ablab
Failed to visualization
Hi developer!!
I ran Isoquant wiht my data generated by RNA004 direct RNa sequencing
but there are some worrying point and error
- 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
- anyway, I ran the visualize.py and it doesn't work...
How can I solve this problem..?
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 https://github.com/ablab/IsoQuant/issues/133
Best Andrey
