Error: Je-demultiplex. Solution: confirm inputs

1

I have been getting this error for Je-demultiplex and I don’t what to do to fix it. What is wrong?

Exception in thread "main" htsjdk.samtools.SAMException: Error opening file for writing: F_AACA_1.txt
	at htsjdk.samtools.util.IOUtil.openFileForWriting(IOUtil.java:551)
	at htsjdk.samtools.util.IOUtil.openFileForWriting(IOUtil.java:529)
	at htsjdk.samtools.fastq.BasicFastqWriter.maybeMd5Wrap(BasicFastqWriter.java:82)
	at htsjdk.samtools.fastq.BasicFastqWriter.<init>(BasicFastqWriter.java:46)
	at htsjdk.samtools.fastq.BasicFastqWriter.<init>(BasicFastqWriter.java:42)
	at org.embl.gbcs.je.jemultiplexer.JemultiplexerFastqWriterFactory.newWriter(JemultiplexerFastqWriterFactory.java:100)
	at org.embl.gbcs.je.jemultiplexer.JemultiplexerFastqWriterFactory.newWriter(JemultiplexerFastqWriterFactory.java:78)
	at org.embl.gbcs.je.jemultiplexer.JemultiplexerFastqWriterFactory.newWriter(JemultiplexerFastqWriterFactory.java:50)
	at org.embl.gbcs.je.jemultiplexer.AbstractJemultiplexer.doWork(AbstractJemultiplexer.java:953)
	at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:209)
	at picard.cmdline.CommandLineProgram.instanceMainWithExit(CommandLineProgram.java:147)
	at org.embl.gbcs.je.Je.main(Je.java:109)
Caused by: java.io.FileNotFoundException: results/FiCLIP_16_Kc/F_AACA_1.txt (No such file or directory)
	at java.io.FileOutputStream.open0(Native Method)
	at java.io.FileOutputStream.open(FileOutputStream.java:270)
	at java.io.FileOutputStream.<init>(FileOutputStream.java:213)
	at htsjdk.samtools.util.IOUtil.openFileForWriting(IOUtil.java:547)
2

Dear @biostaring,
Have you worked with Galaxy, or have you applied the tool via the terminal on your local machine?

The error indicates that it cannot find a file of yours. I assume it does not find the barcode file you have to give to the tool such that the tool can de-multiplex your file. Either the file is malformatted or you typed the wrong name.

Best wishes,
Florian

2 Likes