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Ruitulyu / KAS-Analyzer

New computational framework to process and analyze KAS-seq and spKAS-seq data.
MIT License
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error received on some of the scripts #8

Open sumitra-mohan812 opened 1 year ago

sumitra-mohan812 commented 1 year ago

I get this error when I run peakscalling utility.c(2245):ERROR:50: Cannot open file '/opt/apps/modules/libs/gcc/qt' for 'reading'

Any suggestions on how to fix?

I have also noticed that when I run trim command- the .sh ends up removing trimmed.fq instead of the intermediate files and for mapping I end up with no ext.bed or bg files. but these commands did run and give me some output whereas peakscalling just stops

ecroot commented 1 year ago

Hi, I'm not a developer - just another user of the tool. I can't answer your main question, but regarding the removal of the trimmed.fq files: I also thought these got removed at first, but they actually just get moved into the output directory created by the KAS-seq command (I use KAS-seq -a bwa). It's a bit annoying that they move of course, but you can move them to wherever you like once the mapping is finished.

Ruitulyu commented 1 year ago

Hi, Could you please provide more details? I actually confirm that the trim command will not remove trimmed.fq files. Best, Ruitu

On Fri, Nov 17, 2023 at 4:24 PM sumitra-mohan812 @.***> wrote:

I get this error when I run peakscalling utility.c(2245):ERROR:50: Cannot open file '/opt/apps/modules/libs/gcc/qt' for 'reading'

Any suggestions on how to fix?

I have also noticed that when I run trim command- the .sh ends up removing trimmed.fq instead of the intermediate files and for mapping I end up with no ext.bed or bg files. but these commands did run and give me some output whereas peakscalling just stops

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Ruitulyu commented 1 year ago

Thanks for answering this question. And I have already modified the script that will generate a symbolic link of trimmed.fq files instead of moving them. Best, Ruitu

On Mon, Nov 27, 2023 at 4:03 AM E Croot @.***> wrote:

Hi, I'm not a developer - just another user of the tool. I can't answer your main question, but regarding the removal of the trimmed.fq files: I also thought these got removed at first, but they actually just get moved into the output directory created by the KAS-seq command (I use KAS-seq -a bwa). It's a bit annoying that they move of course, but you can move them to wherever you like once the mapping is finished.

— Reply to this email directly, view it on GitHub https://github.com/Ruitulyu/KAS-Analyzer/issues/8#issuecomment-1827519292, or unsubscribe https://github.com/notifications/unsubscribe-auth/APDPVGAD3JG6LWQUW3B7VMLYGRQODAVCNFSM6AAAAAA7QOF3A6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQMRXGUYTSMRZGI . You are receiving this because you are subscribed to this thread.Message ID: @.***>

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