Hello

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/spades.py --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/config.info

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/config.info 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/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.