search

hartleys / QoRTs

Quality of RNA-Seq Toolset
52 stars 14 forks source link

RuntimeIOException: java.io.FileNotFoundException: --stranded #61

Closed ag009 closed 6 years ago

ag009 commented 6 years ago

Hello, I have a similar question to #21. When I run the commend: java -jar ~/src/QoRTs.jar QC --stranded ~/01bam/OA1316.bam ~/output/count/oa1316

It gives me the result like this: Error info: Exception in thread "main" net.sf.samtools.util.RuntimeIOException: java.io.FileNotFoundException: --stranded (No such file or directory) at net.sf.samtools.SAMFileReader.init(SAMFileReader.java:671) at net.sf.samtools.SAMFileReader.<init>(SAMFileReader.java:184) at net.sf.samtools.SAMFileReader.<init>(SAMFileReader.java:139) at qcUtils.runAllQC$.runOnSeqFile(runAllQC.scala:1012) at qcUtils.runAllQC$.run(runAllQC.scala:960) at qcUtils.runAllQC$allQC_runner.run(runAllQC.scala:672) at runner.runner$.main(runner.scala:97) at runner.runner.main(runner.scala) Caused by: java.io.FileNotFoundException: --stranded (No such file or directory) at java.io.FileInputStream.open0(Native Method) at java.io.FileInputStream.open(FileInputStream.java:195) at java.io.FileInputStream.<init>(FileInputStream.java:138) at net.sf.samtools.SAMFileReader.init(SAMFileReader.java:638) ... 7 more

Does that because I don't provide the gtf file? In order words, gtf is necessary?

Thanks for your helping :)

ag009 commented 6 years ago

After I adding the gtf file, it work!!