Simon C Chu

It looks like an earlier error before the assembly step or the assembly failed. Could you post your config.json file?

The config looks good for me. Would you please try to change `velvet` and `kmc` to the path of absolute folder? Like ``` "velvet": "/gpfs/scratchfs1/chc12015/tools/velvet-master/", "kmc": "/gpfs/scratchfs1/chc12015/tools/kmc2.3/", ```

Could you check whether `/home/progs/GAPPadder/ContigsMerger` and `/home/progs/GAPPadder/TERefiner_1` run properly? Did you compile them or directly use the one contained? On some machines, we need to re-compile them.

Thank you a lot @machadodj and @jorisbertrand for the suggestions. I am trying to release a new version with improvements in installation and project description. I will keep this issue...

Inside the failed ones, there are earlier errors like: multiprocessing.pool.RemoteTraceback: """ Traceback (most recent call last): File "/opt/conda/envs/xtea/lib/python3.9/multiprocessing/pool.py", line 125, in worker result = (True, func(*args, **kwds)) File "/opt/conda/envs/xtea/lib/python3.9/multiprocessing/pool.py", line...

I found the shared workspaces. I checked the failed jobs, and still cannot find out why the errors were triggered. I will download one of the smaller bam and test...

@JialiUMassWengLab Sorry for the late reply. I reinstalled TEMP on another server, and this error doesn't show up now. However, it shows another error: "Illegal division by zero at ../scripts/pickOverlapPair.in.pl...

@JialiUMassWengLab It seems the "getBin" error happen again. Which version of bedtools do you recommend to use? I use the latest one.

@JialiUMassWengLab , I tried the old version of betools and it works. But met another error: "Error: tmp is an empty file." Any suggestion?

I didn't solve the problem, and preferred other tools. @vmerel