index error with a specific file (roadmap data)

[tesa.s...@gmail.com]

Hi Gigglers,

I am trying to run the roadmap example data and run into an error with the H9_Derived_Neuronal_Progenitor_Cultured_Cells_Active_TSS.bed.gz file.
This happens at the index step after sorting.

 ~/tools/giggle/bin/giggle index -i "roadmap_sort/*gz" -o roadmap_sort_b -f -s
Could not open file 'roadmap_sort/H9_Derived_Neuronal_Progenitor_Cultured_Cells_Active_TSS.bed.gz'
giggle: Could not open roadmap_sort/H9_Derived_Neuronal_Progenitor_Cultured_Cells_Active_TSS.bed.gz.


Previously I tried the wget file and it also fails at this file when indexing. Should I remove the offending file?

Thanks for the help,
Tesa

[tesa.s...@gmail.com]

I will answer my own question. It turns out this is also because of the limit to opening files. When I add 'ulimit -Sn 16384' it works.

Cheers,
Tesa


[Ryan Layer]

Great! Thanks.

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[juegaonl...@gmail.com]

The previous solution did not work for me, I am using CentOS.

Instead, I had to modify the file: /etc/security/limits.conf and add the following lines:

(Note that you need sudo permissions)

username soft nofile 16384

username hard nofile  16384

then run:

sysctl -p

Finally, I close your shell session and open it again.