error occurred when running JUM_B.sh

[mhjiang97]

Hi, I got errors when running JUM_B.sh

what I ran:

cd ~/projects/AS/analysis/paper_gb/
sim_1//JUM/JUM_diff/ && bash ~/bin/JUM-JUMv2.0.2_short_user_argument_BSD//JUM_B.sh --Folder ~/bin/JUM-JUMv2.0.2_short
_user_argument_BSD/ --Test adjusted_pvalue --Cutoff 0.05 --TotalFileNum 8 --Condition1_fileNum_threshold 3 --Conditio
n2_fileNum_threshold 3 --Condition1SampleName s1 --Condition2SampleName s2

the error:

ERROR: Sort order was unspecified, and file sample7Aligned.out_coverage_sorted.bed 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 sample8Aligned.out_coverage_sorted.bed 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 sample5Aligned.out_coverage_sorted.bed 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 sample6Aligned.out_coverage_sorted.bed 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 sample3Aligned.out_coverage_sorted.bed 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 sample1Aligned.out_coverage_sorted.bed 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 sample2Aligned.out_coverage_sorted.bed 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 sample4Aligned.out_coverage_sorted.bed 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 sample7Aligned.out_coverage_sorted.bed 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 sample8Aligned.out_coverage_sorted.bed 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 sample5Aligned.out_coverage_sorted.bed 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 sample6Aligned.out_coverage_sorted.bed 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 sample3Aligned.out_coverage_sorted.bed 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 sample1Aligned.out_coverage_sorted.bed 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 sample2Aligned.out_coverage_sorted.bed 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 sample4Aligned.out_coverage_sorted.bed is not sorted lexicographically.
       Please rerun with the -g option for a genome file.
       See documentation for details.
...

The previous steps ran successfully. How can I fix this problem? Thank you very much.

[qqwang-berkeley]

Did you sort your input bam files accordingly to the manual?

Convert and sort the resulted alignment files (please use the exact naming nomenclature as shown below). Here we show ctrl 1 sample as an example but users need to do this for all the samples:
$ samtools view -bS ctrl1Aligned.out.sam > ctrl1Aligned.out.bam
$ samtools sort -o ctrl1Aligned.out_sorted.bam -T ctrl1_temp ctrl1Aligned.out.bam
$ samtools index ctrl1Aligned.out_sorted.bam
$ rm *Aligned.out.bam