlichia	95.0	99.72	99.67	0.99	0.98	9	conclusive
GCF_000632845.1	s__Ehrlichia sp000632845	85.2206	327	392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__Anaplasmataceae;g__Ehrlichia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000508225.1	s__Ehrlichia muris	84.9845	332	392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__Anaplasmataceae;g__Ehrlichia	95.0	96.19	96.19	0.98	0.98	3	-
GCF_000012565.1	s__Ehrlichia canis	82.7014	307	392	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	82.3103	286	392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__Anaplasmataceae;g__Ehrlichia	95.0	99.60	99.60	0.95	0.95	2	-
GCF_000026005.1	s__Ehrlichia ruminantium	78.8881	224	392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__Anaplasmataceae;g__Ehrlichia	95.0	98.02	95.44	1.00	0.99	20	-
--------------------------------------------------------------------------------
[2024-01-25 18:43:40,902] [INFO] GTDB search result was written to GCF_000013145.1_ASM1314v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:43:40,902] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:43:40,904] [INFO] DFAST_QC result json was written to GCF_000013145.1_ASM1314v1_genomic.fna/dqc_result.json
[2024-01-25 18:43:40,905] [INFO] DFAST_QC completed!
[2024-01-25 18:43:40,905] [INFO] Total running time: 0h0m20s