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!
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