[2024-01-24 13:57:12,392] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:12,394] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:12,394] [INFO] DQC Reference Directory: /var/lib/cwl/stg056ca6b1-93f8-4ca7-989e-44cff887bfd6/dqc_reference
[2024-01-24 13:57:13,684] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:13,685] [INFO] Task started: Prodigal
[2024-01-24 13:57:13,685] [INFO] Running command: gunzip -c /var/lib/cwl/stg6aa29b55-674c-44b2-aa61-bdf19ece23d7/GCF_000026005.1_ASM2600v1_genomic.fna.gz | prodigal -d GCF_000026005.1_ASM2600v1_genomic.fna/cds.fna -a GCF_000026005.1_ASM2600v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:15,939] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:15,939] [INFO] Task started: HMMsearch
[2024-01-24 13:57:15,939] [INFO] Running command: hmmsearch --tblout GCF_000026005.1_ASM2600v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg056ca6b1-93f8-4ca7-989e-44cff887bfd6/dqc_reference/reference_markers.hmm GCF_000026005.1_ASM2600v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:16,186] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:16,188] [INFO] Found 6/6 markers.
[2024-01-24 13:57:16,209] [INFO] Query marker FASTA was written to GCF_000026005.1_ASM2600v1_genomic.fna/markers.fasta
[2024-01-24 13:57:16,210] [INFO] Task started: Blastn
[2024-01-24 13:57:16,210] [INFO] Running command: blastn -query GCF_000026005.1_ASM2600v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg056ca6b1-93f8-4ca7-989e-44cff887bfd6/dqc_reference/reference_markers.fasta -out GCF_000026005.1_ASM2600v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:16,872] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:16,875] [INFO] Selected 10 target genomes.
[2024-01-24 13:57:16,876] [INFO] Target genome list was writen to GCF_000026005.1_ASM2600v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:16,882] [INFO] Task started: fastANI
[2024-01-24 13:57:16,883] [INFO] Running command: fastANI --query /var/lib/cwl/stg6aa29b55-674c-44b2-aa61-bdf19ece23d7/GCF_000026005.1_ASM2600v1_genomic.fna.gz --refList GCF_000026005.1_ASM2600v1_genomic.fna/target_genomes.txt --output GCF_000026005.1_ASM2600v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:57:20,575] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:20,576] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg056ca6b1-93f8-4ca7-989e-44cff887bfd6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:57:20,576] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg056ca6b1-93f8-4ca7-989e-44cff887bfd6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:57:20,582] [INFO] Found 4 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:57:20,582] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:57:20,582] [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 ruminantium	strain=Welgevonden	GCA_000026005.1	779	779	type	True	100.0	505	505	95	conclusive
Ehrlichia ruminantium	strain=Welgevonden	GCA_000050425.1	779	779	type	True	99.9723	503	505	95	conclusive
Ehrlichia chaffeensis	strain=Arkansas	GCA_000013145.1	945	945	type	True	78.737	211	505	95	below_threshold
Ehrlichia muris	strain=AS145	GCA_000508225.1	35795	35795	type	True	78.6704	224	505	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:57:20,583] [INFO] DFAST Taxonomy check result was written to GCF_000026005.1_ASM2600v1_genomic.fna/tc_result.tsv
[2024-01-24 13:57:20,584] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:57:20,584] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:57:20,584] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg056ca6b1-93f8-4ca7-989e-44cff887bfd6/dqc_reference/checkm_data
[2024-01-24 13:57:20,585] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:57:20,606] [INFO] Task started: CheckM
[2024-01-24 13:57:20,606] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000026005.1_ASM2600v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000026005.1_ASM2600v1_genomic.fna/checkm_input GCF_000026005.1_ASM2600v1_genomic.fna/checkm_result
[2024-01-24 13:57:35,675] [INFO] Task succeeded: CheckM
[2024-01-24 13:57:35,676] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:57:35,689] [INFO] ===== Completeness check finished =====
[2024-01-24 13:57:35,690] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:57:35,690] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000026005.1_ASM2600v1_genomic.fna/markers.fasta)
[2024-01-24 13:57:35,691] [INFO] Task started: Blastn
[2024-01-24 13:57:35,691] [INFO] Running command: blastn -query GCF_000026005.1_ASM2600v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg056ca6b1-93f8-4ca7-989e-44cff887bfd6/dqc_reference/reference_markers_gtdb.fasta -out GCF_000026005.1_ASM2600v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:36,526] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:36,529] [INFO] Selected 8 target genomes.
[2024-01-24 13:57:36,530] [INFO] Target genome list was writen to GCF_000026005.1_ASM2600v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:57:36,538] [INFO] Task started: fastANI
[2024-01-24 13:57:36,538] [INFO] Running command: fastANI --query /var/lib/cwl/stg6aa29b55-674c-44b2-aa61-bdf19ece23d7/GCF_000026005.1_ASM2600v1_genomic.fna.gz --refList GCF_000026005.1_ASM2600v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000026005.1_ASM2600v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:57:39,119] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:39,129] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:57:39,130] [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_000026005.1	s__Ehrlichia ruminantium	100.0	505	505	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__Anaplasmataceae;g__Ehrlichia	95.0	98.02	95.44	1.00	0.99	20	conclusive
GCF_009728835.1	s__Ehrlichia ruminantium_B	83.2746	374	505	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__Anaplasmataceae;g__Ehrlichia	95.0	99.94	99.90	1.00	1.00	3	-
GCF_000632845.1	s__Ehrlichia sp000632845	78.7431	219	505	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__Anaplasmataceae;g__Ehrlichia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000013145.1	s__Ehrlichia chaffeensis	78.7298	210	505	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	78.7187	226	505	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__Anaplasmataceae;g__Ehrlichia	95.0	99.82	99.82	0.99	0.99	2	-
GCF_000508225.1	s__Ehrlichia muris	78.6891	223	505	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__Anaplasmataceae;g__Ehrlichia	95.0	96.19	96.19	0.98	0.98	3	-
GCF_000825765.1	s__Ehrlichia minasensis	78.5181	220	505	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__Anaplasmataceae;g__Ehrlichia	95.0	99.60	99.60	0.95	0.95	2	-
GCF_000964795.1	s__Neoehrlichia lotoris	76.8982	62	505	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__Anaplasmataceae;g__Neoehrlichia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:57:39,131] [INFO] GTDB search result was written to GCF_000026005.1_ASM2600v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:57:39,132] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:57:39,135] [INFO] DFAST_QC result json was written to GCF_000026005.1_ASM2600v1_genomic.fna/dqc_result.json
[2024-01-24 13:57:39,135] [INFO] DFAST_QC completed!
[2024-01-24 13:57:39,135] [INFO] Total running time: 0h0m27s