Error while running rnaseq_pipeline.sh provided by hisat2

Question

[bioinfo8]

Hi,

I am planning to run hisat2 on my multiple paired-end samples (>20). Hence, I tried to do the test run as per ftp://ccb.jhu.edu/pub/RNAseq_protocol/ and ran ./rnaseq_pipeline.sh out after editing rnaseq_pipeline.config.sh. I am getting the following error:

[2017-10-10 11:00:44] #> START:  ./rnaseq_pipeline.sh out
[2017-10-10 11:00:44] Processing sample: /chrX_data/samples/ERR188044_chrX
[2017-10-10 11:00:44]    * Alignment of reads to genome (HISAT2)
./rnaseq_pipeline.sh: line 92: ./hisat2//chrX_data/samples/ERR188044_chrX.alnstats: No such file or directory

I am unable to resolve why there is // coming up in the last line.

Please guide.

Thanks.

[Russ]

Check the contents of your script, it looks like the path to your samples is incorrect. Try removing the leading / from the samples - this is why the sample file cannot be found, and also why the double // is coming up in the last line.

[bioinfo8]

@russhh : Path to the samples is correct, that is why script is showing first three lines. Issue is with last line. :(

@Russ I tried, but same error:

./rnaseq_pipeline.sh: line 92: ./hisat2/chrX_data/samples/ERR188044_chrX.alnstats: No such file or directory

hisat2 is already in the PATH and should do mapping to generate ERR188044_chrX.alnstats under chrX_data/samples.

[Russ]

Are you calling the script from the appropriate directory?

[bioinfo8]

@Russ: Yes.

[Russ]

I downloaded the files and tested them on my machine; the scripts ran without issue. There must be something in the way your files are organised, or in the edits you made to rnaseq_pipeline.config.sh. Perhaps you can try starting fresh by downloading everything into a new directory and maintaining the directory structure given at the FTP site.

[bioinfo8]

Ok, I will do that again. Thank you.

[russhh]

Does the file exist?

[bioinfo8]

It should but its not. I feel something is wrong inside rnaseq_pipeline.sh

[russhh]

If the example file doesn't exist, obtain it from the hisat2 website, then try running it again. I don't see why the shell script should be considered to be faulty yet: please check that ./hisat2/chrX_data/samples exists (relative to your current working directory) and that ERR188044_chrX.alnstats is present in that folder.

Answer 1

[Karma]

Try running

bin/bash path/to/rnaseq_pipeline.sh

or

sh rnaseq_pipeline.sh

[bioinfo8]

@Snijesh: Did not work. :(