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sdparekh / zUMIs

zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs
GNU General Public License v3.0
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EXITING because of fatal error: buffer size for SJ output is too small Solution: increase input parameter --limitOutSJcollapsed #314

Closed parichitran closed 2 years ago

parichitran commented 2 years ago

Dear christop, Its me here again,Sorry to ask you again and again .Already you helped me a lot to get upto this level.Everything is fine even filteration step it passed successfully for my data. But I got the above mentioned error in the mapping step.

1.Yaml file and terminal output for above error: yamlfileandoutputwithSJbuffer.txt

2.So I increased that to 2000000000 (default=1000000).Now this time no errors regarding SJ output.But mapping is not happening at all and same downstream errors same as before.

yaml file and it output with --limit out Collapsed parameter to 2000000000: yamlfileandoutput.txt

3.So after this i divided my 2684 cells into 5 sets each having 500 cells.And ran zUMIs it ran well for set1(1-500cells),2(501-1000cells).Again set 3,set4 shows the above error

Update: I further divided subsampled cells and ran with single pass mode.All ran successfully.Nothing worked for me in --limit out Collapsed parameter changes as suggessted in STAR issues.If anyone find anyother work around ,pls let me knew it.But here this is the work around i had done.

Thanks in advance