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malonge / RagTag

Tools for fast and flexible genome assembly scaffolding and improvement
MIT License
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The scaffold command was submitted and the assembled result was not available #180

Open LZY19940813 opened 5 months ago

LZY19940813 commented 5 months ago

I assembled scffolds using the contigs file（about 2Gb）that was reassembled from generation 2 by SOAPdenovo2 tool. My scripting have been running for 2 days and I still only have a result file for "ragtag.scaffold.asm.paf". I don't know what the problem is. So, could you tell me if who have any good suggestions. Thank you!

LZY19940813 commented 5 months ago

Traceback (most recent call last): File "/gss1/home/wangzx02/.conda/envs/ragtag/bin/ragtag.py", line 133, in main() File "/gss1/home/wangzx02/.conda/envs/ragtag/bin/ragtag.py", line 89, in main subprocess.call(subcmd) File "/gss1/home/wangzx02/.conda/envs/ragtag/lib/python3.6/subprocess.py", line 289, in call return p.wait(timeout=timeout) File "/gss1/home/wangzx02/.conda/envs/ragtag/lib/python3.6/subprocess.py", line 1477, in wait (pid, sts) = self._try_wait(0) File "/gss1/home/wangzx02/.conda/envs/ragtag/lib/python3.6/subprocess.py", line 1424, in _try_wait (pid, sts) = os.waitpid(self.pid, wait_flags)