Entering edit mode
5.3 years ago
lucia
▴
10
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.
How large is your fastq file? Have you had other assemblies complete successfully?
My fastq file is 7.74G, and I have had other assemblies complete well.
And the log file of another fastq file that also faced this problem shows these:
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.