[2024-01-24 13:49:28,361] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:28,363] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:28,363] [INFO] DQC Reference Directory: /var/lib/cwl/stg004cdfdc-f7b1-4546-bb27-d829781eb1c9/dqc_reference
[2024-01-24 13:49:29,610] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:29,611] [INFO] Task started: Prodigal
[2024-01-24 13:49:29,611] [INFO] Running command: gunzip -c /var/lib/cwl/stgf8c11e35-5a5a-4294-be32-37853e085040/GCF_001656035.1_ASM165603v1_genomic.fna.gz | prodigal -d GCF_001656035.1_ASM165603v1_genomic.fna/cds.fna -a GCF_001656035.1_ASM165603v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:40,335] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:40,336] [INFO] Task started: HMMsearch
[2024-01-24 13:49:40,336] [INFO] Running command: hmmsearch --tblout GCF_001656035.1_ASM165603v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg004cdfdc-f7b1-4546-bb27-d829781eb1c9/dqc_reference/reference_markers.hmm GCF_001656035.1_ASM165603v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:40,728] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:40,729] [INFO] Found 6/6 markers.
[2024-01-24 13:49:40,795] [INFO] Query marker FASTA was written to GCF_001656035.1_ASM165603v1_genomic.fna/markers.fasta
[2024-01-24 13:49:40,796] [INFO] Task started: Blastn
[2024-01-24 13:49:40,796] [INFO] Running command: blastn -query GCF_001656035.1_ASM165603v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg004cdfdc-f7b1-4546-bb27-d829781eb1c9/dqc_reference/reference_markers.fasta -out GCF_001656035.1_ASM165603v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:41,713] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:41,716] [INFO] Selected 14 target genomes.
[2024-01-24 13:49:41,716] [INFO] Target genome list was writen to GCF_001656035.1_ASM165603v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:41,722] [INFO] Task started: fastANI
[2024-01-24 13:49:41,722] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8c11e35-5a5a-4294-be32-37853e085040/GCF_001656035.1_ASM165603v1_genomic.fna.gz --refList GCF_001656035.1_ASM165603v1_genomic.fna/target_genomes.txt --output GCF_001656035.1_ASM165603v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:54,896] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:54,897] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg004cdfdc-f7b1-4546-bb27-d829781eb1c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:54,897] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg004cdfdc-f7b1-4546-bb27-d829781eb1c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:54,912] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:49:54,912] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:54,912] [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 entomophaga	strain=MH96	GCA_001656035.1	935293	935293	type	True	100.0	1424	1425	95	conclusive
Yersinia ruckeri	strain=NCTC12986	GCA_900460715.1	29486	29486	type	True	84.1248	860	1425	95	below_threshold
Yersinia ruckeri	strain=ATCC 29473	GCA_000173755.1	29486	29486	type	True	84.0162	827	1425	95	below_threshold
Yersinia ruckeri	strain=ATCC 29473	GCA_000754815.1	29486	29486	type	True	83.9788	864	1425	95	below_threshold
Yersinia intermedia	strain=NCTC11469	GCA_900635455.1	631	631	type	True	81.5794	659	1425	95	below_threshold
Yersinia enterocolitica subsp. enterocolitica	strain=NCTC12982	GCA_901472495.1	150052	630	type	True	81.4544	684	1425	95	below_threshold
Yersinia rochesterensis	strain=ATCC BAA-2637	GCA_003600645.1	1604335	1604335	type	True	81.4247	659	1425	95	below_threshold
Yersinia aldovae	strain=IP06005	GCA_001091225.1	29483	29483	type	True	81.3634	664	1425	95	below_threshold
Yersinia alsatica	strain=IP38850	GCA_902170305.1	2890317	2890317	type	True	81.2287	682	1425	95	below_threshold
Yersinia pseudotuberculosis	strain=NCTC10275	GCA_900637475.1	633	633	suspected-type	True	80.9707	620	1425	95	below_threshold
Serratia entomophila	strain=A1	GCA_021462285.1	42906	42906	type	True	79.6569	517	1425	95	below_threshold
Serratia nevei	strain=S15	GCA_008364245.1	2703794	2703794	type	True	79.3523	496	1425	95	below_threshold
Serratia bockelmannii	strain=S3	GCA_008011855.1	2703793	2703793	type	True	79.2854	486	1425	95	below_threshold
Rahnella bonaserana	strain=H11b	GCA_019049675.1	2816248	2816248	type	True	79.174	415	1425	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:54,914] [INFO] DFAST Taxonomy check result was written to GCF_001656035.1_ASM165603v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:54,915] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:54,915] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:54,916] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg004cdfdc-f7b1-4546-bb27-d829781eb1c9/dqc_reference/checkm_data
[2024-01-24 13:49:54,917] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:54,967] [INFO] Task started: CheckM
[2024-01-24 13:49:54,967] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001656035.1_ASM165603v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001656035.1_ASM165603v1_genomic.fna/checkm_input GCF_001656035.1_ASM165603v1_genomic.fna/checkm_result
[2024-01-24 13:50:33,203] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:33,205] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:33,226] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:33,227] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:33,227] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001656035.1_ASM165603v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:33,227] [INFO] Task started: Blastn
[2024-01-24 13:50:33,228] [INFO] Running command: blastn -query GCF_001656035.1_ASM165603v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg004cdfdc-f7b1-4546-bb27-d829781eb1c9/dqc_reference/reference_markers_gtdb.fasta -out GCF_001656035.1_ASM165603v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:34,301] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:34,305] [INFO] Selected 16 target genomes.
[2024-01-24 13:50:34,305] [INFO] Target genome list was writen to GCF_001656035.1_ASM165603v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:34,317] [INFO] Task started: fastANI
[2024-01-24 13:50:34,317] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8c11e35-5a5a-4294-be32-37853e085040/GCF_001656035.1_ASM165603v1_genomic.fna.gz --refList GCF_001656035.1_ASM165603v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001656035.1_ASM165603v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:49,389] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:49,408] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:49,408] [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_001656035.1	s__Yersinia entomophaga	100.0	1424	1425	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.84	99.69	0.97	0.94	3	conclusive
GCF_001112925.1	s__Yersinia nurmii	94.7	1298	1425	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000754815.1	s__Yersinia ruckeri	83.9788	864	1425	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.70	97.63	0.94	0.91	69	-
GCF_900635455.1	s__Yersinia intermedia	81.5669	658	1425	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.02	97.82	0.92	0.88	29	-
GCF_001047675.1	s__Yersinia aleksiciae	81.4718	636	1425	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.22	98.37	0.87	0.82	10	-
GCF_901472495.1	s__Yersinia enterocolitica	81.4564	685	1425	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	97.11	96.22	0.89	0.83	185	-
GCF_002082245.2	s__Yersinia enterocolitica_E	81.4276	670	1425	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003600645.1	s__Yersinia rochesterensis	81.4193	661	1425	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.46	98.81	0.94	0.91	13	-
GCF_902726525.1	s__Yersinia enterocolitica_H	81.2501	652	1425	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.97	99.97	0.99	0.99	3	-
GCF_001995075.1	s__Yersinia enterocolitica_F	81.2056	681	1425	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.25	99.14	0.94	0.92	3	-
GCF_001098625.1	s__Yersinia frederiksenii_C	81.197	677	1425	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	98.63	97.69	0.93	0.89	21	-
GCF_900460465.1	s__Yersinia pestis	80.9685	606	1425	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.78	97.10	0.96	0.85	655	-
GCF_001053095.1	s__Yersinia similis	80.8982	582	1425	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.47	99.21	0.94	0.92	9	-
GCF_001152565.1	s__Yersinia pekkanenii	80.8478	652	1425	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.90	99.90	0.98	0.98	2	-
GCF_001902635.1	s__Serratia marcescens_F	79.3886	487	1425	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006438725.1	s__Ewingella americana_A	79.2185	393	1425	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Ewingella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:49,410] [INFO] GTDB search result was written to GCF_001656035.1_ASM165603v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:49,411] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:49,414] [INFO] DFAST_QC result json was written to GCF_001656035.1_ASM165603v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:49,414] [INFO] DFAST_QC completed!
[2024-01-24 13:50:49,414] [INFO] Total running time: 0h1m21s