Freiburg RNA Tools
CRISPRloci - Results
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CRISPRloci 3195732

Input and runtime details for job 3195732 (precomputed example)

Input Parameters

? Sequence(s)[.fa]
? Sequence type Single Genome DNA (FASTA format)

Genome information

? DNA sequence completeness complete

Parameters concerning CRISPR arrays

? CRISPR array orientation prediction Yes
? ML model to use all
? Detect the IS-element Yes
? Compute degenerated repeat Yes
? Fast run mode No
? Enhancement of the predicted array Yes
? Enhancement of the start and end of the array Yes
? Min. repeat length in the array21
? Max. repeat length in the array55
? Min. spacer length in the array18
? Max. spacer length in the array78
? Min. number of repeats in the array3
? Max. edit distance for evaluated array enhancement6
? Max. number of identical spacers in the array4
? Max. number of consecutive identical spacers in the array3
? Max. length of the spacer's margin for the degenerated search30

Parameters concerning Cas genes

? ML model to run combination of both
? Select the classifiers ERT
? Select the regressors ERT
? Max. number of contiguous gaps in a cassette2

Parameters for CRISPR repeat input

? Hit sensitivity (e-value threshold)0.01

Parameters for Virus DNA/RNA input

? Hit sensitivity (e-value threshold)0.000001

Job ID 3195732 (server version trunk)

?Job Submitted & Queued@ Fri Dec 18 07:37:00 CET 2020
?CRISPRloci Started@ Fri Dec 18 07:37:09 CET 2020
?CRISPRloci Finished & Post-Processing@ Fri Dec 18 07:50:33 CET 2020
?Job Completed@ Fri Dec 18 07:50:55 CET 2020
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=3195732&toolName=CRISPRloci ( 30 days expiry )

Description of the job

Synechocystis sp. PCC 6803 plasmid pSYSA (NC_005230)

Output

Download an archive file containing the complete results produced by the job in [.zip] format.

Results file content

/scratch/rna/bisge001/Software/CRISPRloci/1.1.0/CRISPRloci_Webserver/Casboundary Running Prodigal on input Fasta file. Generating Genome DataFrame Searching for potential signature proteins Extracting potential regions. Running hmmsearches. Extracting HMM features and protein properties features. Finding cassette boundaries. Labeling Cas proteins. Merging and saving final predictions. Decomposing into modules. Saving predictions. Total runtime in seconds: 168.63 Running hmmsearch (log and outputs stored in /scratch/rna/bisge001/RNA_results/CARNA-result//CRISPRloci_3195732//tmp/output-CRISPRcasIdentifier/Cassette1/hmmsearch) Annotating proteins Building cassettes Saving cassette(s) to /scratch/rna/bisge001/RNA_results/CARNA-result//CRISPRloci_3195732//tmp/output-CRISPRcasIdentifier/Cassette1/cassette/HMM2019_cassette_arrays.txt -------------------------------------------------- There are 2 unlabeled proteins for cassette # 1 and HMM2019 ERT missing bitscore prediction for cassette #1, HMM2019 and csx18 (1/2): 0.941391 ERT missing bitscore prediction for cassette #1, HMM2019 and cas6 (2/2): 0.015354 -------------------------------------------------- Loading classifiers and running classification Predictions for HMM2019 and ERT regressor Cassette #1 -- ERT classifier: CAS-III-B -------------------------------------------------- Saving class predictions to /scratch/rna/bisge001/RNA_results/CARNA-result//CRISPRloci_3195732//tmp/output-CRISPRcasIdentifier/Cassette1/predictions.csv Running hmmsearch (log and outputs stored in /scratch/rna/bisge001/RNA_results/CARNA-result//CRISPRloci_3195732//tmp/output-CRISPRcasIdentifier/Cassette2/hmmsearch) Annotating proteins Building cassettes Saving cassette(s) to /scratch/rna/bisge001/RNA_results/CARNA-result//CRISPRloci_3195732//tmp/output-CRISPRcasIdentifier/Cassette2/cassette/HMM2019_cassette_arrays.txt -------------------------------------------------- There is 1 unlabeled protein for cassette # 1 and HMM2019 ERT missing bitscore prediction for cassette #1, HMM2019 and cas13 (1/1): 0.000006 -------------------------------------------------- Loading classifiers and running classification Predictions for HMM2019 and ERT regressor Cassette #1 -- ERT classifier: CAS-I-D -------------------------------------------------- Saving class predictions to /scratch/rna/bisge001/RNA_results/CARNA-result//CRISPRloci_3195732//tmp/output-CRISPRcasIdentifier/Cassette2/predictions.csv Running hmmsearch (log and outputs stored in /scratch/rna/bisge001/RNA_results/CARNA-result//CRISPRloci_3195732//tmp/output-CRISPRcasIdentifier/Cassette3/hmmsearch) Annotating proteins Building cassettes Saving cassette(s) to /scratch/rna/bisge001/RNA_results/CARNA-result//CRISPRloci_3195732//tmp/output-CRISPRcasIdentifier/Cassette3/cassette/HMM2019_cassette_arrays.txt -------------------------------------------------- There is 1 unlabeled protein for cassette # 1 and HMM2019 ERT missing bitscore prediction for cassette #1, HMM2019 and csx25 (1/1): 0.060000 -------------------------------------------------- Loading classifiers and running classification Predictions for HMM2019 and ERT regressor Cassette #1 -- ERT classifier: CAS-III-D -------------------------------------------------- Saving class predictions to /scratch/rna/bisge001/RNA_results/CARNA-result//CRISPRloci_3195732//tmp/output-CRISPRcasIdentifier/Cassette3/predictions.csv Executing file /scratch/rna/bisge001/RNA_results/CARNA-result//CRISPRloci_3195732//input.fa 1. Run initial array detection 2. Refine detected arrays 3. Evaluate candidates 4. Enhance evaluated arrays 5. Complement arrays with additional info 6. Write down the results Elapsed time: 54.94071173667908 Building image file with height: 2000 width: 2000 File saved! Parsing XML input. Drawing features.... Positioning and drawing 33 labels.......................... 1 labels were removed. The map has been drawn. Building image file with height: 2500 width: 2500 File saved! Parsing XML input. Drawing features.... Positioning and drawing 33 labels.......................... 1 labels were removed. The map has been drawn. Building image file with height: 3000 width: 3000 File saved! Parsing XML input. Drawing features.... Positioning and drawing 33 labels.......................... 0 labels were removed. Drawing tick marks. Drawing legends. The map has been drawn. Writing picture to /scratch/rna/bisge001/RNA_results/CARNA-result/CRISPRloci_3195732/annotations_details.svg ============================================================ Phage Search using Phaster webservice for input ============================================================ acc_no: NC_005230 phaster_identified_phages /scratch/rna/bisge001/RNA_results/CARNA-result//CRISPRloci_3195732//tmp/output-CRISPRselfTarget/phages_identified_by_phaster.txt find_simi....spacer_number: 1 Bin/fasta36 /scratch/rna/bisge001/RNA_results/CARNA-result//CRISPRloci_3195732//tmp/output-CRISPRidentify/input//Spacers_1.fa /scratch/rna/bisge001/RNA_results/CARNA-result//CRISPRloci_3195732//input.fa -m 8 > /scratch/rna/bisge001/RNA_results/CARNA-result//CRISPRloci_3195732//tmp/output-CRISPRselfTarget/Fasta-simi_Spacers_1_genome.fastab cat /scratch/rna/bisge001/RNA_results/CARNA-result//CRISPRloci_3195732//tmp/output-CRISPRselfTarget/Fasta-simi_Spacers_1_genome.fastab | Bin/hashcol /scratch/rna/bisge001/RNA_results/CARNA-result//CRISPRloci_3195732//tmp/output-CRISPRselfTarget/temp-Spacers1-len | Bin/tabcol2 'abs($13-$4)+$5 $13 $1 $7 $8 $9 $10' | sort -n > /scratch/rna/bisge001/RNA_results/CARNA-result//CRISPRloci_3195732//tmp/output-CRISPRselfTarget/Spacers_1_result2.txt find_simi....spacer_number: 2 Bin/fasta36 /scratch/rna/bisge001/RNA_results/CARNA-result//CRISPRloci_3195732//tmp/output-CRISPRidentify/input//Spacers_2.fa /scratch/rna/bisge001/RNA_results/CARNA-result//CRISPRloci_3195732//input.fa -m 8 > /scratch/rna/bisge001/RNA_results/CARNA-result//CRISPRloci_3195732//tmp/output-CRISPRselfTarget/Fasta-simi_Spacers_2_genome.fastab cat /scratch/rna/bisge001/RNA_results/CARNA-result//CRISPRloci_3195732//tmp/output-CRISPRselfTarget/Fasta-simi_Spacers_2_genome.fastab | Bin/hashcol /scratch/rna/bisge001/RNA_results/CARNA-result//CRISPRloci_3195732//tmp/output-CRISPRselfTarget/temp-Spacers2-len | Bin/tabcol2 'abs($13-$4)+$5 $13 $1 $7 $8 $9 $10' | sort -n > /scratch/rna/bisge001/RNA_results/CARNA-result//CRISPRloci_3195732//tmp/output-CRISPRselfTarget/Spacers_2_result2.txt find_simi....spacer_number: 3 Bin/fasta36 /scratch/rna/bisge001/RNA_results/CARNA-result//CRISPRloci_3195732//tmp/output-CRISPRidentify/input//Spacers_3.fa /scratch/rna/bisge001/RNA_results/CARNA-result//CRISPRloci_3195732//input.fa -m 8 > /scratch/rna/bisge001/RNA_results/CARNA-result//CRISPRloci_3195732//tmp/output-CRISPRselfTarget/Fasta-simi_Spacers_3_genome.fastab cat /scratch/rna/bisge001/RNA_results/CARNA-result//CRISPRloci_3195732//tmp/output-CRISPRselfTarget/Fasta-simi_Spacers_3_genome.fastab | Bin/hashcol /scratch/rna/bisge001/RNA_results/CARNA-result//CRISPRloci_3195732//tmp/output-CRISPRselfTarget/temp-Spacers3-len | Bin/tabcol2 'abs($13-$4)+$5 $13 $1 $7 $8 $9 $10' | sort -n > /scratch/rna/bisge001/RNA_results/CARNA-result//CRISPRloci_3195732//tmp/output-CRISPRselfTarget/Spacers_3_result2.txt ------------------------------- input The number of all spacers: 304 ------------------------------- The number of spacers from type CRISPR: 178 The number of spacers in CasgeneRegion: 47 The number of spacers in ProphageRegion: 12 The number of spacers in GenomicRegion: 67 The total number of spacers written in the end result: 126 Results will be saved to /scratch/rna/bisge001/RNA_results/CARNA-result/CRISPRloci_3195732/CRISPR_Structure! -- current directory /scratch/rna/bisge001/RNA_results/CARNA-result/CRISPRloci_3195732 -- TMP -> /scratch/rna/bisge001/RNA_results/CARNA-result/CRISPRloci_3195732/TMP/ running RNAfold -p --noLP < /scratch/rna/bisge001/RNA_results/CARNA-result/CRISPRloci_3195732/tmp/output-CRISPRidentify/input/ConsensusRepeat1.fa... *------RNAfold -p --noLP ----------- >CRISPR_1 consensus GUUUCAGUCCCGAUCGCCGGGAUUAGUAGAAGGAAAG .....(((((((.....)))))))............. ( -9.50) .,{{{(((((((.....)))))))....,,,...... [-10.25] .....(((((((.....)))))))............. { -9.50 d=2.21} frequency of mfe structure in ensemble 0.296729; ensemble diversity 3.30 running RNAplfold -W 200 -L 150 --noLP -c 0 < /scratch/rna/bisge001/RNA_results/CARNA-result/CRISPRloci_3195732/tmp/output-CRISPRidentify/input/CRISPR_1.fa... running /scratch/rna/bisge001/Software/CRISPRloci/1.1.0/CRISPRloci_Webserver/CRISPRAccuracy/StructureLibrary/dotview.pl -strict -pdf -dot /scratch/rna/bisge001/RNA_results/CARNA-result/CRISPRloci_3195732/CRISPR_Structure/FOLDED_pre-crRNA//CRISPR1_dp.ps -seq "GUUUCAGUCCCGAUCGCCGGGAUUAGUAGAAGGAAAG" -o /scratch/rna/bisge001/RNA_results/CARNA-result/CRISPRloci_3195732/CRISPR_Structure/FOLDED_pre-crRNA//CRISPR1_DRmarked.pdf... Rank Candidate Sequence_Structure Stem Energy Mean_BPaccuracy Median_BPaccuracy Standard_deviation_BPaccuracy 1 CRISPR_1 -guuuc-AGUCCCG-aucgc-CGGGAUU-aguagaaggaaag- NA 0.7132 0.4569 0.1979 running R for plotting... test: .....(((((((.....)))))))............. GUUUCAGUCCCGAUCGCCGGGAUUAGUAGAAGGAAAG .....(((((((.....)))))))............. ( -9.50) .,{{{(((((((.....)))))))....,,,...... [-10.25] .....(((((((.....)))))))............. { -9.50 d=2.21} frequency of mfe structure in ensemble 0.296729; ensemble diversity 3.30 ['CRISPR_Structure_1', 'ConsensusStructure.png'] ConsensusStructure.png RNAplot --infile /scratch/rna/bisge001/RNA_results/CARNA-result//CRISPRloci_3195732//tmp/output-CRISPRidentify/input/ConsensusRepeat_Struct1.fa_tmp -t 4 --output-format=svg mv ConsensusStructure.png CRISPR_Structure_1/ConsensusStructure.png Results will be saved to /scratch/rna/bisge001/RNA_results/CARNA-result/CRISPRloci_3195732/CRISPR_Structure! -- current directory /scratch/rna/bisge001/RNA_results/CARNA-result/CRISPRloci_3195732 -- TMP -> /scratch/rna/bisge001/RNA_results/CARNA-result/CRISPRloci_3195732/TMP/ running RNAfold -p --noLP < /scratch/rna/bisge001/RNA_results/CARNA-result/CRISPRloci_3195732/tmp/output-CRISPRidentify/input/ConsensusRepeat2.fa... *------RNAfold -p --noLP ----------- >CRISPR_2 consensus GUUUCAGUCCCCUGACGGGGAAAAGAGGGUGUUGAAC .((((..(((((....)))))...))))......... ( -8.60) ..(((,.(((((....)))))...,}},....,,,.. [ -9.68] .......(((((....)))))................ { -8.40 d=4.55} frequency of mfe structure in ensemble 0.174288; ensemble diversity 6.98 running RNAplfold -W 200 -L 150 --noLP -c 0 < /scratch/rna/bisge001/RNA_results/CARNA-result/CRISPRloci_3195732/tmp/output-CRISPRidentify/input/CRISPR_2.fa... running /scratch/rna/bisge001/Software/CRISPRloci/1.1.0/CRISPRloci_Webserver/CRISPRAccuracy/StructureLibrary/dotview.pl -strict -pdf -dot /scratch/rna/bisge001/RNA_results/CARNA-result/CRISPRloci_3195732/CRISPR_Structure/FOLDED_pre-crRNA//CRISPR2_dp.ps -seq "GUUUCAGUCCCCUGACGGGGAAAAGAGGGUGUUGAAC" -o /scratch/rna/bisge001/RNA_results/CARNA-result/CRISPRloci_3195732/CRISPR_Structure/FOLDED_pre-crRNA//CRISPR2_DRmarked.pdf... Rank Candidate Sequence_Structure Stem Energy Mean_BPaccuracy Median_BPaccuracy Standard_deviation_BPaccuracy 1 CRISPR_2 -g-UUUC-ag-UCCCC-ugac-GGGGA-aaa-GAGG-guguugaac- NA 0.4758 0.2762 0.1336 running R for plotting... test: .((((..(((((....)))))...))))......... GUUUCAGUCCCCUGACGGGGAAAAGAGGGUGUUGAAC .((((..(((((....)))))...))))......... ( -8.60) ..(((,.(((((....)))))...,}},....,,,.. [ -9.68] .......(((((....)))))................ { -8.40 d=4.55} frequency of mfe structure in ensemble 0.174288; ensemble diversity 6.98 ['CRISPR_Structure_2', 'ConsensusStructure.png'] ConsensusStructure.png RNAplot --infile /scratch/rna/bisge001/RNA_results/CARNA-result//CRISPRloci_3195732//tmp/output-CRISPRidentify/input/ConsensusRepeat_Struct2.fa_tmp -t 4 --output-format=svg mv ConsensusStructure.png CRISPR_Structure_2/ConsensusStructure.png Results will be saved to /scratch/rna/bisge001/RNA_results/CARNA-result/CRISPRloci_3195732/CRISPR_Structure! -- current directory /scratch/rna/bisge001/RNA_results/CARNA-result/CRISPRloci_3195732 -- TMP -> /scratch/rna/bisge001/RNA_results/CARNA-result/CRISPRloci_3195732/TMP/ running RNAfold -p --noLP < /scratch/rna/bisge001/RNA_results/CARNA-result/CRISPRloci_3195732/tmp/output-CRISPRidentify/input/ConsensusRepeat3.fa... *------RNAfold -p --noLP ----------- >CRISPR_3 consensus GUCUCCACUCGUAGGAGAAAUUAAUUGAUUGGAAAC .(((((.......))))).................. ( -6.00) .({(((,.,,...}}}}}..,,...,,,.,,,,... [ -6.52] .(((((.......))))).................. { -6.00 d=6.14} frequency of mfe structure in ensemble 0.431482; ensemble diversity 8.13 running RNAplfold -W 200 -L 150 --noLP -c 0 < /scratch/rna/bisge001/RNA_results/CARNA-result/CRISPRloci_3195732/tmp/output-CRISPRidentify/input/CRISPR_3.fa... running /scratch/rna/bisge001/Software/CRISPRloci/1.1.0/CRISPRloci_Webserver/CRISPRAccuracy/StructureLibrary/dotview.pl -strict -pdf -dot /scratch/rna/bisge001/RNA_results/CARNA-result/CRISPRloci_3195732/CRISPR_Structure/FOLDED_pre-crRNA//CRISPR3_dp.ps -seq "GUCUCCACUCGUAGGAGAAAUUAAUUGAUUGGAAAC" -o /scratch/rna/bisge001/RNA_results/CARNA-result/CRISPRloci_3195732/CRISPR_Structure/FOLDED_pre-crRNA//CRISPR3_DRmarked.pdf... Rank Candidate Sequence_Structure Stem Energy Mean_BPaccuracy Median_BPaccuracy Standard_deviation_BPaccuracy 1 CRISPR_3 -g-UCUCC-acucgua-GGAGA-aauuaauugauuggaaac- NA 0.4729 0.3041 0.2192 running R for plotting... test: .(((((.......))))).................. GUCUCCACUCGUAGGAGAAAUUAAUUGAUUGGAAAC .(((((.......))))).................. ( -6.00) .({(((,.,,...}}}}}..,,...,,,.,,,,... [ -6.52] .(((((.......))))).................. { -6.00 d=6.14} frequency of mfe structure in ensemble 0.431482; ensemble diversity 8.13 ['CRISPR_Structure_3', 'ConsensusStructure.png'] ConsensusStructure.png RNAplot --infile /scratch/rna/bisge001/RNA_results/CARNA-result//CRISPRloci_3195732//tmp/output-CRISPRidentify/input/ConsensusRepeat_Struct3.fa_tmp -t 4 --output-format=svg mv ConsensusStructure.png CRISPR_Structure_3/ConsensusStructure.png ################################################################################### ########## CRISPR: Master Script ######### ################################################################################### Directory already exists: /scratch/rna/bisge001/RNA_results/CARNA-result//CRISPRloci_3195732/ This file does not exist: /scratch/rna/bisge001/RNA_results/CARNA-result//CRISPRloci_3195732//tmp/output-CRISPRidentify/input/Alternative_Candidates.txt This file does not exist: /scratch/rna/bisge001/RNA_results/CARNA-result//CRISPRloci_3195732//tmp/output-CRISPRidentify/input/Possible_Candidates.txt This file does not exist: /scratch/rna/bisge001/RNA_results/CARNA-result//CRISPRloci_3195732//tmp/output-CRISPRidentify/input/Possible_Discarded_Candidates.txt

When using CRISPRloci please cite :

Results are computed with CRISPRloci version 1.1.0