Giter Club home page Giter Club logo

pare's Issues

NFR analysis for randomly distributed nfr regions failed using 100,000 regions,

Hi there,

I run into an error when running PARE. RESULTS.TXT only has one line.
It is taking really long to run. ~6 hours for a 1.5G bam.
anyway to speed it up?
EDIT. I saw a p flag, but is there a way to specify how many cpus the program will use.
I am running PARE on a cluster.

Thanks for your help.

Ming

....
[main_samview] region "chrX:153237367-10020489" specifies an unknown reference name. Continue anyway.
Error: Only a single file was specified. Nothing to combine, exiting.
gzip: PARE-NFR/analysis/my.bam.All.nfr.gz: No such file or directory
PARE-NFR/analysis/myy.sorted.bam.All.nfr: No such file or directory
my.sorted.bedGraph is not case-sensitive sorted at line 29707282.  Please use "sort -k1,1 -k2,2n
(END) 


Check, if all required parameters and files are provided (Wed Feb 17 19:24:06 CST 2016).. done
Determine number of input bam files (Wed Feb 17 19:24:06 CST 2016).. done
Create directory structure (Wed Feb 17 19:24:06 CST 2016).. done
Populating files based on input genome, hg19 (Wed Feb 17 19:24:06 CST 2016).. done
Determine number of bases by which to extend the 3' end of reads (Wed Feb 17 19:24:06 CST 2016).. done
Optimize the threshold for max length and min number of reads in a block group (Wed Feb 17 19:30:19 CST 2016).. do
Create index of input BAM files (Wed Feb 17 20:02:19 CST 2016).. done
Compute size factor for each replicate (Wed Feb 17 20:02:19 CST 2016).. done
Retrieve size factors to normalize the expression of reads... done
Convert input bam file into bed (Wed Feb 17 20:02:19 CST 2016).. convert input bam file into bed
done
Check, if BED files are created properly.. (Wed Feb 17 20:28:16 CST 2016)... done
Predict nucleosome free regions (NFR) for each replicate (Wed Feb 17 20:29:23 CST 2016).. done
Determine common NFR between replicates (Wed Feb 17 23:40:07 CST 2016).. done
Check if size factor files already exist (Wed Feb 17 23:40:07 CST 2016).. done
Create file containing genomic coordinates within which to randomly shuffle the NFRs (Wed Feb 17 23:40:07 CST 2016
NFR analysis for randomly distributed nfr regions (Wed Feb 17 23:40:18 CST 2016).. (failed using 100,000 regions, 
Convert input bam to bigWig format to visualize in UCSC browser (Wed Feb 17 23:40:18 CST 2016).. All done. Bye
(END)

error /risapps/rhel6/python/2.7.6/anaconda/lib/libreadline.so.6: undefined symbol: PC

Hi,
I got an error when running it on our HPC cluster. what's wrong?

Thanks

/risapps/rhel6/R/3.1.0/lib64/R/bin/exec/R: symbol lookup error: /risapps/rhel6/python/2.7.6/anaconda/lib/libreadline.so.6: undefined symbol: PC
/scratch/genomic_med/mtang1/softwares/spundhir-PARE-63c74f7/bin/checkPrerequisite: line 35: [: ==: unary operator expected
/risapps/rhel6/R/3.1.0/lib64/R/bin/exec/R: symbol lookup error: /risapps/rhel6/python/2.7.6/anaconda/lib/libreadline.so.6: undefined symbol: PC
/scratch/genomic_med/mtang1/softwares/spundhir-PARE-63c74f7/bin/checkPrerequisite: line 35: [: ==: unary operator expected
/risapps/rhel6/R/3.1.0/lib64/R/bin/exec/R: symbol lookup error: /risapps/rhel6/python/2.7.6/anaconda/lib/libreadline.so.6: undefined symbol: PC
/scratch/genomic_med/mtang1/softwares/spundhir-PARE-63c74f7/bin/checkPrerequisite: line 35: [: ==: unary operator expected
/risapps/rhel6/R/3.1.0/lib64/R/bin/exec/R: symbol lookup error: /risapps/rhel6/python/2.7.6/anaconda/lib/libreadline.so.6: undefined symbol: PC
/scratch/genomic_med/mtang1/softwares/spundhir-PARE-63c74f7/bin/checkPrerequisite: line 35: [: ==: unary operator expected
/risapps/rhel6/R/3.1.0/lib64/R/bin/exec/R: symbol lookup error: /risapps/rhel6/python/2.7.6/anaconda/lib/libreadline.so.6: undefined symbol: PC
/scratch/genomic_med/mtang1/softwares/spundhir-PARE-63c74f7/bin/checkPrerequisite: line 35: [: ==: unary operator expected
/risapps/rhel6/R/3.1.0/lib64/R/bin/exec/R: symbol lookup error: /risapps/rhel6/python/2.7.6/anaconda/lib/libreadline.so.6: undefined symbol: PC
/scratch/genomic_med/mtang1/softwares/spundhir-PARE-63c74f7/bin/checkPrerequisite: line 35: [: ==: unary operator expected
Can't locate Statistics/Basic.pm in @INC (@INC contains: /opt/moab/lib/perl5 /opt/moab/lib/perl5 /scratch/genomic_med/mtang1/softwares/spundhir-PARE-63c74f7/sha
BEGIN failed--compilation aborted at /scratch/genomic_med/mtang1/softwares/spundhir-PARE-63c74f7/bin/findNFRAll.pl line 24.
Can't locate Statistics/Basic.pm in @INC (@INC contains: /opt/moab/lib/perl5 /opt/moab/lib/perl5 /scratch/genomic_med/mtang1/softwares/spundhir-PARE-63c74f7/sha
BEGIN failed--compilation aborted at /scratch/genomic_med/mtang1/softwares/spundhir-PARE-63c74f7/bin/commonNFR.pl line 24.
gzip: mybam-PARE-NFR/analysis/my.bam.All.nfr.gz: No such file or directory
mybam-PARE-NFR/analysis/my.bam.All.nfr: No such file or directory
cat: mybam-PARE-NFR/analysis/rep0/my.bam.tmp*: No such file or directory
cat: mybam-PARE-NFR/analysis/rep0/my.bam.tmp*: No such file or directory
my.sorted.bedGraph is not case-sensitive sorted at line 29707282.  Please use "sort -k1,1 -k2,2n" with LC_COLLATE=C,  or bedSort and try again
my_pare.e536160 (END)

Defining which perl to use

Several of the scripts in PARE have a #!/usr/bin/perl -w at the top which can lead to a problem with defining which perl version/installation to use if multiple versions are installed.

Changing it to #!/usr/bin/env perl will allow the user to define which perl installation they would like to use based on whatever comes first in PATH.

Happy to set up a pull request.

parallel: command not found

Hi there,
I got something wrong when I use your PARE. It's ok when I use the test data that you provided for us,but there is a error when I use my data :

" Determine common NFR between replicates ~/software/spundhir-PARE-0e89a50/bin/nfrAnaAll: line 402: parallel: command not found"
~/software/spundhir-PARE-0e89a50/bin/nfrAnaAll: line 387: parallel: command not found

This is my code pare -i ENCFF001KOY.bam,ENCFF001KPA.bam -o results -m mm9 -p 10 &> pare.log
and I have tried change my data's name to pare -i h3k4me1_Rep1.bam,h3k4me1_Rep2.bam -o results -m mm9 -p 10 &> pare.log
Thanks for your help.

Gang

Recommend Projects

  • React photo React

    A declarative, efficient, and flexible JavaScript library for building user interfaces.

  • Vue.js photo Vue.js

    🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.

  • Typescript photo Typescript

    TypeScript is a superset of JavaScript that compiles to clean JavaScript output.

  • TensorFlow photo TensorFlow

    An Open Source Machine Learning Framework for Everyone

  • Django photo Django

    The Web framework for perfectionists with deadlines.

  • D3 photo D3

    Bring data to life with SVG, Canvas and HTML. 📊📈🎉

Recommend Topics

  • javascript

    JavaScript (JS) is a lightweight interpreted programming language with first-class functions.

  • web

    Some thing interesting about web. New door for the world.

  • server

    A server is a program made to process requests and deliver data to clients.

  • Machine learning

    Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.

  • Game

    Some thing interesting about game, make everyone happy.

Recommend Org

  • Facebook photo Facebook

    We are working to build community through open source technology. NB: members must have two-factor auth.

  • Microsoft photo Microsoft

    Open source projects and samples from Microsoft.

  • Google photo Google

    Google ❤️ Open Source for everyone.

  • D3 photo D3

    Data-Driven Documents codes.