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wososa / PSI-Sigma

PSI-Sigma
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No such file or directory #56

Closed ESWRKJ closed 1 year ago

ESWRKJ commented 1 year ago

Hello @wososa when I run this command 

singularity exec /public/home/container/psi_sigma_pipeline_4.0.sif perl /usr/local/bin/PSI-Sigma-2.3/dummyai.pl --gtf Gbarbadense_gene.sorted.gtf --name Gbar --type 1 -nread 10 --fmode 3 --groupa PSIsigma.groupa.txt --groupb PSIsigma.groupb.txt

This error occurred

Details

bam_sort_core] merging from 54 files... open: No such file or directory [main_samview] fail to open "leafAligned.sortedByCoord.out.SortedbyName.bam" for reading. [bam_sort_core] merging from 57 files... open: No such file or directory [main_samview] fail to open "rootAligned.sortedByCoord.out.SortedbyName.bam" for reading. mkdir: cannot create directory ‘_wososatmp’: File exists

How to solve it

ESWRKJ commented 1 year ago

And *SJ.out.tab is empty

ESWRKJ commented 1 year ago

Hi @wososa Sorry for my carelessness. It's actually lack “dot”between “BM1” and “Aligned" But why do I always get this error? "mkdir: cannot create directory ‘_wososatmp’: File exists"

wososa commented 1 year ago

Hi @ESWRKJ ,

Please ignore the warning. PSI-Sigma try to create the _wososatmp whenever it is generating temporary IR.out.tab files. Apparently, when PSI-Sigma is processing .bam files in parallel, the first .bam file has already created the folder. It resulted in this warning.

Best, Woody

ESWRKJ commented 1 year ago

OK I see ,thank you