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/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