JUM_A: ERROR: ... not sorted lexicographically

[NeuzaRM]

Hello,
Thank you so much for developing this tool.
I'm running JUM_A and finding the error bellow.
Could you please help me troubleshoot?
Please let me know if you need any more information from me.

Best wishes
Neuza

Sample names are:
ctrl_1_R01_
ctrl_2_R01_
treat_1_R01_
treat_2_R01_
2 input samples to consider under the current condition
2 input samples to consider under the current condition
Preparing for intron retention AS events analyses...
Processing junction overhangs for Sample treat_1_R01_... Success.
Processing junction overhangs for Sample ctrl_2_R01_... Success.
Processing junction overhangs for Sample ctrl_1_R01_... Success.
Processing junction overhangs for Sample treat_2_R01_... Success.
ERROR: Sort order was unspecified, and file output_long_intron_sorted.gff is not sorted lexicographically.
Please rerun with the -g option for a genome file.
See documentation for details.
ERROR: Sort order was unspecified, and file output_long_intron_sorted.gff is not sorted lexicographically.
Please rerun with the -g option for a genome file.
See documentation for details.
ERROR: Sort order was unspecified, and file output_long_intron_sorted.gff is not sorted lexicographically.
Please rerun with the -g option for a genome file.
See documentation for details.
ERROR: Sort order was unspecified, and file output_long_intron_sorted.gff is not sorted lexicographically.
Please rerun with the -g option for a genome file.
See documentation for details.
awk: fatal: cannot open file *intersect_short_intron1.txt' for reading (No such file or directory) awk: fatal: cannot open file *intersect_short_intron2.txt' for reading (No such file or directory)
can't open input1 file: No such file or directory at /labs/mtfuller/Eric/JUM_2.0.2/preparing_intron_retention_count_table_short_intron.pl line 18.

[qqwang-berkeley]

This could be due to the fact that the sorting step was not finished in the previous runs (happens sometimes due to the hardware conditions of users' computer system). Could you run JUM_A.sh again exactly the same way, but use the most updated package v3.0.0? I made a small modification there to ensure the sorting step will be finished before proceeding.