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SPAdes stuck for almost 24h, restart it didn't work

SPAdes stuck for almost 24h, restart it didn't work. I wonder it is because of the fastq file or the software or the server.

39 8 0 nslots: 2147483648 bits per slot: 8 range: 0000008000000000  
0:02:23.951     2G / 2G    INFO   K-mer Counting          
(kmer_data.cpp             : 317)   Processing
/public/home/data/cleandata/NDME07825_output/NDME07825_paired_1.fastq 
0:11:23.927     2G / 2G    INFO   K-mer Counting          
(kmer_data.cpp             : 326)   Processed 23006870 reads  
0:11:23.927     2G / 2G    INFO   K-mer Counting          
(kmer_data.cpp             : 317)   Processing
/public/home/data/cleandata/NDME07825_output/NDME07825_paired_2.fastq

Has anyone had this problem before? Dying for suggestions and solutions.

spades
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updated by Joe Joe • written by lucia • lucia

How large is your fastq file? Have you had other assemblies complete successfully?

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written by Joe Joe

My fastq file is 7.74G, and I have had other assemblies complete well.

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written by lucia • lucia

And the log file of another fastq file that also faced this problem shows these:

=== Stack Trace === [0x40a709] [0x40a876] [0x5b3220] [0x48a3f7] [0x441977] [0x439b98] [0x59a7ae] [0x5ab8c4] [0x60b969]


== Error ==  system call for: "['/public/home/biotools/SPAdes-3.12.0-Linux/bin/spades-hammer', '/public/home/data/assembly/NDME07821/corrected/configs/config.info']" finished abnormally, err code: 1

In case you have troubles running SPAdes, you can write to spades.support@cab.spbu.ru or report an issue on our GitHub repository github.com/ablab/spades Please provide us with params.txt and spades.log files from the output directory.
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updated by GenoMax GenoMax • written by lucia • lucia

Hello Lucia, good to see you. Try to increase the number of threads with -t parameter, e.g., -t 8 is 8 threads. Error code 1 is a segmentation fault, I believe. Obviously, also ensure that you are using enough RAM.

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written by Kevin Blighe Kevin Blighe

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