Question: rnaSPADES, assembly problems
gravatar for leonardomajul
3.8 years ago by
leonardomajul0 wrote:


I am doing a Transcriptome of a mushroom and I trying to make the assembly with rnaSPAdes (a tool of SPAdes 3.9). I did the sequenciation with Illumina and trimmed the sequencies with trimmomatic to take out the adapters. When I start running rnaSPAdes and BayesHammer starts the analysis something goes wrong, finishing with an error code 6. Do you know how can I fix it?

Command line: /opt/perun/bin/ --rna -1 /misc/home/majul/hongo1_S1_L001_R2_001_paired.fq.gz -2 /misc/home/majul/hongo1_S1_L001_R2_001_reverse_paired.fq.gz -o /misc/home/majul/spagsch13_output

System information: SPAdes version: 3.9.0 Python version: 2.7.6 OS: Linux-3.13.0-53-generic-x86_64-with-Ubuntu-14.04-trusty

Output dir: /misc/home/majul/spagsch13_output Mode: read error correction and assembling Debug mode is turned OFF

Dataset parameters: RNA-seq mode Reads: Library number: 1, library type: paired-end orientation: fr left reads: ['/misc/home/majul/hongo1_S1_L001_R2_001_paired.fq.gz'] right reads: ['/misc/home/majul/hongo1_S1_L001_R2_001_reverse_paired.fq.gz'] 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: [55] Repeat resolution is enabled Mismatch careful mode is turned OFF MismatchCorrector will be SKIPPED Coverage cutoff is turned OFF Other parameters: Dir for temp files: /misc/home/majul/spagsch13_output /tmp Threads: 16 Memory limit (in Gb): 141

======= SPAdes pipeline started. Log can be found here: /misc/home/majul/spagsch13_output /spades.log

===== Read error correction started.

== Running read error correction tool: /misc/scratch1/software-ubuntu/SPAdes-3.9.0-Linux/bin/hammer /misc/home/majul/spagsch13_output /corrected/configs/

0:00:00.001 4M / 4M INFO General (main.cpp : 83) Starting BayesHammer, built from N/A, git revision N/A 0:00:00.004 4M / 4M INFO General (main.cpp : 84) Loading config from /misc/home/majul/spagsch13_output /corrected/configs/ Failed to load file /misc/home/majul/spagsch13_outputterminate called without an active exception

== Error == system call for: "['/misc/scratch1/software-ubuntu/SPAdes-3.9.0-Linux/bin/hammer', '/misc/home/majul/spagsch13_output\r/corrected/configs/']" finished abnormally, err code: -6

In case you have troubles running SPAdes, you can write to Please provide us with params.txt and spades.log files from the output directory.

rna spades assembly • 2.0k views
ADD COMMENTlink written 3.8 years ago by leonardomajul0

With larger genomes you may want to stick with Trinity. It does have specific hardware requirements that you should consider before starting. A publicly accessible Trinity instance is at Galaxy @Indiana if you don't have necessary hardware available locally.

ADD REPLYlink modified 3.8 years ago • written 3.8 years ago by genomax91k
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