[2024-01-24 14:10:15,910] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:10:15,915] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:10:15,915] [INFO] DQC Reference Directory: /var/lib/cwl/stg2ebca4bd-100b-43f3-a2d2-7e05447428e9/dqc_reference
[2024-01-24 14:10:17,287] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:10:17,288] [INFO] Task started: Prodigal
[2024-01-24 14:10:17,288] [INFO] Running command: gunzip -c /var/lib/cwl/stg2e19d883-4359-4786-bb28-96fe4753316f/GCF_001053095.1_5139_1_3_genomic.fna.gz | prodigal -d GCF_001053095.1_5139_1_3_genomic.fna/cds.fna -a GCF_001053095.1_5139_1_3_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:10:29,319] [INFO] Task succeeded: Prodigal
[2024-01-24 14:10:29,319] [INFO] Task started: HMMsearch
[2024-01-24 14:10:29,319] [INFO] Running command: hmmsearch --tblout GCF_001053095.1_5139_1_3_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2ebca4bd-100b-43f3-a2d2-7e05447428e9/dqc_reference/reference_markers.hmm GCF_001053095.1_5139_1_3_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:10:29,611] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:10:29,612] [INFO] Found 6/6 markers.
[2024-01-24 14:10:29,654] [INFO] Query marker FASTA was written to GCF_001053095.1_5139_1_3_genomic.fna/markers.fasta
[2024-01-24 14:10:29,655] [INFO] Task started: Blastn
[2024-01-24 14:10:29,655] [INFO] Running command: blastn -query GCF_001053095.1_5139_1_3_genomic.fna/markers.fasta -db /var/lib/cwl/stg2ebca4bd-100b-43f3-a2d2-7e05447428e9/dqc_reference/reference_markers.fasta -out GCF_001053095.1_5139_1_3_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:10:30,469] [INFO] Task succeeded: Blastn
[2024-01-24 14:10:30,473] [INFO] Selected 19 target genomes.
[2024-01-24 14:10:30,474] [INFO] Target genome list was writen to GCF_001053095.1_5139_1_3_genomic.fna/target_genomes.txt
[2024-01-24 14:10:30,482] [INFO] Task started: fastANI
[2024-01-24 14:10:30,483] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e19d883-4359-4786-bb28-96fe4753316f/GCF_001053095.1_5139_1_3_genomic.fna.gz --refList GCF_001053095.1_5139_1_3_genomic.fna/target_genomes.txt --output GCF_001053095.1_5139_1_3_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:10:48,969] [INFO] Task succeeded: fastANI
[2024-01-24 14:10:48,970] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2ebca4bd-100b-43f3-a2d2-7e05447428e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:10:48,970] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2ebca4bd-100b-43f3-a2d2-7e05447428e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:10:48,983] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:10:48,983] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:10:48,984] [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 similis	strain=Y228	GCA_001053095.1	367190	367190	type	True	100.0	1565	1568	95	conclusive
Yersinia similis	strain=228	GCA_000582515.1	367190	367190	type	True	99.9828	1566	1568	95	conclusive
Yersinia pseudotuberculosis	strain=NCTC10275	GCA_900637475.1	633	633	suspected-type	True	94.8811	1357	1568	95	below_threshold
Yersinia intermedia	strain=NCTC11469	GCA_900635455.1	631	631	type	True	82.8375	918	1568	95	below_threshold
Yersinia intermedia	strain=ATCC 29909	GCA_000168035.1	631	631	type	True	82.734	875	1568	95	below_threshold
Yersinia thracica	strain=IP34646	GCA_902170565.1	2890319	2890319	type	True	82.6537	850	1568	95	below_threshold
Yersinia aldovae	strain=IP06005	GCA_001091225.1	29483	29483	type	True	82.5952	876	1568	95	below_threshold
Yersinia frederiksenii	strain=ATCC 33641	GCA_000168015.1	29484	29484	suspected-type	True	82.5576	881	1568	95	below_threshold
Yersinia alsatica	strain=IP38850	GCA_902170305.1	2890317	2890317	type	True	82.5388	922	1568	95	below_threshold
Yersinia rochesterensis	strain=ATCC BAA-2637	GCA_003600645.1	1604335	1604335	type	True	82.5289	890	1568	95	below_threshold
Yersinia aldovae	strain=ATCC 35236	GCA_000173735.1	29483	29483	type	True	82.5068	864	1568	95	below_threshold
Yersinia vastinensis	strain=IP38594	GCA_902726565.1	2890318	2890318	type	True	82.4415	870	1568	95	below_threshold
Serratia entomophila	strain=A1	GCA_021462285.1	42906	42906	type	True	79.0393	363	1568	95	below_threshold
Serratia nevei	strain=S15	GCA_008364245.1	2703794	2703794	type	True	78.9284	327	1568	95	below_threshold
Serratia bockelmannii	strain=S3	GCA_008011855.1	2703793	2703793	type	True	78.8436	322	1568	95	below_threshold
Rahnella bonaserana	strain=H11b	GCA_019049675.1	2816248	2816248	type	True	78.7528	310	1568	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:10:48,985] [INFO] DFAST Taxonomy check result was written to GCF_001053095.1_5139_1_3_genomic.fna/tc_result.tsv
[2024-01-24 14:10:48,986] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:10:48,986] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:10:48,986] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2ebca4bd-100b-43f3-a2d2-7e05447428e9/dqc_reference/checkm_data
[2024-01-24 14:10:48,987] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:10:49,037] [INFO] Task started: CheckM
[2024-01-24 14:10:49,038] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001053095.1_5139_1_3_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001053095.1_5139_1_3_genomic.fna/checkm_input GCF_001053095.1_5139_1_3_genomic.fna/checkm_result
[2024-01-24 14:11:28,541] [INFO] Task succeeded: CheckM
[2024-01-24 14:11:28,542] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:11:28,567] [INFO] ===== Completeness check finished =====
[2024-01-24 14:11:28,568] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:11:28,568] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001053095.1_5139_1_3_genomic.fna/markers.fasta)
[2024-01-24 14:11:28,569] [INFO] Task started: Blastn
[2024-01-24 14:11:28,569] [INFO] Running command: blastn -query GCF_001053095.1_5139_1_3_genomic.fna/markers.fasta -db /var/lib/cwl/stg2ebca4bd-100b-43f3-a2d2-7e05447428e9/dqc_reference/reference_markers_gtdb.fasta -out GCF_001053095.1_5139_1_3_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:11:29,548] [INFO] Task succeeded: Blastn
[2024-01-24 14:11:29,552] [INFO] Selected 15 target genomes.
[2024-01-24 14:11:29,552] [INFO] Target genome list was writen to GCF_001053095.1_5139_1_3_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:11:29,842] [INFO] Task started: fastANI
[2024-01-24 14:11:29,843] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e19d883-4359-4786-bb28-96fe4753316f/GCF_001053095.1_5139_1_3_genomic.fna.gz --refList GCF_001053095.1_5139_1_3_genomic.fna/target_genomes_gtdb.txt --output GCF_001053095.1_5139_1_3_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:11:45,443] [INFO] Task succeeded: fastANI
[2024-01-24 14:11:45,456] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:11:45,457] [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_001053095.1	s__Yersinia similis	100.0	1565	1568	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.47	99.21	0.94	0.92	9	conclusive
GCF_900460465.1	s__Yersinia pestis	94.7237	1318	1568	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.78	97.10	0.96	0.85	655	-
GCF_001152565.1	s__Yersinia pekkanenii	83.124	996	1568	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.90	99.90	0.98	0.98	2	-
GCF_001047675.1	s__Yersinia aleksiciae	82.8597	816	1568	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.22	98.37	0.87	0.82	10	-
GCF_900635455.1	s__Yersinia intermedia	82.8464	917	1568	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.02	97.82	0.92	0.88	29	-
GCF_002082245.2	s__Yersinia enterocolitica_E	82.7307	954	1568	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001098625.1	s__Yersinia frederiksenii_C	82.6776	900	1568	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	98.63	97.69	0.93	0.89	21	-
GCF_001123825.1	s__Yersinia kristensenii_C	82.5517	861	1568	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.60	99.58	0.95	0.93	4	-
GCF_000754805.1	s__Yersinia frederiksenii	82.5424	919	1568	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.36	98.91	0.95	0.85	11	-
GCF_003600645.1	s__Yersinia rochesterensis	82.5292	890	1568	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.46	98.81	0.94	0.91	13	-
GCF_000173735.1	s__Yersinia aldovae	82.4978	865	1568	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.00	96.65	0.94	0.91	11	-
GCF_014639435.1	s__Ewingella psychrotolerans	78.4778	281	1568	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Ewingella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002095535.1	s__Pantoea cypripedii	77.788	222	1568	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	99.97	99.97	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:11:45,458] [INFO] GTDB search result was written to GCF_001053095.1_5139_1_3_genomic.fna/result_gtdb.tsv
[2024-01-24 14:11:45,459] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:11:45,462] [INFO] DFAST_QC result json was written to GCF_001053095.1_5139_1_3_genomic.fna/dqc_result.json
[2024-01-24 14:11:45,462] [INFO] DFAST_QC completed!
[2024-01-24 14:11:45,462] [INFO] Total running time: 0h1m30s