#11 Get reditools merged result, but not all scaffolds

[Liuxiang]

Dear developer：

I am sorry to disturb you, but I get something wrong when using your software, reditools to search RNA editing sites. I used PBS to submit my tasking codes. However, I get the merged result "outTable_322300956", which is just part of all scaffolds. And PBS said this task is sleeping, and not finished. I don't kown what is wrong and how to deal with it. Could you please take me some advices. I really hope your reply.

here is my codes:

python $redtoolsBin/REDItoolDnaRna.py \
-i $RNA.bam \
-j $DNA.bam \
-f $genome.scaffold.fa \
-o $cw/$i \
-C 10000000 \
-t 10 \
-c 4,4 \
-m 25,25 \
-s 2 \
-S \
-X \
-u \
-U \
-N 0.0 \
-n 0.0 \
-a 5-5 \
-l \
-L \
-r 5 \
-v 1 \
-g 1 \
-Q 33,33 \
-q 25,25 \
-O 7,7 \
-R \
-V \
-p -e -E -d -D

And there is no error reported.
In addition, some samples may get novel lines, like:
"scaffold540 2384767 A 0 4 40.00 [0, 0, 0, 4] AT 1.00 23 38.65 scaffold541 480099 C 0 9 38.56 [0, 3, 0, 6] C0.67 10 40.20 [0, 6, 0, 4] CT 0.40" , indicating something is wrong.

from liuxiang