Failed to visualization

[Seongmin-Jang-1165]

Hi developer!!

I ran Isoquant wiht my data generated by RNA004 direct RNa sequencing

but there are some worrying point and error

1. I can't see the contents in the output folder like below.

so I check the log and there is error like below

the code I use is like this:

#!/bin/bash

isoquant.py -d nanopore --stranded forward --fastq /home/rnagenomics/sm/Nanopore/20240923_Histone_Direct_RNA_seq/analysis/POD5/Real/basecalling/fastq/DORADO_barcode1.fastq
--reference /home/rnagenomics/sm/Nanopore/20240923_Histone_Direct_RNA_seq/Reference/Reference/gencode.v43.transcripts.fa --genedb /home/rnagenomics/sm/Nanopore/20240923_Histone_Direct_RNA_seq/Reference/Reference/GENCODE/GENCODE_Homo_sapiens_hg38/GRCh38.gencode.v43.basic.annotation.gtf --complete_genedb
--output /home/rnagenomics/sm/Nanopore/20240923_Histone_Direct_RNA_seq/analysis/IsoQuant/output --prefix siCTR_ -t 20

isoquant.py -d nanopore --stranded forward --fastq /home/rnagenomics/sm/Nanopore/20240923_Histone_Direct_RNA_seq/analysis/POD5/Real/basecalling/fastq/DORADO_barcode2.fastq
--reference /home/rnagenomics/sm/Nanopore/20240923_Histone_Direct_RNA_seq/Reference/Reference/gencode.v43.transcripts.fa --genedb /home/rnagenomics/sm/Nanopore/20240923_Histone_Direct_RNA_seq/Reference/Reference/GENCODE/GENCODE_Homo_sapiens_hg38/GRCh38.gencode.v43.basic.annotation.gtf --complete_genedb
--output /home/rnagenomics/sm/Nanopore/20240923_Histone_Direct_RNA_seq/analysis/IsoQuant/output --prefix siMETTL3_ -t 20

2. anyway, I ran the visualize.py and it doesn't work...

How can I solve this problem..?

[andrewprzh]

Dear @Seongmin-Jang-1165

Your ran failed due to the operating system limit on the number of open files, which can be changed using

ulimit -n

I presume setting something like 10000 should be enough. Increase it if you see the same error again.

This issue was also resolved previously #133

Best
Andrey