Missing forward library error in MaSuRCA run

Question

[catheason09]

Hello, I am trying to run MaSuRCA on a subset of a bacterial genome. The data is paired -end and I have followed the documentation on how to run the program but it hits an error and says Missing forward file for PE library pe at ///path to MaSuRCA directory/bin/masurca line 298, <FILE> line 13. I am not sure what is going wrong and why it won't recognize the file.

My configuration file

!/bin/bash

# config file for my first test run of V_gazogenes data
SCRATCH_DIR=/lustre/medusa/catheason

DATA_ROOT=/$SCRATCH_DIR/assemblydata/rdikow_bacteria_ABYSS_or_VELVET/V_gazogenes/trimmomatic

DATA
PE= pe 100 20 $DATA_ROOT/paired1.fq $DATA_ROOT/paired2.fq
END

PARAMETERS

# values between 25 and 101 are supported, auto will compute the optimal size
GRAPH_KMER_SIZE=auto

# set this to 1 for Illumina-only assemblies and to 0 if you have 1x or more long (Sanger, 454) reads

USE_LINKING_MATES=1

# Typically set it to 60 for bacteria and something large (300) for mammals
LIMIT_JUMP_COVERAGE = 60

# these are the additional parameters to Celera Assembler.
CA_PARAMETERS = ovlMerSize=30 cgwErrorRate=0.25 ovlMemory=4GB

# minimum count k-mers used in error correction 1 means all k-mers are used. one can increase to 2 if coverage >100

KMER_COUNT_THRESHOLD = 1

# auto-detected number of cpus to use
NUM_THREADS= $NUM_THREADS

# this is mandatory jellyfish hash size
JF_SIZE=63065410

# this specifies if we do (1) or do not (0) want to trim long runs of homopolymers (e.g. # GGGGGGG) from 3' read ends, use it for high GC genomes

DO_HOMOPOLYMER_TRIM=0

END

My job file

#!/bin/bash
#PBS -j oe
#PBS -S /bin/bash
#PBS -A UT-INTERN
#PBS -l ncpus=16,mem=64000MB

cd $PBS_O_WORKDIR

SCRATCH_DIR=/lustre/medusa/catheason
MaS_PATH=/$SCRATCHDIR/MaSuRCA-2.2.1
MaS_BIN=/$MaS_PATH/bin
CONFIG_PATH=/$MaS_PATH/firsttestrun

$MaS_BIN/masurca $CONFIG_PATH/firstconfig.txt

Answer 1

[rtliu]

My suggestion:

1. Use the latest version of MaSuRCA (ftp://ftp.genome.umd.edu/pub/MaSuRCA/MaSuRCA-2.3.0rc1.tar.gz). There existed some problems in certain distribution of Linux with MaSuRCA-2.2.1, which may be fixed in MaSuRCA-2.2.0 or MaSuRCA-2.3.0rc1.

diff MaSuRCA-2.2.1/bin/expand_fastq MaSuRCA-2.3.0rc1/bin/expand_fastq
31c31
<     (text/plain*)
---
>     (text/*)
...

2. Provide the full path to fastq files in config file, make sure there is no space in the /full/path/to/fastq. e.g.

DATA
PE=pe 100 20 /full/path/to/paired1.fq /full/path/to/paired2.fq
END

Good luck!