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hellosunking / Msuite2

Msuite2: integrated DNA methylation data analysis toolkit with enhanced performance
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FATAL: Could not open file per.chr/chrx.sam for write. #5

Open ikaramichali opened 1 year ago

ikaramichali commented 1 year ago

Hello!

I am trying to run the command /mnt/g/Programs/Msuite2-master/bin/T2C.pe.m3 /mnt/g/Programs/Msuite2-master/index/Vfaba/chr.info Msuite2.raw.sam per.chr 10 && touch Msuite2.split.OK

But I am keep getting the same error: FATAL: Could not open file per.chr/chrcontig_6894.sam for write.

I have checked the folders permissions and I do run the command as sudo. I don't ha a space problem either. I even tried to run it within the same folder I have placed Msuite2. I still get the same error.

I am using the precompiled files and indexing and mapping worked just fine. Can you please help me? Kind regards, Ioanna

hellosunking commented 1 year ago

Hi Ioanna,

I guess the error is because either you are not running the program in the correct directory or "per.chr/" directory doesnot exist due to some reasons. You can change to the output directory of Msuite2, which contains both "Msuite2.raw.sam" file and "per.chr/" directory (which will be generated during Msuite2 makefile generation) and run the command; if "per.chr/" directory doesnot exist, you can make one manually and re-run the command.

B.T.W., we do not recommend the user to run "T2C.pe.m3" manually. Please run "Msuite2" to generate makefile then use "make" command to perform the analysis.

Kun