Error that GTF file does not exist

[qianzhao613]

Hi Youngbin and Dominik,

I tried running Nextflow on some public datasets and set the directory according to the requirements. However, I encountered an error indicating that the GTF file could not be found. I have verified that the path is correct and that the GTF file can be printed. Could you please help me resolve this issue?

Cheers,
Qian

[4li77l3n00b]

execute export NXF_SINGULARITY_HOME_MOUNT=true in bash.
referring to https://www.nextflow.io/docs/latest/container.html#id21

[qianzhao613]

execute export NXF_SINGULARITY_HOME_MOUNT=true in bash. referring to https://www.nextflow.io/docs/latest/container.html#id21

Thanks for your reply. The code I used is

export NXF_SINGULARITY_HOME_MOUNT=true

nextflow run main.nf -profile singularity --sample_type "mouse"

but the problem still exists. Do you have any suggestions? Thanks.

[ymoon06]

Hi, I tried to replicate the issue, but it ran normally. Could you please confirm if you ran it in a Slurm environment? Currently, we only support Slurm environments, and the test was conducted on Slurm. May I ask which environment you used? Did you run it on your local computer?

[qianzhao613]

Hi, I tried to replicate the issue, but it ran normally. Could you please confirm if you ran it in a Slurm environment? Currently, we only support Slurm environments, and the test was conducted on Slurm. May I ask which environment you used? Did you run it on your local computer?

Hi,

Thanks for your answer. I used the SGE batch system. I guess that's the problem.

Best,
Qian