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ababaian / LIONS

LIONS is a bioinformatic analysis pipeline which brings together a few pieces of software and some home-brewed scripts to annotate a paired-end RNAseq library to detect TE-intiated transcripts
GNU General Public License v3.0
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java.io.IOException #23

Closed WalterHK closed 3 years ago

WalterHK commented 3 years ago

Hello,

     Since I have multiple files need to do analysis, I separately use tophat to complete alignment first which is following by LIONS analysis. But I encountered following error after Inspecting reads and determining fragment length distribution. The code and the reference genome used for tophat alignement is following those listed in LIONS except -r = 100 since I used PE100 sequenceing. Please help taking a look what are the potential problem. Thank you.

java.io.IOException: Stream closed

at java.io.BufferedReader.ensureOpen(BufferedReader.java:122) at java.io.BufferedReader.readLine(BufferedReader.java:317) at java.io.BufferedReader.readLine(BufferedReader.java:389) at src.tools.BAM2WIG.generateWig(BAM2WIG.java:921) at src.tools.BAM2WIG.run(BAM2WIG.java:377) at src.tools.BAM2WIG.main(BAM2WIG.java:116)

My java version openjdk version "1.8.0_152-release" openJDK Runtime Enviroment (build 1.8.0_152-release-1056-b12) OpenJDK 64-Bit Server VM(build 25.152-b12, mixed mode)