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ZijieJin / scFusion

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Docker/Singularity Issue #24

Open Sogand65 opened 3 weeks ago

Sogand65 commented 3 weeks ago

Hi ZijieJin,

I tried the docker using first on my local but since the base image is not defined and my system is Mac I got incompatibility error! I tried on our hpc, since npc uses singularity I had to use singularity/apptainer. Using your testdata, I am facing error from the beginning, the BuildSTARIndex command cause the error occur due to Log.Out file which can not be created on. the container since I have no permission to create any folder of file there! Is there anyway we can specify the output so I can specify it on my home directory, I appreciate if you could help me to use your model for my single cell data. For more info about my issue please see below.

Thanks, Sogi Apptainer> python /usr/local/src/scFusion/scFusion.py BuildSTARIndex -g /usr/local/src/scFusion/data/hg19.fa -a /usr/local/src/scFusion/data/ref_annot.gtf -s /home/sssajedi/proj/scFusion/hg19STARIndex/ -t20

EXITING because of FATAL ERROR: could not create output file: ./Log.out Check if the path ./ exists and you have permissions to write there

Aug 21 11:12:46 ...... FATAL ERROR, exiting

I tried to see if I have permission to generate a file: Apptainer> touch test touch: cannot touch 'test': Read-only file system

ZijieJin commented 3 weeks ago

Sorry, I am not familiar with the singularity. I had no idea about your problem. Sorry~~ By the way, as a reminder, please ensure your scRNA-seq data were Smart-seq data, rather than 10X.