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Error in converting sai to sam #25

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ErikaAndrade opened this issue Oct 29, 2019 · 0 comments
Open

Error in converting sai to sam #25

ErikaAndrade opened this issue Oct 29, 2019 · 0 comments

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@ErikaAndrade
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Hello,
First, thank you for developing this very useful tool. I have been trying to use the UI and keep getting stuck at sai to sam conversion. I get the following error:

[E::bwa_set_rg] the read group line contained literal characters -- replace with escaped tabs: \t
*** ERROR: convert sai to sam failed!!! ***
*** ERROR: RnaEditor Failed ***

When I try using bwa independently using the same commands, it seems to work just fine.

Version info:
Program: bwa (alignment via Burrows-Wheeler transformation)
Version: 0.7.17-r1188

java version "1.7.0_80"
Java(TM) SE Runtime Environment (build 1.7.0_80-b15)
Java HotSpot(TM) 64-Bit Server VM (build 24.80-b11, mixed mode)

Python 2.7.15 |Anaconda, Inc.| (default, Dec 14 2018, 13:10:39)
[GCC 4.2.1 Compatible Clang 4.0.1 (tags/RELEASE_401/final)]

Also, when i try dropping a sorted bam using the same commands used by RNAeditor, I get the following error:

ERROR: Bam File was not mapped with RnaEditor, this is not supported. Please provide the fastq Files to RnaEditor ***
*** ERROR: RnaEditor Failed ***

Anything else I should try?

Thank you.
Erika

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