Filterbytile.sh - Exception in thread "main" java.lang.RuntimeException: Can't read file ...

Question

[duplessisantzel]

Hello there.

I am doing my research project and this is the first time I am working with RNA sequenced data. I ran my FastQC and now I want to run filterbytile.sh to refine my data, but it being my first time doing this type of computer work, I don't know what to do with the following:

filterbytile.sh in=Resc5815_rep1.2.fastq.gz out=filtered_resc5815_rep1.2.fq.gz

java -ea -Xmx753m -Xms753m -cp /usr/local/bin/current/ hiseq.AnalyzeFlowCell in=Resc5815_rep1.2.fastq.gz out=filtered_resc5815_rep1.2.fq.gz

Executing hiseq.AnalyzeFlowCell [in=Resc5815_rep1.2.fastq.gz, out=filtered_resc5815_rep1.2.fq.gz]

Exception in thread "main" java.lang.RuntimeException: Can't read file 'Resc5815_rep1.2.fastq.gz'
at shared.Tools.testInputFiles(Tools.java:188)
at hiseq.AnalyzeFlowCell.checkFileExistence(AnalyzeFlowCell.java:261)
at hiseq.AnalyzeFlowCell.checkFiles(AnalyzeFlowCell.java:228)
at hiseq.AnalyzeFlowCell.<init>(AnalyzeFlowCell.java:108)
at hiseq.AnalyzeFlowCell.main(AnalyzeFlowCell.java:51)

I don't know what this means, I did read the guide on the filterbytile.sh command and it does accept fastqc files but it seems like it can't, or am I reading this message wrong. Please can I ask for some assistance, I am a self-learner in Bioinformatics so I don't have a lot of background. Thank you.

[GenoMax]

Can't read file 'Resc5815_rep1.2.fastq.gz'

It means the file is not present in directory where you are running this command from. You could try providing full path the file.

[duplessisantzel]

HI. Thank you very much for clarifying. How would it look if I add the full path? Can you please give an example.

[GenoMax]

If the file is in /user/you/fastq/Resc5815_rep1.2.fastq.gz, then you will use this full string as in=/user/you/fastq/Resc5815_rep1.2.fastq.gz.

If you are new to command line/UNIX it would help if you spend a few hours getting familiar with UNIX. Use: http://korflab.ucdavis.edu/Unix_and_Perl/current.html#part1