Error while running rnaseq_pipeline.sh provided by hisat2
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.
1 answer
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Does the file exist?
It should but its not. I feel something is wrong inside
rnaseq_pipeline.shIf 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.
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.@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:
hisat2is already in the PATH and should do mapping to generate ERR188044_chrX.alnstats under chrX_data/samples.Are you calling the script from the appropriate directory?
@Russ: Yes.
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.Ok, I will do that again. Thank you.