Hello, I would like to request your help to troubleshoot a problem.
I am using P_RNA_scaffolder to improve a de novo plant genome for which I have several RNAseq libraries. As I have several libraries, I put all the reads together (keeping the order) and merged the bams generated by each individual alignment and sort it. So my cmd went like this:
$P_RNA: P_RNA_scaffolder path
$genome: the path to my assembly
$folder: Working directory
$threads: # of threads
The thing is, after running a few minutes (~25 min), when I look at the output folder:
ls -gh output:
So, I do not why it is happening, but from the very first moment when the intron.txt is generated, as it is empty, it causes that the input to downstream processes is empty as well. In the end P_RNA_scaffold.fasta is the same assembly that I gave as input.
Thus, I wonder if you have any ideas of what is happening here and how to address it.
Hello, I would like to request your help to troubleshoot a problem.
I am using P_RNA_scaffolder to improve a de novo plant genome for which I have several RNAseq libraries. As I have several libraries, I put all the reads together (keeping the order) and merged the bams generated by each individual alignment and sort it. So my cmd went like this:
$P_RNA -d $(dirname $P_RNA) -i $folder/input/merged_sorted.sam -j $genome -F $folder/input/left_rna.fastq -R $folder/input/right_rna.fastq -o $folder/output -t $threads$P_RNA: P_RNA_scaffolder path$genome: the path to my assembly$folder: Working directory$threads: # of threadsThe thing is, after running a few minutes (~25 min), when I look at the output folder:
ls -gh output:So, I do not why it is happening, but from the very first moment when the
intron.txtis generated, as it is empty, it causes that the input to downstream processes is empty as well. In the endP_RNA_scaffold.fastais the same assembly that I gave as input.Thus, I wonder if you have any ideas of what is happening here and how to address it.
Thanks in advance