Error: mapping to rRNA failed

[hemingwang]

Dear Dr.Han,

I have a problem about mapping when I used the small RNA pipeline. I follow the "install" and install the genome. But I failed in mapping and I don't know how to solve it.
Here is my code and program.

$ piPipes small -i Sample_A.fastq -g mm9 -c 24 -o output
[2016-12-30 23:56:48 CST] sort is using:
/media/heming/新加卷/seq/pirna/piPipes/bin/sort
[2016-12-30 23:56:48 CST] md5sum is using:
/usr/bin/md5sum
[2016-12-30 23:56:48 CST] awk is using:
/usr/bin/awk
[2016-12-30 23:56:48 CST] grep is using:
/bin/grep
[2016-12-30 23:56:48 CST] python is using:
/usr/bin/python
[2016-12-30 23:56:48 CST] samtools is using:
/media/heming/新加卷/seq/pirna/piPipes/bin/samtools
[2016-12-30 23:56:48 CST] gs is using:
/usr/bin/gs
[2016-12-30 23:56:48 CST] Rscript is using:
/usr/bin/Rscript
[2016-12-30 23:56:48 CST] bowtie is using:
/media/heming/新加卷/seq/pirna/piPipes/bin/bowtie
[2016-12-30 23:56:48 CST] ParaFly is using:
/media/heming/新加卷/seq/pirna/piPipes/bin/ParaFly
[2016-12-30 23:56:48 CST] bedtools_piPipes is using:
/media/heming/新加卷/seq/pirna/piPipes/bin/bedtools_piPipes
[2016-12-30 23:56:48 CST] bedGraphToBigWig is using:
/media/heming/新加卷/seq/pirna/piPipes/bin/bedGraphToBigWig
[2016-12-30 23:56:48 CST] piPipes_bed2Summary is using:
/media/heming/新加卷/seq/pirna/piPipes/bin/piPipes_bed2Summary
[2016-12-30 23:56:48 CST] piPipes_fastq_to_insert is using:
/media/heming/新加卷/seq/pirna/piPipes/bin/piPipes_fastq_to_insert
[2016-12-30 23:56:48 CST] piPipes_insertBed_to_bed2 is using:
/media/heming/新加卷/seq/pirna/piPipes/bin/piPipes_insertBed_to_bed2
[2016-12-30 23:56:48 CST] ---------------------------------------------------------------------------------
[2016-12-30 23:56:48 CST] Beginning running [piPipes] small RNA pipeline single library mode version 1.1.0
[2016-12-30 23:56:48 CST] Converting fastq format into insert format
[2016-12-30 23:56:48 CST] Mapping to rRNA, with mismatch(es) allowed
[2016-12-30 23:56:49 CST] Error: mapping to rRNA failed

Thank you,
heming

[bowhan]

When you ran install, it should ask you to input a few parameters. Seems that you have at least some of them missing. Please edit /common/mm9/variables file and fill the missing variables, and then try again. If it is not the case, please let me know! Thanks!

[dingailuma]

Hi, here is my parameters used :

export rRNA_MM=2
export hairpin_MM=2
export genome_MM=2
export transposon_MM=2
export siRNA_bot=21
export siRNA_top=26
export piRNA_bot=26
export piRNA_top=31

However, there is still the error 'mapping to rRNA failed'. I don't know why. Could you please give some tips ? Thx !!

[bowhan]

Can you please paste the content of the XXX.rRNA.log in the output directory?

[adds89]

Hi..
I am having the same problem when running pipeline for small RNA seq.
"Error: mapping to rRNA failed"

I've tried different configurations of "/common/hg19/variables", but the error remains.
Also, there is no file being created in the output directory, only empty folders was created.
How can I fix this?

Thank you!