stampy error during mapping
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15 months ago

Hello! I'm running stampy.py (version 1.0.28) on a HPC but after hours of running I get this error message:

"terminate called after throwing an instance of 'std::bad_array_new_length'
  what():  std::bad_array_new_length

stampy: Error: Detected unexpected failure of a child -- waiting for other children to terminate"

When running the same reads and genome locally on my Mac I get this other error:

"libc++abi.dylib: terminating with uncaught exception of type std::bad_alloc: std::bad_alloc
Abort trap: 6"

Python version is 2.7.10

Any help is appreciated!

Thanks!

Giulia

software error RNA-Seq alignment • 333 views
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For mac manual says:

For Mac, only Python 2.6 with 2-byte Unicode is supported.

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The reads I am mapping are paired end Illumina (SRR8755631) and the genome is that of Parasteatoda tepidariorum (GCF_000365465.2_Ptep_2.0).

First, I have prepared the genome index and hash table with the commands:

stampy.py -G GCF_000365465.2_Ptep_2.0 GCF_000365465.2_Ptep_2.0.fa
stampy.py -g GCF_000365465.2_Ptep_2.0 -H GCF_000365465.2_Ptep_2.0

Then, I sent the job through SLURM using this sbatch script:

#!/bin/bash
# SLURM options:
# *************
#SBATCH --job-name stampy
#SBATCH --partition ax-normal
#SBATCH --output %x_%j.out
#SBATCH --error %x_%j.err
#SBATCH --nodes 1
#SBATCH --ntasks 1
#SBATCH --cpus-per-task 4
#SBATCH --mail-type ALL
#SBATCH --export=NONE

##SBATCH --mem 30G
##SBATCH --time 5:00:00

stampy.py -t 4 -g GCF_000365465.2_Ptep_2.0 -h GCF_000365465.2_Ptep_2.0
-o SRR8755631 -M SRR8755631_1.fastq.gz SRR8755631_2.fastq.gz

Thank you

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