perl: symbol lookup error:
-bash-4.1$ perl /group/bioinfo/apps/apps/diffReps-1.55.4/bin/diffReps.pl
perl: symbol lookup error: /home/xie186/perl5/lib/perl5/x86_64-linux-thread-multi/auto/ Math/CDF/CDF.so: undefined symbol: Perl_Gthr_key_ptr
I checked the perl version.
$ perl -v
This is perl 5, version 20, subversion 1 (v5.20.1) built for x86_64-linux-thread-multi
Copyright 1987-2014, Larry Wall
Perl may be copied only under the terms of either the Artistic License or the
GNU General Public License, which may be found in the Perl 5 source kit.
Complete documentation for Perl, including FAQ lists, should be found on
this system using "man perl" or "perldoc perl". If you have access to the
Internet, point your browser at http://www.perl.org/, the Perl Home Page.
-bash-4.1$ /usr/bin/perl -v
This is perl, v5.10.1 (*) built for x86_64-linux-thread-multi
Copyright 1987-2009, Larry Wall
Perl may be copied only under the terms of either the Artistic License or the
GNU General Public License, which may be found in the Perl 5 source kit.
Complete documentation for Perl, including FAQ lists, should be found on
this system using "man perl" or "perldoc perl". If you have access to the
Internet, point your browser at http://www.perl.org/, the Perl Home Page.
$ /usr/bin/perl /group/bioinfo/apps/apps/diffReps-1.55.4/bin/diffReps.pl
diffReps - Detect Differential Sites from ChIP-seq with Biological Replicates.
Usage: diffReps.pl --treatment bed_file1...[bed_fileN] --control bed_file1...[bed_fileN] --report output_results \
[--gname genome_name|--chrlen chrom_length_file]
**Chromosome lengths can be specified through a text file or given a genome name.
**Currently built-in genomes: mm9, hg19, rn4.
Optional parameters(defaults in parentheses):
- Background samples(DNA input or IgG control):
--btr Treatment group background: bed_file1...[bed_fileN].
--bco Control group background: bed_file1...[bed_fileN].
Hint: If background is only specified for one group, it will automatically be used for both groups.
- Genomic region parameters:
--mode(peak) Scanning mode: a selection implies a different window size.
Set window and step size manually to override.
(p)eak (=1000) Histone mark peak (Default).
(n)ucleosome(=200) Single nucleosome (+DNAlinker).
(b)lock (=10000) Large chromatin modification block.
--window(1000) Window size (default=Histone mark peak size).
--step(1/10 win) Window moving step size.
--gap(0) Gap allowed between two consecutive windows.
- Background filtering using: mean + nsd*deviation.
--std Use standard estimation of mean and deviation (Default=Robust estimation).
In robust estimation, median absolute deviation is used in place of standard deviation.
--nsd(broad) Z-score cutoff for low read count. Choose from two default modes or set your own.
(b)road (=2) Broad peak such as H3K36me3.
(s)harp (=20) Sharp peak such as H3K4me3 or Transcription factors.
--alpha(0.05) Alpha for right-trimmed mean, must be in: [0, 0.5).
--bkg(0) Use fold enrichment vs. background as filter instead. Set a float number such as 2.0 here.
Default is to use the Z-score as filter.
- Statistical testing parameters:
--meth(nb) Statistical test (nb=Negative binomial; gt=G-test; tt=T-test; cs=Chi-square test).
--pval(0.0001) P-value cutoff for significant windows.
- Normalization can be done externally and be supplied as a text file:
--nrpass(1) Do normalization on bins pass nsd cutoff?
--norm File name to specify pre-determined norm constants (Default=Estimate by diffReps).
- Misc. parameters:
--frag(100) ChIP-seq library fragment size. Use to shift read positions.
--nproc(1) Number of processors to use.
--noanno Switch off genomic annotation for differential sites (Default=Do annotation).
--nohs Switch off looking for chromatin modification hotspots (Default=Find hotspots).
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