[2024-01-25 19:46:20,460] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:46:20,462] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:46:20,462] [INFO] DQC Reference Directory: /var/lib/cwl/stgddee929b-0d5d-4de7-a33d-a8c5d59e8326/dqc_reference
[2024-01-25 19:46:21,569] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:46:21,570] [INFO] Task started: Prodigal
[2024-01-25 19:46:21,570] [INFO] Running command: gunzip -c /var/lib/cwl/stgd6d91a19-5c2f-44dd-a8ec-e7ad6a840ad3/GCF_000511675.1_ASM51167v1_genomic.fna.gz | prodigal -d GCF_000511675.1_ASM51167v1_genomic.fna/cds.fna -a GCF_000511675.1_ASM51167v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:46:31,085] [INFO] Task succeeded: Prodigal
[2024-01-25 19:46:31,086] [INFO] Task started: HMMsearch
[2024-01-25 19:46:31,086] [INFO] Running command: hmmsearch --tblout GCF_000511675.1_ASM51167v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgddee929b-0d5d-4de7-a33d-a8c5d59e8326/dqc_reference/reference_markers.hmm GCF_000511675.1_ASM51167v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:46:31,345] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:46:31,346] [INFO] Found 6/6 markers.
[2024-01-25 19:46:31,385] [INFO] Query marker FASTA was written to GCF_000511675.1_ASM51167v1_genomic.fna/markers.fasta
[2024-01-25 19:46:31,385] [INFO] Task started: Blastn
[2024-01-25 19:46:31,385] [INFO] Running command: blastn -query GCF_000511675.1_ASM51167v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgddee929b-0d5d-4de7-a33d-a8c5d59e8326/dqc_reference/reference_markers.fasta -out GCF_000511675.1_ASM51167v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:46:32,195] [INFO] Task succeeded: Blastn
[2024-01-25 19:46:32,198] [INFO] Selected 15 target genomes.
[2024-01-25 19:46:32,198] [INFO] Target genome list was writen to GCF_000511675.1_ASM51167v1_genomic.fna/target_genomes.txt
[2024-01-25 19:46:32,209] [INFO] Task started: fastANI
[2024-01-25 19:46:32,209] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6d91a19-5c2f-44dd-a8ec-e7ad6a840ad3/GCF_000511675.1_ASM51167v1_genomic.fna.gz --refList GCF_000511675.1_ASM51167v1_genomic.fna/target_genomes.txt --output GCF_000511675.1_ASM51167v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:46:46,572] [INFO] Task succeeded: fastANI
[2024-01-25 19:46:46,573] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgddee929b-0d5d-4de7-a33d-a8c5d59e8326/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:46:46,573] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgddee929b-0d5d-4de7-a33d-a8c5d59e8326/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:46:46,583] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:46:46,583] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:46:46,583] [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
Yersinia pseudotuberculosis	strain=NCTC10275	GCA_900637475.1	633	633	suspected-type	True	99.9958	1431	1432	95	conclusive
Yersinia similis	strain=Y228	GCA_001053095.1	367190	367190	type	True	94.9547	1295	1432	95	below_threshold
Yersinia similis	strain=228	GCA_000582515.1	367190	367190	type	True	94.9044	1328	1432	95	below_threshold
Yersinia intermedia	strain=NCTC11469	GCA_900635455.1	631	631	type	True	82.7178	877	1432	95	below_threshold
Yersinia alsatica	strain=IP38850	GCA_902170305.1	2890317	2890317	type	True	82.7106	878	1432	95	below_threshold
Yersinia intermedia	strain=ATCC 29909	GCA_000168035.1	631	631	type	True	82.6983	846	1432	95	below_threshold
Yersinia thracica	strain=IP34646	GCA_902170565.1	2890319	2890319	type	True	82.6799	843	1432	95	below_threshold
Yersinia frederiksenii	strain=ATCC 33641	GCA_000168015.1	29484	29484	suspected-type	True	82.6428	862	1432	95	below_threshold
Yersinia aldovae	strain=IP06005	GCA_001091225.1	29483	29483	type	True	82.5502	848	1432	95	below_threshold
Yersinia vastinensis	strain=IP38594	GCA_902726565.1	2890318	2890318	type	True	82.5349	830	1432	95	below_threshold
Yersinia rochesterensis	strain=ATCC BAA-2637	GCA_003600645.1	1604335	1604335	type	True	82.5271	845	1432	95	below_threshold
Serratia bockelmannii	strain=S3	GCA_008011855.1	2703793	2703793	type	True	78.8662	328	1432	95	below_threshold
Serratia nevei	strain=S15	GCA_008364245.1	2703794	2703794	type	True	78.8465	335	1432	95	below_threshold
Hafnia paralvei	strain=ATCC 29927	GCA_023698525.1	546367	546367	type	True	78.5659	244	1432	95	below_threshold
Rahnella perminowiae	strain=SL6	GCA_019049755.1	2816244	2816244	type	True	78.5253	293	1432	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:46:46,585] [INFO] DFAST Taxonomy check result was written to GCF_000511675.1_ASM51167v1_genomic.fna/tc_result.tsv
[2024-01-25 19:46:46,585] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:46:46,585] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:46:46,585] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgddee929b-0d5d-4de7-a33d-a8c5d59e8326/dqc_reference/checkm_data
[2024-01-25 19:46:46,586] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:46:46,631] [INFO] Task started: CheckM
[2024-01-25 19:46:46,632] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000511675.1_ASM51167v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000511675.1_ASM51167v1_genomic.fna/checkm_input GCF_000511675.1_ASM51167v1_genomic.fna/checkm_result
[2024-01-25 19:47:18,618] [INFO] Task succeeded: CheckM
[2024-01-25 19:47:18,618] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:47:18,652] [INFO] ===== Completeness check finished =====
[2024-01-25 19:47:18,652] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:47:18,652] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000511675.1_ASM51167v1_genomic.fna/markers.fasta)
[2024-01-25 19:47:18,652] [INFO] Task started: Blastn
[2024-01-25 19:47:18,652] [INFO] Running command: blastn -query GCF_000511675.1_ASM51167v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgddee929b-0d5d-4de7-a33d-a8c5d59e8326/dqc_reference/reference_markers_gtdb.fasta -out GCF_000511675.1_ASM51167v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:47:19,877] [INFO] Task succeeded: Blastn
[2024-01-25 19:47:19,879] [INFO] Selected 12 target genomes.
[2024-01-25 19:47:19,879] [INFO] Target genome list was writen to GCF_000511675.1_ASM51167v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:47:19,894] [INFO] Task started: fastANI
[2024-01-25 19:47:19,895] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6d91a19-5c2f-44dd-a8ec-e7ad6a840ad3/GCF_000511675.1_ASM51167v1_genomic.fna.gz --refList GCF_000511675.1_ASM51167v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000511675.1_ASM51167v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:47:32,160] [INFO] Task succeeded: fastANI
[2024-01-25 19:47:32,169] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:47:32,169] [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_900460465.1	s__Yersinia pestis	99.1338	1339	1432	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.78	97.10	0.96	0.85	655	conclusive
GCF_001053095.1	s__Yersinia similis	94.9389	1296	1432	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.47	99.21	0.94	0.92	9	-
GCF_001047675.1	s__Yersinia aleksiciae	82.9139	810	1432	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.22	98.37	0.87	0.82	10	-
GCF_001098625.1	s__Yersinia frederiksenii_C	82.8927	882	1432	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	98.63	97.69	0.93	0.89	21	-
GCF_002082245.2	s__Yersinia enterocolitica_E	82.8251	911	1432	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013282745.1	s__Yersinia bercovieri	82.7792	849	1432	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.12	95.38	0.94	0.87	18	-
GCF_001155565.1	s__Yersinia frederiksenii_A	82.7571	824	1432	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.53	99.44	0.95	0.92	10	-
GCF_900635455.1	s__Yersinia intermedia	82.7243	876	1432	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.02	97.82	0.92	0.88	29	-
GCF_000754805.1	s__Yersinia frederiksenii	82.6763	863	1432	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.36	98.91	0.95	0.85	11	-
GCF_001123825.1	s__Yersinia kristensenii_C	82.6243	840	1432	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.60	99.58	0.95	0.93	4	-
GCF_001152565.1	s__Yersinia pekkanenii	82.6027	935	1432	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.90	99.90	0.98	0.98	2	-
GCF_003600645.1	s__Yersinia rochesterensis	82.5139	847	1432	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.46	98.81	0.94	0.91	13	-
--------------------------------------------------------------------------------
[2024-01-25 19:47:32,170] [INFO] GTDB search result was written to GCF_000511675.1_ASM51167v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:47:32,171] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:47:32,174] [INFO] DFAST_QC result json was written to GCF_000511675.1_ASM51167v1_genomic.fna/dqc_result.json
[2024-01-25 19:47:32,174] [INFO] DFAST_QC completed!
[2024-01-25 19:47:32,174] [INFO] Total running time: 0h1m12s