[2024-01-24 13:32:41,990] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:41,991] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:41,991] [INFO] DQC Reference Directory: /var/lib/cwl/stgfb275b2a-7f5c-4a6f-8804-eeb8564e4354/dqc_reference
[2024-01-24 13:32:43,190] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:43,192] [INFO] Task started: Prodigal
[2024-01-24 13:32:43,192] [INFO] Running command: gunzip -c /var/lib/cwl/stgde26132c-01f3-45e0-8ea3-d59e889d9012/GCF_000409285.1_Cmuy_final_contigs_genomic.fna.gz | prodigal -d GCF_000409285.1_Cmuy_final_contigs_genomic.fna/cds.fna -a GCF_000409285.1_Cmuy_final_contigs_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:54,586] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:54,586] [INFO] Task started: HMMsearch
[2024-01-24 13:32:54,587] [INFO] Running command: hmmsearch --tblout GCF_000409285.1_Cmuy_final_contigs_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfb275b2a-7f5c-4a6f-8804-eeb8564e4354/dqc_reference/reference_markers.hmm GCF_000409285.1_Cmuy_final_contigs_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:54,940] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:54,944] [INFO] Found 6/6 markers.
[2024-01-24 13:32:54,985] [INFO] Query marker FASTA was written to GCF_000409285.1_Cmuy_final_contigs_genomic.fna/markers.fasta
[2024-01-24 13:32:54,985] [INFO] Task started: Blastn
[2024-01-24 13:32:54,985] [INFO] Running command: blastn -query GCF_000409285.1_Cmuy_final_contigs_genomic.fna/markers.fasta -db /var/lib/cwl/stgfb275b2a-7f5c-4a6f-8804-eeb8564e4354/dqc_reference/reference_markers.fasta -out GCF_000409285.1_Cmuy_final_contigs_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:56,034] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:56,038] [INFO] Selected 11 target genomes.
[2024-01-24 13:32:56,039] [INFO] Target genome list was writen to GCF_000409285.1_Cmuy_final_contigs_genomic.fna/target_genomes.txt
[2024-01-24 13:32:56,040] [INFO] Task started: fastANI
[2024-01-24 13:32:56,041] [INFO] Running command: fastANI --query /var/lib/cwl/stgde26132c-01f3-45e0-8ea3-d59e889d9012/GCF_000409285.1_Cmuy_final_contigs_genomic.fna.gz --refList GCF_000409285.1_Cmuy_final_contigs_genomic.fna/target_genomes.txt --output GCF_000409285.1_Cmuy_final_contigs_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:33:07,375] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:07,376] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfb275b2a-7f5c-4a6f-8804-eeb8564e4354/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:33:07,376] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfb275b2a-7f5c-4a6f-8804-eeb8564e4354/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:33:07,390] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:33:07,390] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:33:07,390] [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
Cronobacter muytjensii	strain=ATCC 51329	GCA_000409285.1	413501	413501	type	True	100.0	1406	1411	95	conclusive
Cronobacter muytjensii	strain=ATCC 51329	GCA_001277195.1	413501	413501	type	True	99.9971	1411	1411	95	conclusive
Cronobacter dublinensis subsp. lactaridi	strain=LMG 23825	GCA_000409345.1	413499	413497	type	True	92.597	1264	1411	95	below_threshold
Cronobacter dublinensis subsp. lausannensis	strain=LMG 23824	GCA_000409365.1	413500	413497	type	True	92.5484	1265	1411	95	below_threshold
Cronobacter dublinensis subsp. dublinensis	strain=LMG 23823	GCA_001277235.1	413498	413497	type	True	92.3128	1262	1411	95	below_threshold
Cronobacter dublinensis subsp. dublinensis	strain=LMG 23823	GCA_000409225.1	413498	413497	type	True	92.2849	1268	1411	95	below_threshold
Cronobacter sakazakii	strain=ATCC 29544	GCA_001971035.1	28141	28141	type	True	89.3838	1143	1411	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	80.8745	820	1411	95	below_threshold
Klebsiella pneumoniae	strain=PartO-Kpneumoniae-RM8376	GCA_022869665.1	573	573	type	True	80.8486	751	1411	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	80.832	814	1411	95	below_threshold
Pseudocitrobacter corydidari		GCA_021172065.1	2891570	2891570	type	True	80.6759	749	1411	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:33:07,392] [INFO] DFAST Taxonomy check result was written to GCF_000409285.1_Cmuy_final_contigs_genomic.fna/tc_result.tsv
[2024-01-24 13:33:07,393] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:33:07,393] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:33:07,394] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfb275b2a-7f5c-4a6f-8804-eeb8564e4354/dqc_reference/checkm_data
[2024-01-24 13:33:07,396] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:33:07,438] [INFO] Task started: CheckM
[2024-01-24 13:33:07,438] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000409285.1_Cmuy_final_contigs_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000409285.1_Cmuy_final_contigs_genomic.fna/checkm_input GCF_000409285.1_Cmuy_final_contigs_genomic.fna/checkm_result
[2024-01-24 13:33:45,128] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:45,129] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:45,153] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:45,153] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:45,154] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000409285.1_Cmuy_final_contigs_genomic.fna/markers.fasta)
[2024-01-24 13:33:45,154] [INFO] Task started: Blastn
[2024-01-24 13:33:45,154] [INFO] Running command: blastn -query GCF_000409285.1_Cmuy_final_contigs_genomic.fna/markers.fasta -db /var/lib/cwl/stgfb275b2a-7f5c-4a6f-8804-eeb8564e4354/dqc_reference/reference_markers_gtdb.fasta -out GCF_000409285.1_Cmuy_final_contigs_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:46,668] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:46,673] [INFO] Selected 7 target genomes.
[2024-01-24 13:33:46,673] [INFO] Target genome list was writen to GCF_000409285.1_Cmuy_final_contigs_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:46,675] [INFO] Task started: fastANI
[2024-01-24 13:33:46,676] [INFO] Running command: fastANI --query /var/lib/cwl/stgde26132c-01f3-45e0-8ea3-d59e889d9012/GCF_000409285.1_Cmuy_final_contigs_genomic.fna.gz --refList GCF_000409285.1_Cmuy_final_contigs_genomic.fna/target_genomes_gtdb.txt --output GCF_000409285.1_Cmuy_final_contigs_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:55,166] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:55,178] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:55,179] [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_001277195.1	s__Cronobacter muytjensii	99.9971	1411	1411	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cronobacter	95.0	99.13	98.83	0.94	0.91	9	conclusive
GCF_001277235.1	s__Cronobacter dublinensis	92.3128	1262	1411	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cronobacter	95.0	97.74	96.92	0.93	0.89	42	-
GCF_001277175.1	s__Cronobacter universalis	90.054	1254	1411	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cronobacter	95.0	99.87	99.62	0.99	0.98	4	-
GCA_000027065.2	s__Cronobacter turicensis	89.7521	1250	1411	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cronobacter	95.0	97.17	96.06	0.93	0.89	18	-
GCF_001277215.2	s__Cronobacter malonaticus	89.5025	1236	1411	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cronobacter	95.0	98.86	98.11	0.94	0.89	62	-
GCF_000982825.1	s__Cronobacter sakazakii	89.4803	1237	1411	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cronobacter	95.0	98.00	97.39	0.92	0.86	440	-
GCF_001277255.1	s__Cronobacter condimenti	88.6174	1216	1411	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cronobacter	95.0	99.97	99.97	0.99	0.97	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:55,180] [INFO] GTDB search result was written to GCF_000409285.1_Cmuy_final_contigs_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:55,181] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:55,184] [INFO] DFAST_QC result json was written to GCF_000409285.1_Cmuy_final_contigs_genomic.fna/dqc_result.json
[2024-01-24 13:33:55,184] [INFO] DFAST_QC completed!
[2024-01-24 13:33:55,184] [INFO] Total running time: 0h1m13s