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CRISPRloci 0109488

Input and runtime details for job 0109488 (precomputed example)

Input Parameters

? Sequence(s)[.fa]
? Sequence type Protein sequence(s) (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 0109488 (server version trunk)

?Job Submitted & Queued@ Fri Dec 18 08:01:24 CET 2020
?CRISPRloci Started@ Fri Dec 18 08:01:41 CET 2020
?CRISPRloci Finished & Post-Processing@ Fri Dec 18 08:10:41 CET 2020
?Job Completed@ Fri Dec 18 08:10:47 CET 2020
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=0109488&toolName=CRISPRloci ( 30 days expiry )

Description of the job

Protein mode

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 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: 187.49 Running hmmsearch (log and outputs stored in /scratch/rna/bisge001/RNA_results/CARNA-result//CRISPRloci_0109488//tmp/output-CRISPRcasIdentifier/Cassette1/hmmsearch) Annotating proteins Building cassettes Saving cassette(s) to /scratch/rna/bisge001/RNA_results/CARNA-result//CRISPRloci_0109488//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_0109488//tmp/output-CRISPRcasIdentifier/Cassette1/predictions.csv Running hmmsearch (log and outputs stored in /scratch/rna/bisge001/RNA_results/CARNA-result//CRISPRloci_0109488//tmp/output-CRISPRcasIdentifier/Cassette2/hmmsearch) Annotating proteins Building cassettes Saving cassette(s) to /scratch/rna/bisge001/RNA_results/CARNA-result//CRISPRloci_0109488//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_0109488//tmp/output-CRISPRcasIdentifier/Cassette2/predictions.csv Running hmmsearch (log and outputs stored in /scratch/rna/bisge001/RNA_results/CARNA-result//CRISPRloci_0109488//tmp/output-CRISPRcasIdentifier/Cassette3/hmmsearch) Annotating proteins Building cassettes Saving cassette(s) to /scratch/rna/bisge001/RNA_results/CARNA-result//CRISPRloci_0109488//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_0109488//tmp/output-CRISPRcasIdentifier/Cassette3/predictions.csv ################################################################################### ########## CRISPR: Master Script ######### ################################################################################### Directory already exists: /scratch/rna/bisge001/RNA_results/CARNA-result//CRISPRloci_0109488/

When using CRISPRloci please cite :

Results are computed with CRISPRloci version 1.1.0
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