Spladder test stuck

[zyh4482]

Following is my computer setup. CPU: i7-11700. RAM: 102GB

I have around 200 tumor and 100 normal bams. I tried with the following command: spladder test --conditionA tumor.txt --conditionB normal.txt --labelA tumor --labelB normal --parallel 8 --outdir ~/project/as -v

But it has been stuck for a few days. I have no idea what should I do. Part of the latest log is as below:

[################################################# ] 130087 / 130094 (100%) - to[################################################# ] 130088 / 130094 (100%) - to[################################################# ] 130089 / 130094 (100%) - to[################################################# ] 130090 / 130094 (100%) - to[################################################# ] 130091 / 130094 (100%) - to[################################################# ] 130092 / 130094 (100%) - to[##################################################] 130093 / 130094 (100%) - to[##################################################] 130094 / 130094 (100%) - took 10105 sec (ETA: 0 sec) Found dispersion fit Estimating adjusted dispersions.

Should I halt it and re-run the command? Or just wait? Is it the reason that my computer is low grade and does not fulfill computation expenses?

Thank you.

[zyh4482]

I re-ran the test and checked the task manager this time. I found that after calculating exon skip events, spladder did not proceed on the next task anymore. It just left only four diagnositic plots for exon skip. I have 135 normal bams and 237 tumor bams. I don't know if it is caused by too many input files. Could you please help me with it?

[akahles]

Dear @zyh4482 ,

sorry for the late reply. Is this issue still relevant for you? Did you try running the test with a smaller subset of samples?

Thanks,

Andre