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ablab / spades

SPAdes Genome Assembler
http://ablab.github.io/spades/
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Trouble running SPAdes on IonTorrent data #679

Closed BCMollett closed 3 years ago

BCMollett commented 3 years ago

Hi, I have limited knowledge of processing IonTorrent data but running into a consistent error when running SPAdes. I cant figure out what the issue is... sorry if its simple and thanks in advance for your help.

Is the below error being caused by my input?

0:00:00.059 95M / 95M ERROR General (mmapped_reader.hpp : 81) unlink(2) failed. Reason: No such file or directory. Error code: 2

It also appears that the kmer temp folders might not be being deleted? It is saying that the folder is not empty

params.txt spades.log

Thanks, Ben

asl commented 3 years ago

Hello

The log reads:

  0:00:00.029     3G / 3G    INFO   K-mer Splitting          (kmer_data.cpp             :  89)   Processed 0 reads

So, either the input file is empty or corrupted.

PS: For assembling Influenza data you may want to use coronaSPAdes (see https://www.biorxiv.org/content/10.1101/2020.07.28.224584v2 for more information)