Question: Error while running rnaseq_pipeline.sh provided by hisat2
0
gravatar for bioinfo8
10 months ago by
bioinfo890
bioinfo890 wrote:

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.

ADD COMMENTlink modified 10 months ago • written 10 months ago by bioinfo890
1

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.

ADD REPLYlink written 10 months ago by Russ310

@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.

ADD REPLYlink modified 10 months ago • written 10 months ago by bioinfo890
1

Are you calling the script from the appropriate directory?

ADD REPLYlink written 10 months ago by Russ310

@Russ: Yes.

ADD REPLYlink written 10 months ago by bioinfo890
1

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.

ADD REPLYlink written 10 months ago by Russ310

Ok, I will do that again. Thank you.

ADD REPLYlink written 10 months ago by bioinfo890

Does the file exist?

ADD REPLYlink written 10 months ago by russhh3.6k

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

ADD REPLYlink modified 10 months ago • written 10 months ago by bioinfo890
1

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.

ADD REPLYlink written 10 months ago by russhh3.6k
0
gravatar for Snijesh VP
10 months ago by
Snijesh VP190
India
Snijesh VP190 wrote:

Try running

bin/bash path/to/rnaseq_pipeline.sh

or

sh rnaseq_pipeline.sh
ADD COMMENTlink written 10 months ago by Snijesh VP190

@Snijesh: Did not work. :(

ADD REPLYlink written 10 months ago by bioinfo890
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