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View Code? Open in Web Editor NEWAn ultrafast and versatile algorithm that searches for potential off-target sites of CRISPR/Cas-derived RNA-guided endonucleases.
License: Other
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rodoyle martinsaip alenzhao ryys1122 springtan justinashworth andylaw asad projectitus vijaywebs andreaclausenlind richardkmichael intellia gue-ho healthvivo godotgildor drofish6390 ghahfarokhi benblack769 honestant positive-song latchbio mvattiku bowhan furkanozdenn wangdong-ls xiahaohao pnucolabcas-offinder's Issues
clFinish Failed: -36 -- error message during chunk loading
I received this error message clFinish Failed: -36 when I attempted to run a couple of random sequences. Here's the specs...
The input named test.fasta:
/data/index/hg19chr
NNNNNNNNNNNNNNNNNNNNNRG
GACTGATGCTGTAGTCGTACNNN 3
TAGCTGTGTAGTCGTGTCGGNNN 2
The reference was acquired from:
wget http://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/chromFa.tar.gz
My desktop is running 64-bit:
4.4.0-97-generic #120-Ubuntu SMP Tue Sep 19 17:28:18 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
Binary cas-offinder was acquired from:
https://sourceforge.net/projects/cas-offinder/files/Binaries/2.4/Linux64/cas-offinder/download
Executing cas-offinder gave me this info:
$ ./cas-offinder
[Output]
./cas-offinder: /usr/local/cuda-8.0/targets/x86_64-linux/lib/libOpenCL.so.1: no version information available (required by ./cas-offinder)
Cas-OFFinder v2.4 (Aug 17 2016)
Copyright (c) 2013 Jeongbin Park and Sangsu Bae
Website: http://github.com/snugel/cas-offinder
Usage: cas-offinder {input_file} {C|G|A}[device_id(s)] {output_file}
(C: using CPUs, G: using GPUs, A: using accelerators)
Example input file:
/var/chromosomes/human_hg19
NNNNNNNNNNNNNNNNNNNNNRG
GGCCGACCTGTCGCTGACGCNNN 5
CGCCAGCGTCAGCGACAGGTNNN 5
ACGGCGCCAGCGTCAGCGACNNN 5
GTCGCTGACGCTGGCGCCGTNNN 5
Available device list:
Type: GPU, ID: 0, <NVS 510> on <NVIDIA CUDA>
*Note that an warning pop up at the first line of stdout. The file libOpenCL.so.1 was existed in the folder it showed in the warning message.
Running test.fasta:
$ ./cas-offinder ../raw_data/test.fasta G0 ../processed_data/test.out
[Output]
./cas-offinder: /usr/local/cuda-8.0/targets/x86_64-linux/lib/libOpenCL.so.1: no version information available (required by ./cas-offinder)
Total 1 device(s) found.
Loading input file...
Reading /data/index/hg19chr/chrUn_gl000223.fa...
Sending data to devices...
Chunk load started.
1 devices selected to analyze...
Finding pattern in chunk #1...
Comparing patterns in chunk #1...
Reading /data/index/hg19chr/chr9_gl000201_random.fa...
Sending data to devices...
Chunk load started.
1 devices selected to analyze...
Finding pattern in chunk #2...
Comparing patterns in chunk #2...
Reading /data/index/hg19chr/chrUn_gl000228.fa...
Sending data to devices...
Chunk load started.
1 devices selected to analyze...
Finding pattern in chunk #3...
Comparing patterns in chunk #3...
Reading /data/index/hg19chr/chr6.fa...
Sending data to devices...
Chunk load started.
1 devices selected to analyze...
Finding pattern in chunk #4...
clFinish Failed: -36
The last line in the stdout clFinish Failed: -36 kept showed up and stopped my runs.
Could someone diagnose the type of error and take a guess why it could not complete the runs?
Looks like a bug with .2bit input
I have one target sequence in t.fa
I create t.2bit using: faToTwoBit t.fa t.2bit
The query sequence is taken from the target sequence.
If I run: cas-offinder t.fa.in C t.fa.ou, I get the correct output, where it finds an exact match.
ATGGCCAACACTCACCTTCACGG chr5:64476990-64477249 234 ATGGCCAACACTCACCTTCACGG - 0
If I run: cas-offinder t.2bit.in C t.2bit.ou, I get a wrong output, which finds a mismatch that does not exist.
ATGGCCAACACTCACCTTCACGG chr5:64476990-64477249 234 cTGGCCAACACTCACCTTCACGG - 1
Seems like a bug associated with the 2bit input format. Thanks!
Randomly occurring error with clFinish
clFinish Failed: -36
There seems to be no pattern or possible cause. If I rerun the same command, it sometimes runs successfully and sometimes returns this error code. Could you please add some details in error reporting to enable better debugging?
Diffrenet results via webserver vs commnad line exe
Some erroneous output alongwith correct results
Hi,
I have been trying to run CAS-OFFINDER using the binary files that i have downloaded from https://github.com/snugel/cas-offinder/releases/tag/3.0.0b3.
The input to the binary file is as follows
var/chromosome/human_hg38
NNNNNNNNNNNNNNNNNNNNNGG 0 0
GACCCCCTCCACCCCGCCTCNNN 5 Seq0
Looking at the output, i see it does expected output for the test case, GACCCCCTCCACCCCGCCTC with selected PAM as SpCas9 from Streptococcus pyogenes: 5'-NGG-3'. However, there are some erroneous rows as shown below
| #Id | Bulge Type | crRNA | DNA | Chromosome | Location | Direction | Mismatches | Bulge Size |
|---|
Seq0 | X | GACCCCCTCCACCCCGCCTCNNN | GACCCCCTCCACCCCGCCTCCGG | chr6 | 43770818 | - | 0 | 0
Seq0 | X | GACCCCCTCCACCCCGCCTCNNN | cttaCataagtCgCaGatggTGG | chr16 | 90227832 | - | 0 | 0
Seq0 | X | GACCCCCTCCACCCCGCCTCNNN | tgaCttacatAagtCGCagaTGG | chr16 | 90227835 | - | 0 | 0
Seq0 | X | GACCCCCTCCACCCCGCCTCNNN | aAaaCCacagtgtCtGtaTCTGG | chr16 | 90227868 | - | 0 | 0
Seq0 | X | GACCCCCTCCACCCCGCCTCNNN | tttCtCactgttgaaGtgggAGG | chr16 | 90227801 | - | 0 | 0
Seq0 | X | GACCCCCTCCACCCCGCCTCNNN | agCtttCTCactgttGaagtGGG | chr16 | 90227804 | - | 0 | 0
Seq0 | X | GACCCCCTCCACCCCGCCTCNNN | GAatagaatCtgtagGCtgaAGG | chr16 | 90227965 | - | 0 | 0
Seq0 | X | GACCCCCTCCACCCCGCCTCNNN | tgCCCtCagCcCgCCcgCcCGGG | chr13 | 114353556 | - | 0 | 0
Seq0 | X | GACCCCCTCCACCCCGCCTCNNN | GtgCCCtcagcCCgCcCgcCCGG | chr13 | 114353557 | - | 0 | 0
Seq0 | X | GACCCCCTCCACCCCGCCTCNNN | ccgCCCtcgCgatgCtCtcCGGG | chr13 | 114353464 | - | 0 | 0
Seq0 | X | GACCCCCTCCACCCCGCCTCNNN | tcCgCCCTCgcgatgctCTCCGG | chr13 | 114353465 | - | 0 | 0
Seq0 | X | GACCCCCTCCACCCCGCCTCNNN | acttgaaTgacCttatgagaAGG | chr20 | 64330031 | + | 0 | 0
Seq0 | X | GACCCCCTCCACCCCGCCTCNNN | tAttgCtTtgtttCtcagctTGG | chr20 | 64333338 | + | 0 | 0
Seq0 | X | GACCCCCTCCACCCCGCCTCNNN | cttgtgCTCtgCaCatatatTGG | chr20 | 64330056 | + | 0 | 0
Seq0 | X | GACCCCCTCCACCCCGCCTCNNN | agCttttTgagtgagtgCTCAGG | chr20 | 64333448 | + | 0 | 0
Seq0 | X | GACCCCCTCCACCCCGCCTCNNN | GctttttgagtgagtGCtcaGGG | chr20 | 64333449 | + | 0 | 0
Seq0 | X | GACCCCCTCCACCCCGCCTCNNN | GtgagtgctCAgggtGttctAGG | chr20 | 64333458 | + | 0 | 0
Seq0 | X | GACCCCCTCCACCCCGCCTCNNN | tcttCCtagCAaaCtttCTtTGG | chr20 | 64330126 | + | 0 | 0
Seq0 | X | GACCCCCTCCACCCCGCCTCNNN | ctttggtaaagaatgaataaAGG | chr20 | 64330143 | + | 0 | 0
Seq0 | X | GACCCCCTCCACCCCGCCTCNNN | cttatCCaCagCtgaGCtcaCGG | chr20 | 64330169 | + | 0 | 0
Seq0 | X | GACCCCCTCCACCCCGCCTCNNN | ccaCagCTgagCtCacggTtAGG | chr20 | 64330174 | + | 0 | 0
Seq0 | X | GACCCCCTCCACCCCGCCTCNNN | cACagCtgagctCaCGgtTaGGG | chr20 | 64330175 | + | 0 | 0
Seq0 | X | GACCCCCTCCACCCCGCCTCNNN | cttCagtataAtgttGgCTgTGG | chr20 | 64333669 | + | 0 | 0
Seq0 | X | GACCCCCTCCACCCCGCCTCNNN | ttCagtaTaatgttgGCtgtGGG | chr20 | 64333670 | + | 0 | 0
Seq0 | X | GACCCCCTCCACCCCGCCTCNNN | GgCtgtgggtttgtCaCagaTGG | chr20 | 64333684 | + | 0 | 0
Seq0 | X | GACCCCCTCCACCCCGCCTCNNN | agatggCTtttattacCtTaAGG | chr20 | 64333701 | + | 0 | 0
Seq0 | X | GACCCCCTCCACCCCGCCTCNNN | tttCtatgtagattttgtTgAGG | chr20 | 64333732 | + | 0 | 0
Seq0 | X | GACCCCCTCCACCCCGCCTCNNN | ttCtatgTagAttttGttgaGGG | chr20 | 64333733 | + | 0 | 0
Seq0 | X | GACCCCCTCCACCCCGCCTCNNN | tAaCaaaaattCtgtttaTgTGG | chr20 | 64333820 | + | 0 | 0
Seq0 | X | GACCCCCTCCACCCCGCCTCNNN | cAttCaagtCtggCacCacgTGG | chr20 | 64330017 | - | 0 | 0
Seq0 | X | GACCCCCTCCACCCCGCCTCNNN | ctCataaggtcattCaagTCTGG | chr20 | 64330027 | - | 0 | 0
Seq0 | X | GACCCCCTCCACCCCGCCTCNNN | agCaCaagttcCttCtCaTaAGG | chr20 | 64330041 | - | 0 | 0
Seq0 | X | GACCCCCTCCACCCCGCCTCNNN | aAtgaatTCagtaaaGttTCAGG | chr20 | 64333412 | - | 0 | 0
Seq0 | X | GACCCCCTCCACCCCGCCTCNNN | agtttgCTaggaagataaatGGG | chr20 | 64330118 | - | 0 | 0
Seq0 | X | GACCCCCTCCACCCCGCCTCNNN | aAgtttgctaggaagataaaTGG | chr20 | 64330119 | - | 0 | 0
Seq0 | X | GACCCCCTCCACCCCGCCTCNNN | tttaCCaaagAaagtttgctAGG | chr20 | 64330130 | - | 0 | 0
Seq0 | X | GACCCCCTCCACCCCGCCTCNNN | cctaaCCgtgAgCtCagCTgTGG | chr20 | 64330174 | - | 0 | 0
Seq0 | X | GACCCCCTCCACCCCGCCTCNNN | cAgCCaacattataCtgaagGGG | chr20 | 64333666 | - | 0 | 0
Seq0 | X | GACCCCCTCCACCCCGCCTCNNN | acagCCaaCattatactgaaGGG | chr20 | 64333667 | - | 0 | 0
Seq0 | X | GACCCCCTCCACCCCGCCTCNNN | cACagCCaaCAttataCtgaAGG | chr20 | 64333668 | - | 0 | 0
Seq0 | X | GACCCCCTCCACCCCGCCTCNNN | atagaaaaaaACatacCtTaAGG | chr20 | 64333716 | - | 0 | 0
Seq0 | X | GACCCCCTCCACCCCGCCTCNNN | tggaaaggaCACgggaagTCTGG | chrY | 57214618 | + | 0 | 0
Seq0 | X | GACCCCCTCCACCCCGCCTCNNN | GgaaaggaCacgggaagtctGGG | chrY | 57214619 | + | 0 | 0
Seq0 | X | GACCCCCTCCACCCCGCCTCNNN | tggCaCaggCcagCaGttgCTGG | chrY | 57214533 | + | 0 | 0
Seq0 | X | GACCCCCTCCACCCCGCCTCNNN | tACaCatgaacagaaagaagAGG | chrY | 57214657 | + | 0 | 0
Seq0 | X | GACCCCCTCCACCCCGCCTCNNN | GAaagaagaggtCaaagaaaAGG | chrY | 57214669 | + | 0 | 0
Seq0 | X | GACCCCCTCCACCCCGCCTCNNN | GAggtCaaagAaaagGCtgaCGG | chrY | 57214676 | + | 0 | 0
Seq0 | X | GACCCCCTCCACCCCGCCTCNNN | GcaaCtgctggCCtgtgCcaGGG | chrY | 57214530 | - | 0 | 0
Seq0 | X | GACCCCCTCCACCCCGCCTCNNN | agCaaCtgCtggCCtGtgcCAGG | chrY | 57214531 | - | 0 | 0
Seq0 | X | GACCCCCTCCACCCCGCCTCNNN | GtCtgaCTtCcagCaaCtgCTGG | chrY | 57214542 | - | 0 | 0
This is different from the output that i get on the hosted server at http://www.rgenome.net/cas-offinder/
Is there something wrong in the input? or Is there something that is dont post processing?
Missing potential off-targets of length less than 23 with gaps?
Hello,
First, thank you for your amazing work.
Second, I tried to find off-targets with indels, where the cRNA will be of length 23 (it can't have bulges), and the DNA would be of length less than 23 with gaps. For example, In some experimental data, I got for the target (cRNA) "GTCCCTAGTGGCCCCACTGTNGG" the following off-target:
"GTCCTGTGCCCCCACTGTGGG", and the alignment is:
C A G
G T C C T G T G C C C C A C T G T N G G
| | | | | | | | | | | | | | | | | | | |
G T C C - T - G T G C C C C A C T G T G G G
C
I tried different variations of running cas-offinder, but could found any that generates such examples, even more, simple with off-targets (DNA) of length 22 for example. Do you support those kinds of off-targets?
Moreover, It seems that the tool is providing cRNA with 24 nuclides (when the original size is 23), meaning that it seems like it contains insertion in the guide RNA. How is it possible? The insertion or deletion should be only in the DNA.
Thank you
Segemetation fault when match is at the very first location
To reproduce, use Fasta file:
s1
GGCCGACCTGTCGCTGACGCAGG
Use input file:
NNNNNNNNNNNNNNNNNNNNNNN
GGCCGACCTGTCGCTGACGCAGG 5
Get a segmentation fault. However, if we use Fasta file, it works.
s1
AGGCCGACCTGTCGCTGACGCAGG
Could you help take a look? Thanks!
conda-installed cas-offinder doesn't find GPU
cas-offinder installed via conda running on AWS p3.2xlarge instance can't "see" the GPUs (when running with arg "G" doesn't work and receive error "No OpenCL devices found", but arg "C" works fine).
When installed from source not in a conda environment it works fine with arg "G". It could be an issue of opencl, or of conda, but I wanted to let you know.
Thanks for the great program!
Add summary table?
As with the online version of Cas-OFFinder, providing a summary table along with the result could be helpful.
Similar to VCF file, this table can be provided on top of the result, starting double #. For example:
##Id=0;Bulge Type=DNA;Bulge Size=1;Mismatches=0;Number of Found Targets=3
##Id=0;Bulge Type=DNA;Bulge Size=1;Mismatches=1;Number of Found Targets=6
##Id=0;Bulge Type=DNA;Bulge Size=1;Mismatches=2;Number of Found Targets=52
##Id=0;Bulge Type=RNA;Bulge Size=1;Mismatches=0;Number of Found Targets=2
##Id=0;Bulge Type=RNA;Bulge Size=1;Mismatches=1;Number of Found Targets=7
##Id=0;Bulge Type=RNA;Bulge Size=1;Mismatches=2;Number of Found Targets=124
##Id=0;Bulge Type=RNA;Bulge Size=2;Mismatches=0;Number of Found Targets=1
##Id=0;Bulge Type=RNA;Bulge Size=2;Mismatches=1;Number of Found Targets=12
##Id=0;Bulge Type=RNA;Bulge Size=2;Mismatches=2;Number of Found Targets=411
##Id=0;Bulge Type=X;Bulge Size=0;Mismatches=0;Number of Found Targets=1
##Id=0;Bulge Type=X;Bulge Size=0;Mismatches=2;Number of Found Targets=2
##Id=1;Bulge Type=DNA;Bulge Size=1;Mismatches=1;Number of Found Targets=1
##Id=1;Bulge Type=DNA;Bulge Size=1;Mismatches=2;Number of Found Targets=16
##Id=1;Bulge Type=RNA;Bulge Size=1;Mismatches=1;Number of Found Targets=1
##Id=1;Bulge Type=RNA;Bulge Size=1;Mismatches=2;Number of Found Targets=67
##Id=1;Bulge Type=RNA;Bulge Size=2;Mismatches=1;Number of Found Targets=14
##Id=1;Bulge Type=RNA;Bulge Size=2;Mismatches=2;Number of Found Targets=200
##Id=1;Bulge Type=X;Bulge Size=0;Mismatches=0;Number of Found Targets=1
##Id=1;Bulge Type=X;Bulge Size=0;Mismatches=2;Number of Found Targets=1
#Id Bulge type crRNA DNA Chromosome Location Direction Mismatches Bulge Size
0 X CAGCAACTCCAGGGGGCCGCNGG CAGCAACTCCAGaaGGCCGCTGG chr8 37610874 - 2 0
0 DNA C-AGCAACTCCAGGGGGCCGCNGG CCAGCAACTCCAGaaGGCCGCTGG chr8 37610874 - 2 1
0 RNA CAGCAACTCCAGGGGGCCGCNGG CA-CAACTCCAGGGGGgCcCAGG chr8 23557969 - 2 1
0 RNA CAGCAACTCCAGGGGGCCGCNGG CAGC--CTCCAGGGaGCaGCGGG chr8 142250982 + 2 2
0 RNA CAGCAACTCCAGGGGGCCGCNGG CAGCgACTCC--GGGGaCGCAGG chr8 11704733 + 2 2
0 RNA CAGCAACTCCAGGGGGCCGCNGG CgGCAACcCCAGGGGGC--CTGG chr8 19084840 - 2 2
0 RNA CAGCAACTCCAGGGGGCCGCNGG CAGCAgCaCCAGGGGGC--CGGG chr8 142474507 - 2 2
0 RNA CAGCAACTCCAGGGGGCCGCNGG CAGCAtCTCCAGtGGGC--CTGG chr8 143464948 - 2 2
1 DNA AA-AGGAAACCATTGTGTTAANGG AAGAGaAAAaCATTGTGTTAAAGG chr8 58745275 - 2 1
1 DNA AAAGGAAACCATTGTGTTA-ANGG AAAGGAAACacTTGTGTTACAGGG chr8 75004203 - 2 1
1 RNA AAAGGAAACCATTGTGTTAANGG AAA-GAAACCAaTGTGTTtAAGG chr8 121965290 - 2 1
1 RNA AAAGGAAACCATTGTGTTAANGG AAAG-AAACCAaTGTGTTtAAGG chr8 121965290 - 2 1
1 RNA AAAGGAAACCATTGTGTTAANGG AAAGGAAACtA-TGTaTTAATGG chr8 11047256 - 2 1
1 RNA AAAGGAAACCATTGTGTTAANGG AAAGGAAACtAT-GTaTTAATGG chr8 11047256 - 2 1
1 RNA AAAGGAAACCATTGTGTTAANGG A--GaAAAaCATTGTGTTAAAGG chr8 58745275 - 2 2
1 RNA AAAGGAAACCATTGTGTTAANGG AA--tAAtCCATTGTGTTAATGG chr8 64904883 + 2 2
1 RNA AAAGGAAACCATTGTGTTAANGG AA--GAAACCAaTGTGTTtAAGG chr8 121965290 - 2 2
...
The off-target zero-based position doesn't match the UCSC zero-based position
Cas-offinder positions for off-target sites don't match UCSC blat results. UCSC blat results are zero-based. Below is an example:
Cas-offinder output: CTCCCACACGAGTTGCCCCACGCT + 483173
Blat Result using the above sequence: chr8 + 483174 483197
So, it seems the cas-offinder position is off by one base. Could you please advice?
Many Thanks,
Azita
Failure on Mac OSX Catalina
Hi,
Getting :
$ ./cas-offinder ./input.txt C ./output.txt
clBuildProgram Failed: -11
Log from device 0:
System info:
MacBook Pro (15-inch, 2018)
2.2 GHz 6-Core Intel Core i7
GPU:
Radeon Pro 555X 4 GB
Intel UHD Graphics 630 1536 MB
Mac OS: 10.15.7 (19H1323)
Can you help debug this?
Thanks!
Fred
parameter setting
Is there any empiric value for maximum mismatch numbers in input file?
Time to process
for a list of 300 guides, the time to compute the off target score is a lot. Do you have any recommendations for how I can speed up the process? Or alternative faster resources.
Thanks
Tagging of input sequences
When running a large amount of sequences with cas-offinder, additional steps are needed to match the input and output data for further analysis.
In order to make it easier to use cas-offinder results further in e.g. pipelines it would be beneficial to add an identifying column to the input and output.
Example input
/var/chromosomes/human_hg19
NNNNNNNNNNNNNNNNNNNNNRG
GGCCGACCTGTCGCTGACGCNNN 5 ID1
CGCCAGCGTCAGCGACAGGTNNN 5 ID2
ACGGCGCCAGCGTCAGCGACNNN 5 ID3
GTCGCTGACGCTGGCGCCGTNNN 5 ID4
Example output
GGCCGACCTGTCGCTGACGCNNN chr8 49679 GGgCatCCTGTCGCaGACaCAGG + 5 ID1
GGCCGACCTGTCGCTGACGCNNN chr8 517739 GcCCtgCaTGTgGCTGACGCAGG + 5 ID1
GGCCGACCTGTCGCTGACGCNNN chr8 599935 tGCCGtCtTcTCcCTGACGCCAG - 5 ID1
GGCCGACCTGTCGCTGACGCNNN chr8 5308348 GGCaGgCCTGgCttTGACGCAGG - 5 ID2
GGCCGACCTGTCGCTGACGCNNN chr8 9525579 GGCCcAgCTGTtGCTGAtGaAAG + 5 ID2
GGCCGACCTGTCGCTGACGCNNN chr8 12657177 GGCCcACCTGTgGCTGcCcaTAG - 5 ID3
GGCCGACCTGTCGCTGACGCNNN chr8 12808911 GGCCGACCaGgtGCTccCGCCGG + 5 ID3
GGCCGACCTGTCGCTGACGCNNN chr8 21351922 GGCCcACCTGaCtCTGAgGaCAG - 5 ID3
GGCCGACCTGTCGCTGACGCNNN chr8 21965064 GGCCGtCCTGcgGCTGctGCAGG - 5 ID4
GGCCGACCTGTCGCTGACGCNNN chr8 22409058 GcCCGACCccTCcCcGACGCCAG + 5 ID4
Input files - Positions issues
Hello,
Thanks for making such a great documentation. I have a question regarding some strange results I have been getting depending on the input files. I have changed my original error message and put real guides and examples to make it easier to replicate.
Say you have a guide for Myod: “TTTGTGGTTAAGGAAAGCGG”. If I run it on the terminal with one mismatch, one dna bulge and one rna bulge, I get the following wrong position (off by one 0-based) for no mismatches: X TTTGTGGTTAAGGAAAGCGGNRG TTTGTGGTTAAGGAAAGCGGCGG chr11 17719597 - 0 0
If I run the same guide in the cas-offinder website with the same parameters (1 mismatch, one bulge in dna and rna), I get the correct position: X TTTGTGGTTAAGGAAAGCGGNRG TTTGTGGTTAAGGAAAGCGGCGG chr11 17719596 - 0 0
Now, if you run the guide in the terminal with just one mismatch (no bulges), you get the correct position again as in the website, so it seems that adding bulges to the parameters triggers something that makes the position to be off. I tried to replicate, and strangely it does not happen with all guides. So I tested a few and from those, the one I mention in this example gave those weird results.
The guides I tested are:
TCCTTAACCACAAATCAGGC
TTTGTGGTTAAGGAAAGCGG (only one where I detected this problem)
CAAATCAGGCCGGACAGGAG
AACCACAAATCAGGCCGGAC
GCTTTCCTTAACCACAAATC
Thank you so much, Carmen
cas-offinder-bulge targe sequence change
Hi,
I ran cas-offinder-bulge and noticed that the target sequences in my output .txt file are different from my input sequences. Specifically, the first base of the target sequence is gone, and there is an "N" inserted at the end of the sequence, right before the PAM sequence. The issue is present for both RNA and DNA bulges.
input:
./Cas-OFFinder/chromosomes
NNNNNNNNNNNNNNNNNNNNNRG 1 1
CTAACAGTTGCTTTTATCACNGG 3
output (crRNA):
TAACAGTTGCTTTTATCACNNRG
I don't have this problem when I run the original cas-offinder.
I've also submitted this issue in cas-offinder-bulge. hyugel/cas-offinder-bulge#1
Thanks!
multicore issue
Hi,
I am running cas-offinder as a part of a pipeline on a cluster and my job is failing because a demand for more cores than I configure.
I wonder if cas-offinder automatically uses multicore?
Thank you
please tag updates
For the purposes of reproducible science could you please tag your project. I would also recommend using a 3 or 4 digit semantic versioning scheme; Magor.Minor.Patch. Please do not follow the git examples by putting a "v" as the leading character. Github will create a "release" once you push a tag.
git tag 2.4.0
git push origin 2.4.0
Position seems off-by-1
I am sorry, I am not sure if this is a bug or if I misunderstand Cas-OFFinder "position".
I know the documentation indicates the Cas-OFFinder position is according to "Bowtie convention". However, I do not know what "Bowtie convention" means-- does it mean "position is the last bp just before the matched sequence begins" (i.e., n-1) ? (I looked at the Bowtie documentation but I did not find and explanation of position, a link or reference would be appreciated, I will add it to Cas-OFFinder documentation.)
Using GRCh38, Cas-OFFinder returns:
query_sequence,chromosome,position,matched_sequence,direction,mismatches
GACCCCCTCCACCCCGCCTCNGG,"1 dna:chromosome chromosome:GRCh38:1:1:248956422:1 REF",9830673,aACCtCCaCCtCCCgGatTCAaG,+,8
Using the IGV viewer, at chr1:9,830,653-9,830,692, we see the matched sequence aACCtCCaCCtCCCgGatTCAaG begins at 9,830,674, not 9,830,673, which is off by 1 bp.
I also see this unmerged commit e89b48e on the develop branch, which appears to fix an off-by-1 problem; is it related ?
Diffrenet results via webserver vs commnad line exe and error input length
Hello,
Running an targetseq on the webserver with buldge sizes of 0 and till 6 missmatches against hg38 genome gives different amount of results comparing to the command line output file.
for example: running the tragetseq: AACTGAGTCCCAAGGTGGGTNGG with parameters mentioned gives around 11k results on the web server but in the commnad line there are around 35k results.
further more in the version 2.4.1 trying to run your input file example as:
/var/chromosomes/human_hg38
NNNNNNNNNNNNNNNNNNNNNRG 2 1
GGCCGACCTGTCGCTGACGCNNN 5
gives an critical error that sequences lengths arnt the same. giving any bulge number to dna\rna and not keeping them empty will give that error.
thanks!
PAM site for Cpf1
The tool seems to find the PAM site for Cpf1 on the 3' side instead of the 5' side. It's supposed to look at the 5' side. Is it possible to add a parameter to specify this?
Segmentation fault in GPU mode on Mac
Hi
Thank you for this excellent application. I was able to get it to work on Linux without a problem on CPU and GPU.
However when I tried using your supplied binary and a self-compiled binary on Mac OSX 10.9.2 (64 bit) with a Iris 1024 OpenCL supported GPU, the program gives a "Segmentation fault" as soon as it starts. On the Mac, the CPU mode works fine but takes a while.
Here is what the debugger says :
Haris-MacBook-Pro:~ hari$ ./cas-offinder_mac testinput.txt G cas_gpu_official
Segmentation fault: 11
The debugger outputs:
(lldb) run
Process 7356 launched: './cas-offinder_mac' (x86_64)
Process 7356 stopped
- thread #1: tid = 0x5a2a6, 0x00001234003c3d79 AppleIntelHD5000GraphicsGLDriver
gldBuildComputeProgram + 84, queue = 'com.apple.main-thread', stop reason = EXC_BAD_ACCESS (code=1, address=0xc) frame #0: 0x00001234003c3d79 AppleIntelHD5000GraphicsGLDrivergldBuildComputeProgram + 84
AppleIntelHD5000GraphicsGLDriver`gldBuildComputeProgram + 84:
-> 0x1234003c3d79: movl 0xc(%rdi), %eax
0x1234003c3d7c: leaq 0x18(%rax,%rdi), %rax
0x1234003c3d81: movq 0x8(%rbx), %rcx
0x1234003c3d85: movq %rax, 0x28(%rcx)
I also compiled my own binary from source and that too segmentation faults on the same Macbook
Apples web page suggest that OpenCl MacBook Pro (Retina, 13-inch, Late 2013)
Intel Iris Graphics support OpenCL 1.2. I was also able to run Apples demo OpenCL application on the same hardware.
Any ideas on how to get GPU mode working on Mac.
Thanks
Hari
Failing to parse input file
cas-offinder fails to parse the input file even when using the example.
I receive the following error message: Critical error! The length of target sequences should match with the length of pattern sequence.
Any ideas as to what is causing this or any possible solutions for remedying it?
Wrong number of predicted mismatches
Hi,
I'm trying to use Cas-Offinder (conda version or v.2.4) with Cas-designer (v.1.2 standalone) and Cas-Offinder-bulge (v.1.2 beta), and – although the pipeline runs – I'm getting some wrong results regarding the number of mismatches.
command:
python3 cas-designer file.config
where 'file.config' looks like this:
/path-to/genome.fasta
/path-to/target.fasta
20
NGG
NGG
5
0
0I noticed the mismatch count is wrong by inspecting the output 'file-offtargets.txt', for example:
#Bulge type crRNA DNA Chromosome Position Direction Mismatches Bulge Size
X TTCACCCGGATAAGCGACACNGG TTttCtaGatTttcgGgaAaAAA NC_071671.1 5197491 + 2 0
X TTCACCCGGATAAGCGACACNGG TTtctagattTtcGgGAaAaAAT NC_071671.1 5197492 + 1 0
X TTCACCCGGATAAGCGACACNGG TTCtagatttTcgGgaAaAaATA NC_071671.1 5197493 + 1 0
X TTCACCCGGATAAGCGACACNGG TctAgattttcggGaaAaAaTAA NC_071671.1 5197494 + 1 0I also noticed that these off-targets above don't have a PAM (NGG), but some others do:
#Bulge type crRNA DNA Chromosome Position Direction Mismatches Bulge Size
X TTCACCCGGATAAGCGACACNGG cctttggGaAagttttttttGGG NC_016056.1 15617 + 3 0
X TTCACCCGGATAAGCGACACNGG TTtcgggGttTtttaccaAtTGG NC_016056.1 15484 + 4 0
X TTCACCCGGATAAGCGACACNGG TTttttaccAattGgtcCAaTGG NC_016056.1 15492 + 3 0Even if I just use Cas-Offinder I got wierd results.
running cas-offinder offinder.conf G offinder.out where offinder.conf looks like this:
/path_to/genome.fasta
NNNNNNNNNNNNNNNNNNNNNGG 0 0
TTCACCCGGATAAGCGACACCGG 5I get this:
#gRNA target strand mismatches
TTCACCCGGATAAGCGACACCGG TTCACCCGGATAAGCGACACCGGAAAC + 0
TTCACCCGGATAAGCGACACCGG TgtAaCCtcATAAGCGACACCGGTGTC + 5
TTCACCCGGATAAGCGACACCGG aTCACtCGGAgAAGgGACAgCGGCTGT + 5
TTCACCCGGATAAGCGACACCGG acttCaCccgcctctGcCACaccGGGT - 5
TTCACCCGGATAAGCGACACCGG acttaaaccggAtatcAgACaccGGAT - 5Above, the last two sequences have way more than 5 mismatches
I don't know why this is happening, can you help me?
Thank you,
Dani.
statistics?
Could the outcome be integrated with statistics, to guide further wet experiments to detect high risk off target event? Thanks
Cannot compile 3.0.0.b (develop branch) on macOS 10.14.6
I noticed development is starting on 3.0.0b on the develop branch, and I wanted to test it.
I am unable to compile it on macOS 10.14.6 (clang 10), due to a problem with the new add_compare macro:
source/cas-offinder/cas-offinder.cpp:559:4: error: expected
'(' for function-style cast or type construction
add_compare(string(m_dnabulgesize, 'N') + sline[0], ci, bi);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
source/cas-offinder/cas-offinder.cpp:13:49: note: expanded from
macro 'add_compare'
m_compares[a] = make_pair(b, vector<bulgeinfo>{c});\
~~~~~~~~~~~~~~~~~^
source/cas-offinder/cas-offinder.cpp:564:6: error: expected
'(' for function-style cast or type construction
...add_compare(string(preNcnt, 'N') + sline[0].substr(0, j) + string(i, 'N') + sline[0].substr(j), ci, bi);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
source/cas-offinder/cas-offinder.cpp:13:49: note: expanded from
macro 'add_compare'
m_compares[a] = make_pair(b, vector<bulgeinfo>{c});\
~~~~~~~~~~~~~~~~~^
source/cas-offinder/cas-offinder.cpp:571:6: error: expected
'(' for function-style cast or type construction
...add_compare(string(preNcnt, 'N') + sline[0].substr(0, j) + sline[0].substr(j + i), ci, bi);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
source/cas-offinder/cas-offinder.cpp:13:49: note: expanded from
macro 'add_compare'
m_compares[a] = make_pair(b, vector<bulgeinfo>{c});\
~~~~~~~~~~~~~~~~~^
25 warnings and 3 errors generated.
make[2]: *** [CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o] Error 1
make[1]: *** [CMakeFiles/cas-offinder.dir/all] Error 2
make: *** [all] Error 2
simple-build-changes *$ $ clang++ --version
Apple LLVM version 10.0.1 (clang-1001.0.46.4)
Target: x86_64-apple-darwin18.7.0
Thread model: posix
InstalledDir: /Library/Developer/CommandLineTools/usr/bin
Add summary table to README
cas-offinder-bulge
Hi Thanks for the excellent software!
I am trying to run a simple analysis to find all the sequences with 6 mismatches and 1nt bulge either DNA or RNA.
This is my input file:
/data/genomes/hg19.2bit
NNNNNNNNNNNNNNNNNNNNNNN 1 1
GAGTCCGAGCAGAAGAAGAAGGG 6
This is the command I run:
cas-offinder-bulge input_file.txt G output_file.txt
In the output file I see the RNA bulges but not DNA.
Is this a known bug?
Issue with running command
I am trying to run the executable following the example:
./cas-offinder.exe input_010.txt G output_010.txt
The code seems to be working as it should, the output in the terminal displays the chunk number, the loading the reading and the sending of the information to the device. However, as soon as I run the command, the output_010.txt files deletes (i can see it being deleted from my directory), and thus there is no output file. What could be causing this? How can I access the output?
Missing off-targets
I have encountered several instances where cas-offinder misses an off-target. I get the same result with macOS 10.13 and Ubuntu 18.04. I show one such example below. Can you please advise if I'm doing something wrong with my input file or something else? Using version Cas-OFFinder v2.4 (Jul 1 2018)
My source of hg19;
wget http://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/chromFa.tar.gz
Here is my input file;
/var/chromosome/human_hg19
NNNNNNNNNNNNNNNNNNNNNNNN
GCTCGGGCTGTTTGCTGTTGGCTG 1
and output file;
GCTCGGGCTGTTTGCTGTTGGCTG chr2 191829773 GCTCGGGCTGTTTGCTGTTGGCTG + 0
However, BLAT and other off-target software will find an off-target in chr7 (BLAT output shown below);
browser details YourSeq 24 1 24 24 100.0% chr2 + 191829774 191829797 24
browser details YourSeq 20 1 22 24 95.5% chr7 + 128327881 128327902 22
"skipping non acceptable file" issue
I keep running into a problem in which every time I try to run the script it skips over the executable, then the input, and then the output files, giving the message "skipping non acceptable file". I've tried it on multiple machines and get the same result each time
[Cas-Offinder-Bulge] IOError: [Errno 2] No such file or directory line 103
Running Cas-Offinder-Bulge returns an error on line 103.
Total 1 device(s) found.
Loading input file...
1.05135 seconds elapsed.
Processing output file...
Traceback (most recent call last):
File "/home/jake/cas-offinder/cas-offinder-bulge", line 154, in <module>
main()
File "/home/jake/cas-offinder/cas-offinder-bulge", line 103, in main
with open(outfn) as fi, open(argv[3], 'w+') as fo:
IOError: [Errno 2] No such file or directory: '/tmp/tmpQyCBJt_bulgeout.txt'
Fixed by updating line 103:
with open(outfn, 'w+') as fi, open(argv[3], 'w+') as fo:
Problem with running binary or compiling cas-offinder with Linux Catalyst on Ubuntu 14.04
Hello, Sorry to email this in as an issue but I am having some issues getting cas-offinder running on my system.
When I try the binary I get the message:
hari@hjubuntu:~/cas-offinder$ ./cas-offinder
clGetPlatformIDs Failed: -1001
When I tried compiling I get the message:
cmake -DOPENCL_INCLUDE_DIRS=/opt/AMDAPPSDK-3.0/include -DOPENCL_LIBRARIES=/opt/AMDAPPSDK-3.0/lib/x86_64/libOpenCL.so .
hari@hjubuntu:~/cas-offinder$ make
Scanning dependencies of target cas-offinder
[ 25%] Building CXX object CMakeFiles/cas-offinder.dir/main.cpp.o
[ 50%] Building CXX object CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o
In file included from /home/hari/cas-offinder/cas-offinder.cpp:4:0:
/home/hari/cas-offinder/oclfunctions.h: In function ‘_cl_command_queue* oclCreateCommandQueue(cl_context, cl_device_id, cl_command_queue_properties)’:
/home/hari/cas-offinder/oclfunctions.h:131:35: warning: ‘_cl_command_queue* clCreateCommandQueue(cl_context, cl_device_id, cl_command_queue_properties, cl_int*)’ is deprecated (declared at /opt/AMDAPPSDK-3.0/include/CL/cl.h:1359) [-Wdeprecated-declarations]
cl_command_queue command_queue = clCreateCommandQueue(context, device, properties, &err);
^
/home/hari/cas-offinder/oclfunctions.h:131:89: warning: ‘_cl_command_queue* clCreateCommandQueue(cl_context, cl_device_id, cl_command_queue_properties, cl_int*)’ is deprecated (declared at /opt/AMDAPPSDK-3.0/include/CL/cl.h:1359) [-Wdeprecated-declarations]
cl_command_queue command_queue = clCreateCommandQueue(context, device, properties, &err);
^
[ 75%] Building CXX object CMakeFiles/cas-offinder.dir/read_fasta.cpp.o
[100%] Building CXX object CMakeFiles/cas-offinder.dir/read_twobit.cpp.o
Linking CXX executable cas-offinder
CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o: In function `oclCreateBuffer(_cl_context*, unsigned long, unsigned long, void*)':
cas-offinder.cpp:(.text+0x9): undefined reference to `clCreateBuffer'
CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o: In function `oclGetPlatformIDs(unsigned int, _cl_platform_id**, unsigned int*)':
cas-offinder.cpp:(.text+0x42): undefined reference to `clGetPlatformIDs'
CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o: In function `oclGetDeviceIDs(_cl_platform_id*, unsigned long, unsigned int, _cl_device_id**, unsigned int*)':
cas-offinder.cpp:(.text+0x82): undefined reference to `clGetDeviceIDs'
CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o: In function `oclCreateContext(long*, unsigned int, _cl_device_id* const*, void (*)(char const*, void const*, unsigned long, void*), void*)':
cas-offinder.cpp:(.text+0xc9): undefined reference to `clCreateContext'
CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o: In function `oclCreateProgramWithSource(_cl_context*, unsigned int, char const**, unsigned long const*)':
cas-offinder.cpp:(.text+0x109): undefined reference to `clCreateProgramWithSource'
CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o: In function `oclBuildProgram(_cl_program*, unsigned int, _cl_device_id* const*, char const*, void (*)(_cl_program*, void*), void*)':
cas-offinder.cpp:(.text+0x157): undefined reference to `clBuildProgram'
cas-offinder.cpp:(.text+0x1c0): undefined reference to `clGetProgramBuildInfo'
cas-offinder.cpp:(.text+0x1ea): undefined reference to `clGetProgramBuildInfo'
CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o: In function `oclCreateKernel(_cl_program*, char const*)':
cas-offinder.cpp:(.text+0x229): undefined reference to `clCreateKernel'
CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o: In function `oclCreateCommandQueue(_cl_context*, _cl_device_id*, unsigned long)':
cas-offinder.cpp:(.text+0x269): undefined reference to `clCreateCommandQueue'
CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o: In function `oclGetDeviceInfo(_cl_device_id*, unsigned int, unsigned long, void*, unsigned long*)':
cas-offinder.cpp:(.text+0x2a2): undefined reference to `clGetDeviceInfo'
CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o: In function `oclReleaseKernel(_cl_kernel*)':
cas-offinder.cpp:(.text+0x2e7): undefined reference to `clReleaseKernel'
CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o: In function `oclReleaseCommandQueue(_cl_command_queue*)':
cas-offinder.cpp:(.text+0x327): undefined reference to `clReleaseCommandQueue'
CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o: In function `oclReleaseContext(_cl_context*)':
cas-offinder.cpp:(.text+0x367): undefined reference to `clReleaseContext'
CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o: In function `oclEnqueueWriteBuffer(_cl_command_queue*, _cl_mem*, unsigned int, unsigned long, unsigned long, void const*, unsigned int, _cl_event* const*, _cl_event**)':
cas-offinder.cpp:(.text+0x3c1): undefined reference to `clEnqueueWriteBuffer'
CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o: In function `oclFinish(_cl_command_queue*)':
cas-offinder.cpp:(.text+0x402): undefined reference to `clFinish'
CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o: In function `oclSetKernelArg(_cl_kernel*, unsigned int, unsigned long, void const*)':
cas-offinder.cpp:(.text+0x442): undefined reference to `clSetKernelArg'
CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o: In function `oclEnqueueNDRangeKernel(_cl_command_queue*, _cl_kernel*, unsigned int, unsigned long const*, unsigned long const*, unsigned long const*, unsigned int, _cl_event* const*, _cl_event**)':
cas-offinder.cpp:(.text+0x4a1): undefined reference to `clEnqueueNDRangeKernel'
CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o: In function `oclEnqueueReadBuffer(_cl_command_queue*, _cl_mem*, unsigned int, unsigned long, unsigned long, void*, unsigned int, _cl_event* const*, _cl_event**)':
cas-offinder.cpp:(.text+0x501): undefined reference to `clEnqueueReadBuffer'
CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o: In function `clearbufvec(std::vector<_cl_mem*, std::allocator<_cl_mem*> >*)':
cas-offinder.cpp:(.text+0x572): undefined reference to `clReleaseMemObject'
CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o: In function `Cas_OFFinder::releaseLociinfo()':
cas-offinder.cpp:(.text+0x852): undefined reference to `clReleaseMemObject'
cas-offinder.cpp:(.text+0x8ca): undefined reference to `clReleaseMemObject'
cas-offinder.cpp:(.text+0x932): undefined reference to `clReleaseMemObject'
CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o: In function `Cas_OFFinder::compareAll(char const*)':
cas-offinder.cpp:(.text+0xe8d): undefined reference to `clEnqueueWriteBuffer'
cas-offinder.cpp:(.text+0xeda): undefined reference to `clEnqueueWriteBuffer'
cas-offinder.cpp:(.text+0xf25): undefined reference to `clEnqueueWriteBuffer'
cas-offinder.cpp:(.text+0xf3a): undefined reference to `clFinish'
cas-offinder.cpp:(.text+0xf66): undefined reference to `clSetKernelArg'
cas-offinder.cpp:(.text+0xfc4): undefined reference to `clEnqueueNDRangeKernel'
cas-offinder.cpp:(.text+0x1172): undefined reference to `clFinish'
cas-offinder.cpp:(.text+0x11c3): undefined reference to `clEnqueueReadBuffer'
cas-offinder.cpp:(.text+0x122a): undefined reference to `clEnqueueReadBuffer'
cas-offinder.cpp:(.text+0x127d): undefined reference to `clEnqueueReadBuffer'
cas-offinder.cpp:(.text+0x12d4): undefined reference to `clEnqueueReadBuffer'
cas-offinder.cpp:(.text+0x12ec): undefined reference to `clFinish'
CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o: In function `Cas_OFFinder::init_platforms()':
cas-offinder.cpp:(.text+0x19d1): undefined reference to `clGetPlatformIDs'
CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o: In function `Cas_OFFinder::print_usage()':
cas-offinder.cpp:(.text+0x1fb4): undefined reference to `clGetDeviceIDs'
cas-offinder.cpp:(.text+0x2021): undefined reference to `clGetDeviceInfo'
cas-offinder.cpp:(.text+0x20fb): undefined reference to `clGetDeviceIDs'
cas-offinder.cpp:(.text+0x2169): undefined reference to `clGetDeviceInfo'
cas-offinder.cpp:(.text+0x2241): undefined reference to `clGetDeviceIDs'
cas-offinder.cpp:(.text+0x22b1): undefined reference to `clGetDeviceInfo'
CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o: In function `Cas_OFFinder::~Cas_OFFinder()':
cas-offinder.cpp:(.text+0x25fa): undefined reference to `clReleaseKernel'
cas-offinder.cpp:(.text+0x265a): undefined reference to `clReleaseKernel'
cas-offinder.cpp:(.text+0x26b1): undefined reference to `clReleaseCommandQueue'
cas-offinder.cpp:(.text+0x26ce): undefined reference to `clReleaseContext'
cas-offinder.cpp:(.text+0x271a): undefined reference to `clReleaseMemObject'
cas-offinder.cpp:(.text+0x2782): undefined reference to `clReleaseMemObject'
cas-offinder.cpp:(.text+0x27ea): undefined reference to `clReleaseMemObject'
cas-offinder.cpp:(.text+0x2852): undefined reference to `clReleaseMemObject'
cas-offinder.cpp:(.text+0x28ba): undefined reference to `clReleaseMemObject'
CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o: In function `Cas_OFFinder::initOpenCL()':
cas-offinder.cpp:(.text+0x327d): undefined reference to `clGetDeviceIDs'
cas-offinder.cpp:(.text+0x32f1): undefined reference to `clCreateKernel'
cas-offinder.cpp:(.text+0x3346): undefined reference to `clCreateKernel'
cas-offinder.cpp:(.text+0x33aa): undefined reference to `clCreateCommandQueue'
cas-offinder.cpp:(.text+0x3428): undefined reference to `clGetDeviceInfo'
cas-offinder.cpp:(.text+0x3468): undefined reference to `clCreateContext'
cas-offinder.cpp:(.text+0x34c2): undefined reference to `clCreateProgramWithSource'
cas-offinder.cpp:(.text+0x34ec): undefined reference to `clBuildProgram'
cas-offinder.cpp:(.text+0x3510): undefined reference to `clCreateKernel'
cas-offinder.cpp:(.text+0x37be): undefined reference to `clGetProgramBuildInfo'
cas-offinder.cpp:(.text+0x37e9): undefined reference to `clGetProgramBuildInfo'
CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o: In function `Cas_OFFinder::setChrData()':
cas-offinder.cpp:(.text+0x3f0a): undefined reference to `clReleaseMemObject'
cas-offinder.cpp:(.text+0x3f7a): undefined reference to `clReleaseMemObject'
cas-offinder.cpp:(.text+0x3fea): undefined reference to `clReleaseMemObject'
cas-offinder.cpp:(.text+0x408d): undefined reference to `clCreateBuffer'
cas-offinder.cpp:(.text+0x40f8): undefined reference to `clCreateBuffer'
cas-offinder.cpp:(.text+0x415c): undefined reference to `clSetKernelArg'
cas-offinder.cpp:(.text+0x418a): undefined reference to `clSetKernelArg'
cas-offinder.cpp:(.text+0x41b8): undefined reference to `clSetKernelArg'
cas-offinder.cpp:(.text+0x41e3): undefined reference to `clSetKernelArg'
cas-offinder.cpp:(.text+0x4211): undefined reference to `clSetKernelArg'
CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o:cas-offinder.cpp:(.text+0x423f): more undefined references to `clSetKernelArg' follow
CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o: In function `Cas_OFFinder::setChrData()':
cas-offinder.cpp:(.text+0x4311): undefined reference to `clCreateBuffer'
CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o: In function `Cas_OFFinder::loadNextChunk()':
cas-offinder.cpp:(.text+0x45db): undefined reference to `clEnqueueWriteBuffer'
cas-offinder.cpp:(.text+0x468e): undefined reference to `clEnqueueWriteBuffer'
CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o: In function `Cas_OFFinder::findPattern()':
cas-offinder.cpp:(.text+0x4851): undefined reference to `clEnqueueWriteBuffer'
cas-offinder.cpp:(.text+0x489c): undefined reference to `clEnqueueNDRangeKernel'
cas-offinder.cpp:(.text+0x498f): undefined reference to `clEnqueueReadBuffer'
cas-offinder.cpp:(.text+0x4ab0): undefined reference to `clCreateBuffer'
cas-offinder.cpp:(.text+0x4b1b): undefined reference to `clCreateBuffer'
cas-offinder.cpp:(.text+0x4b85): undefined reference to `clCreateBuffer'
cas-offinder.cpp:(.text+0x4bec): undefined reference to `clSetKernelArg'
cas-offinder.cpp:(.text+0x4c1a): undefined reference to `clSetKernelArg'
cas-offinder.cpp:(.text+0x4c48): undefined reference to `clSetKernelArg'
cas-offinder.cpp:(.text+0x4c7a): undefined reference to `clFinish'
cas-offinder.cpp:(.text+0x4cfd): undefined reference to `clEnqueueReadBuffer'
CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o: In function `Cas_OFFinder::readInputFile(char const*)':
cas-offinder.cpp:(.text+0x6214): undefined reference to `clCreateBuffer'
cas-offinder.cpp:(.text+0x62a0): undefined reference to `clEnqueueWriteBuffer'
cas-offinder.cpp:(.text+0x62f0): undefined reference to `clEnqueueWriteBuffer'
cas-offinder.cpp:(.text+0x631d): undefined reference to `clCreateBuffer'
cas-offinder.cpp:(.text+0x638b): undefined reference to `clCreateBuffer'
cas-offinder.cpp:(.text+0x63f7): undefined reference to `clCreateBuffer'
cas-offinder.cpp:(.text+0x6482): undefined reference to `clEnqueueWriteBuffer'
cas-offinder.cpp:(.text+0x649a): undefined reference to `clFinish'
cas-offinder.cpp:(.text+0x64c9): undefined reference to `clSetKernelArg'
cas-offinder.cpp:(.text+0x64f8): undefined reference to `clSetKernelArg'
cas-offinder.cpp:(.text+0x6527): undefined reference to `clSetKernelArg'
cas-offinder.cpp:(.text+0x6556): undefined reference to `clSetKernelArg'
cas-offinder.cpp:(.text+0x6585): undefined reference to `clSetKernelArg'
CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o:cas-offinder.cpp:(.text+0x65b4): more undefined references to `clSetKernelArg' follow
CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o: In function `Cas_OFFinder::readInputFile(char const*)':
cas-offinder.cpp:(.text+0x670b): undefined reference to `clCreateBuffer'
collect2: error: ld returned 1 exit status
make[2]: *** [cas-offinder] Error 1
make[1]: *** [CMakeFiles/cas-offinder.dir/all] Error 2
make: *** [all] Error 2
I have tried to add the include library to my LD_LIBRARY_PATH but still dont get it to compile. Please can you help with with what may be a specific issue with the way my GPU drivers are setup. I am running Catalyst on Ubuntu 14.04 with AMD Radeon dual HD 7870.
hari@hjubuntu:~/cas-offinder$ fglrxinfo
display: :0 screen: 0
OpenGL vendor string: Advanced Micro Devices, Inc.
OpenGL renderer string: AMD Radeon HD 7800 Series
OpenGL version string: 4.5.13399 Compatibility Profile Context 15.201.1151
ii fglrx-updates 2:15.201-0ubuntu0.14.04.1 amd64 Video driver for the AMD graphics accelerators
ii fglrx-updates-core 2:15.201-0ubuntu0.14.04.1 amd64 Minimal video driver for the AMD graphics accelerators
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