problem in combined_depletion_coverage.pl

[e-lerat]

hi,
I have installed TIDAL and I am trying to use it on our cluster.
I currently have an error message but I cannot figure out what is wrong. In the nohup.out, I have thousand of the following lines

Argument "AAAAACCCAACAGCCAAGAGCCAAAACCGAGCGAGCCAAATCCGCTTTTGTCCAAT..." isn't numeric in sort at /usr/remote/TIDAL/CODE/combined_depletion_coverage.pl line 62.
Argument "CCTTCCCCGTCAAGAAACTGCATTGTTGCTTCTTGAAGACCAGTTTTGGTAACATC..." isn't numeric in sort at /usr/remote/TIDAL/CODE/combined_depletion_coverage.pl line 62.
etc.

The input files seem ok but maybe they are not? Here is an example:

the 5prime_refgene_count.xls is like that:

chr2R 1097 1248 ATTTTGACCGCTTAAAATGACATAACTTAGTCAATTTATTGTTTTTGTGTACCAGGTTTAAATAATCTTTAGAAGGTATCTTCTGTTTGTCTGGTACTTGAAATCGAAAAATCACCCATTTTGACCGATTAAAATGTTAAACT
TAGGCAAT:1 21 - 1097 1248 0,0,0 1 151, 0, 0 0 151 0.0000000
chr2R 1493 1616 GAAATCGGAAATTCACCCATTTGACCGCTTAAAATGACATAACTTAGTCAATTTATTGTTTTTGTGTACCAGGATTAAATAATCTGTAGAAGGTATCTTCTGTTTGTCTGGTTCTTGAAATC:1 14 - 1493 1616 0,0,0 1 123, 0, 0 0 123 0.0000000
etc.

the 3prime_refgene_count.xls looks like that also.

If it may be useful, I put the nohup.out as an attachment

If you have any idea what is the problem, that would be great because I am stuck on this since several days!
thank you in advance !
Emmanuelle
nohup.out.tar.gz

[laulabbrandeis]

I believe this error is due to using the latest version of bedtools. Please try using: bedtools suite (v. 2.17.0)

If you still encounter more problems, please let me know. Sorry for the delayed response.