Can't find SJ.out.tab

[ktruve]

I have softlinks to SJ.out.tab but still I get this error message while trying to run:

Generating .SJ.out.tab will need to re-sort consi_cytoRNA_2_SRR17621747.Aligned.sortedByCoord.out.bam file by read names. It will consume a lot of time, do you want to proceed? (Y/N)

Problem one why can't it find the SJ file and why does it want to sort the bam file by name? And also even if I answer N it will start to sort. I'm using version PSI-Sigma-2.1

Best,

Katarina

[wososa]

Hi Katarina,

thanks for reporting this issue. Could you provide an example name of your .SJ.out.tab files? File name could be the cause.

Thanks, Woody

[ktruve]

Hi, here is a name example: Hela_consi1_SRR17621735.SJ.out.tab I did copy the SJ files to the working dir instead and then it worked. Seemed to be something with the softlinks. Best, Katarina

[wososa]

Hi @ktruve ,

Thanks for figuring it out. If you are using singularity or docker, you probably need to mount the drive where your SJ.out.tab files are. To mount the drive (e.g., /folder/path/x.SJ.out.tab), you can edit the --bind /mnt:/mnt to --bind /folder/path:/folder/path so that singularity can recognize the folder. This might be the cause of softlinks not working. Let me know if I can help further.

Best, Woody