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Errors with nextPolish.sh.e #87
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Hi, could you paste the content of |
Hi,
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As the log says, there is no |
I made the reinstall, but now I receive the log below from the Thanks!
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The RAM is too small |
Is there a proper way to increase it? According to the FAQ of NextPolish it should be possible to increase it from the default 3G for Paralleltask, but I cannot see an effect in changing it in the Also how is that the memory isn't enough for only 3G? |
The computer node you submitted only have ~6Gb memory, you can not change it by adjusting parameters, you need to change another computer nodes to run it. EDITED: |
Good to know. At least it's not a problem with my installation or files submitted. These errors come from a local test. When the tool is used in a cluster it runs perfectly. I was trying to figure out why there was such different behavior, but if it's due to a hardware restriction then there's nothing to do by now. Thanks. |
Hi all. I'm trying to polish an assembly from Flye for nanopore reads. However, I cannot make the command work as I receive errors that I cannot determine the source, or how to proceed. These errors appear also with the test data (
nextPolish test_data/run.cfg
).Operating system
Linux Mint 20.2 Uma (Ubuntu Focal base)
GCC
gcc version 9.3.0 (Ubuntu 9.3.0-17ubuntu1~20.04)
Python
Python 3.9.7
NextPolish
nextPolish v1.4.0
Input files
(https://nextpolish.readthedocs.io/en/latest/TUTORIAL.html#polishing-using-long-reads-only)
lgs.fofn:
I have only one FASTQ file because I'm testing the tool to adapt it to CWL, proceeding with
ls /path/to/fastq_runid.fastq > lgs.fofn
run.cfg:
modified parts are commented
Log
Regards,
Alex
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