install custom genome error

[gongyy-sumhs]

Dear Bo Han,

I am trying to install orycun2 genome which is without iGenome support, I have provided all the files that you have mentioned: genome sequence in fasta format, transposon sequence in fasta format, piRNA cluster in bed format, genes annotation in gtf format, miRNA hairpin sequence in fasta format, miRNA sequence in fasta format. However, there was a error when performing repBase transposon annotation:
[2023-02-16 16:30:58 CST] Begining installing the genome orycun2
[2023-02-16 16:30:58 CST] Testing/Installing missing R packages
[2023-02-16 16:30:58 CST] Preparing genomic sequence/annotation and making indexes
[2023-02-16 16:30:58 CST] Building STAR index for genome
[2023-02-16 16:30:58 CST] Building mrFast index for genome
[2023-02-16 16:30:58 CST] Building Bowtie/Bowtie2 index for rRNA
[2023-02-16 16:30:58 CST] Building index for microRNA hairpin, still using fasta from mirBase
[2023-02-16 16:30:58 CST] Building Bowtie/BWA index for repBase transposon annotation
Can't open repBase/L2a::LINE/L2::chr1:51-174.fa to write: No such file or directory
[2023-02-16 16:30:58 CST] Building Bowtie/BWA index for piRNA cluster
[2023-02-16 16:30:58 CST] Building Bowtie/BWA index for repBase + piRNA cluster + genes
Do you have any idea about that?

By the way, could piPipes handle multiple sample for small RNA-Seq and RNA-Seq, thank you!

Yuan

[rubenolbrechts]

Hi Yuan!

I had the same error, and I think it's because of the name repbase gave to the transposon.
piPipes doesn't like the "/" inside the name and interprets it as a directory.
So just run

cat genome.repBase.fa | tr "/" _ > genome.repBase_tmp.fa

to remove all "/" in the names and change them to "_" (be sure to rename the output file again to genome.repBase.fa).
This worked for me!

I hope this is still useful for you, seeing as it's 2 years after your problem 😅

Best,
Ruben