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6.0 years ago
Menia_gavr
•
0
Hi guys,
I am new to bionformatics. I am trying to run my assembly with SPAdes and I get this error. I tried to decrease the RAM and threads that are occupied, but I still get the error. Any ideas?
Command line: /home/programs/assembly/SPAdes-3.0.0-Linux/bin/spades.py -1 B9_trimmed.1.fastq -2 B9_trimmed.2.fastq --careful -o /home/gavri003/B9_Assembly
System information:
SPAdes version: 3.0.0
Python version: 2.7.6
OS: Linux-3.13.0-93-generic-x86_64-with-Ubuntu-14.04-trusty
Output dir: /home/gavri003/B9_Assembly
Mode: read error correction and assembling
Debug mode is turned OFF
Dataset parameters:
Multi-cell mode (you should set '--sc' flag if input data was obtained with MDA (single-cell) technology
Reads:
Library number: 1, library type: paired-end
orientation: fr
left reads: ['/home/gavri003/B9_Assembly/B9_trimmed.1.fastq']
right reads: ['/home/gavri003/B9_Assembly/B9_trimmed.2.fastq']
interlaced reads: not specified
single reads: not specified
Read error correction parameters:
Iterations: 1
PHRED offset will be auto-detected
Corrected reads will be compressed (with gzip)
Assembly parameters:
k: automatic selection based on read length
MismatchCorrector will be used
Repeat resolution is enabled
Other parameters:
Dir for temp files: /home/gavri003/B9_Assembly/tmp
Threads: 16
Memory limit (in Gb): 250
======= SPAdes pipeline started. Log can be found here: /home/gavri003/B9_Assembly/spades.log
===== Read error correction started.
== Running read error correction tool: /home/programs/assembly/SPAdes-3.0.0-Linux/bin/hammer /home/gavri003/B9_Assembly/corrected/configs/config.info
0:00:00.000 4M / 4M INFO General (main.cpp : 82) Loading config from /home/gavri003/B9_Assembly/corrected/configs/config.info
0:00:00.001 4M / 4M INFO General (memory_limit.hpp : 29) Memory limit set to 250 Gb
0:00:00.001 4M / 4M INFO General (main.cpp : 91) Trying to determine PHRED offset
0:00:00.001 4M / 4M INFO General (main.cpp : 97) Determined value is 33
0:00:00.002 4M / 4M INFO General (hammer_tools.cpp : 49) Hamming graph threshold tau=1, k=21, subkmer positions = [ 0 10 ]
=== ITERATION 0 begins ===
0:00:00.002 4M / 4M INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index
0:00:00.002 4M / 4M INFO K-mer Splitting (kmer_data.cpp : 127) Splitting kmer instances into 256 buckets. This might take a while.
0:00:00.003 4M / 4M INFO General (file_limit.hpp : 29) Open file limit set to 1024
0:00:00.003 4M / 4M INFO K-mer Splitting (kmer_data.cpp : 150) Memory available for splitting buffers: 5.20825 Gb
0:00:00.003 4M / 4M INFO K-mer Splitting (kmer_data.cpp : 159) Using cell size of 262144
0:00:43.883 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 181) Processed 3315276 reads
0:01:03.099 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 181) Processed 4886811 reads
0:01:47.794 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 181) Processed 8340219 reads
0:02:06.279 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 181) Processed 9773622 reads
0:02:06.281 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 186) Processed 9773622 reads
0:02:07.223 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting.
0:02:13.019 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 186015006 kmers in total.
0:02:13.020 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets.
0:02:15.173 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices
0:02:57.154 68M / 9G INFO General (kmer_index.hpp : 371) Merging final buckets.
0:03:10.101 68M / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 64349595 bytes occupied (2.7675 bits per kmer).
0:03:10.101 68M / 9G INFO K-mer Counting (kmer_data.cpp : 267) Arranging kmers in hash map order
0:04:22.334 68M / 9G INFO K-mer Counting (kmer_data.cpp : 280) Done. Total swaps: 186014738
0:04:23.129 1G / 9G INFO General (main.cpp : 151) Clustering Hamming graph.
0:04:23.129 1G / 9G INFO Hamming Clustering (hamcluster.cpp : 115) Serializing sub-kmers.
0:04:23.129 1G / 9G INFO Hamming Clustering (hamcluster.cpp : 120) Serializing: [0, 10)
0:05:53.899 1G / 9G INFO Hamming Clustering (hamcluster.cpp : 120) Serializing: [10, 21)
0:07:24.190 1G / 9G INFO Hamming Clustering (hamcluster.cpp : 129) Splitting sub-kmers, pass 1.
0:09:24.241 1G / 9G INFO Hamming Clustering (hamcluster.cpp : 134) Splitting done. Processed 2 blocks. Produced 5242482 blocks.
0:09:24.241 1G / 9G INFO Hamming Clustering (hamcluster.cpp : 145) Merge sub-kmers, pass 1
0:16:19.822 1G / 9G INFO Hamming Clustering (hamcluster.cpp : 170) Merge done, total 2249504 new blocks generated.
0:16:20.228 1G / 9G INFO Hamming Clustering (hamcluster.cpp : 175) Spliting sub-kmers, pass 2.
=== Stack Trace ===
[0x4027fa]
[0x428065]
[0x4289f9]
[0x416533]
[0x55f110]
[0x4001b9]
hammer: /home/yasha/gitrep2/algorithmic-biology/assembler/src/hammer/hamcluster.cpp:54: std::pair<long unsigned int, long unsigned int> SubKMerSplitter::split(): Assertion `!ofs.fail()' failed.
== Error == system call for: "['/home/programs/assembly/SPAdes-3.0.0-Linux/bin/hammer', '/home/gavri003/B9_Assembly/corrected/configs/config.info']" finished abnormally, err code: -6
In case you have troubles running SPAdes, you can write to spades.support@bioinf.spbau.ru
Please provide us with params.txt and spades.log files from the output directory.
Thanks a lot! Menia
I see that you are running an old version of SPAdes. It is currently in version 3.11.1. You may want to start by getting it upgraded to latest and see if the error goes away.