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4ureliek / TEanalysis

Analysis of TE contribution to features (transcripts or simple features). Includes utils to test enrichment.
MIT License
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TE-analysis_Shuffle_bed.pl_V4.4 error #2

Closed wolfQK closed 6 years ago

wolfQK commented 6 years ago

Hi Aurelie, I am playing with TE-analysis_Shuffle_bed.pl to test enrichment of TE in ATACseq peaks. The script reports errors"Invalid version format (non-numeric data) at /zfssz2/Perl/lib/perl5/site_perl/5.26.1/Statistics/R.pm line 369.". Can you take a look and help me with this problem? Thank you very much! My command is the following: perl /zfssz2/script/TEanalysis-master/TE-analysis_Shuffle_bed.pl -q /zfssz2/mydata/TE_hg38_class/5_s.bed -f /zfssz2/mydata/Neural_ATAC_hg38/t-iPS129.EB.68.stage.bed -s bed
-r /zfssz2/mydata/hg38.chrom.sizes -e /zfssz2/mydata/gap.txt.bed
-w /zfssz2/software/bedtools2/bedtools2/bin/ -o 1 -n 100 Besides,the two bed files are both 3 columns(chr start end).

4ureliek commented 6 years ago

Hi, This is an error in the R module itself; you should have in the error message the line where the R module is called in my code, that would be very helpful (I need to know why something non numerical was passed to the R module). Even better for me to debug is if you share with me small files that reproduce the error! Cheers, Aurelie

4ureliek commented 6 years ago

I just tried a test run with a fake input file being a bunch of mouse mm10 TEs, and got no errors - so I definitely need sample files to be able to help you out! Quick question though, is this file: /zfssz2/mydata/TE_hg38_class/5_s.bed a repeat masker output file? Even if in bed format, the code is written to parse repeat masker output info, so if not that could be the source of the issue.

wolfQK commented 6 years ago

Hi Aurelie, Thank you for your prompt reply. There is no flaw in your code, I use the wrong type of file, which is a subset of repeat masker output file. And my problem has been solved. Thank you!