Error with NeoFuse execution

[Prathyusha-konda]

Hi, I am trying to execute neofuse with the following command and I am getting error about unable to create folder in a non-existent path (/mnt/out - I am not sure why it's trying to write here, this path does not exist - I'm running on a cluster). Can you please help me with this? Thank you very much.

Command: NeoFuse -o ./NeoFuse_data/output/ \ -1 ./p2/a2/celllinedata/B10/B10_1.fq \ -2 ./p2/a2/celllinedata/B10/B10_2.fq \ -s ./Reference/STARindex/ \ -g ./Reference/GRCh38.primary_assembly.genome.fa \ -a ./Reference/gencode.v31.annotation.gtf \ -M 11 --docker

Error: mkdir: cannot create directory '/mnt/out/output/B10_1.fq': Permission denied mkdir: cannot create directory '/mnt/out/output/B10_1.fq': Permission denied mkdir: cannot create directory '/mnt/out/output/B10_1.fq': Permission denied mkdir: cannot create directory '/mnt/out/output/B10_1.fq': Permission denied mkdir: cannot create directory '/mnt/out/output/B10_1.fq': Permission denied mkdir: cannot create directory '/mnt/out/output/B10_1.fq': Permission denied mkdir: cannot create directory '/mnt/out/output/B10_1.fq': Permission denied mkdir: cannot create directory '/mnt/out/output/B10_1.fq': Permission denied mkdir: cannot create directory '/mnt/out/output/B10_1.fq': Permission denied mkdir: cannot create directory '/mnt/out/output/B10_1.fq': Permission denied mkdir: cannot create directory '/mnt/out/output/B10_1.fq': Permission denied mkdir: cannot create directory '/mnt/out/output/B10_1.fq': Permission denied [-------------------------------- [NeoFuse] --------------------------------]

[18:21:45] Paired End (PE) Reads detected: commencing processing [18:21:45] Processing files B10_1.fq - B10_2.fq [18:21:45] STAR Run started /usr/local/bin/NeoFuse_single: line 224: /mnt/out/output/B10_1.fq/LOGS/B10_1.fq.STAR.err: No such file or directory /usr/local/bin/NeoFuse_single: line 234: /mnt/out/output/B10_1.fq/LOGS/B10_1.fq.samtools.log: No such file or directory [18:21:45] Arriba Run started /usr/local/bin/NeoFuse_single: line 250: /mnt/out/output/B10_1.fq/LOGS/B10_1.fq.arriba.log: No such file or directory

EXITING because of FATAL ERROR: could not create output file: /mnt/out/output/B10_1.fq/Arriba/B10_1.fq.Log.out Check if the path /mnt/out/output/B10_1.fq/Arriba/B10_1.fq. exists and you have permissions to write there

Aug 09 18:21:45 ...... FATAL ERROR, exiting An error occured during STAR/Arriba run, check the log files in /home/pk576/NeoFuse_data/output/B10_1.fq/LOGS/ for more details

[abyssum]

Hello @Prathyusha-konda,

The /mnt/out NeoFuse is trying to access is the actual mount point to /home/pk576/NeoFuse_data/output/. So this should not cause any problems. You are getting a Permission denied tho, which means that the container does not have permission to write on this specific path. I don't know what's the configuration on your cluster but Docker containers run as super user (sudo), also keep in mind that the container environment runs as user: NeoFuse (there's a reason for that).

I am afraid there's not much we can do from our side atm (but I will try to figure out a workaround), what I can suggest for now is to:

1. Report the issue to your sys admin.
2. Check if there's a singularity installation on your HPC and run NeoFuse with the --singularity flag.

[Prathyusha-konda]

Hi @abyssum,

Thank you so much for responding so quickly, really appreciate it. This is my first time using docker so I was not sure what that error meant - I'll ask the bioinformatics core if they can enable permissions :)

I don't think we have singularity, unfortunately.