masurca invalid forward file for PE library

Question

[mariachiaracascarano]

Hi everybody! I am trying to assemble a bacterial genome from miseq paired end reads in masurca 3.3.0. I compiled the configuration file as follows

DATA

Illumina paired end reads supplied as
if single-end, do not specify
MUST HAVE Illumina paired end reads to use MaSuRCA
PE=pe 267 57 ~/projects/miseq/pant_bact/DLK2/frag_1.fastq ~/projects/miseq/pant_bact/DLK2/frag_2.fastq

Illumina mate pair reads supplied as
JUMP= sh 3600 200
pacbio OR nanopore reads must be in a single fasta or fastq file with absolute path, can be gzipped
if you have both types of reads supply them both as NANOPORE type
PACBIO=/FULL_PATH/pacbio.fa
NANOPORE=/FULL_PATH/nanopore.fa
Other reads (Sanger, 454, etc) one frg file, concatenate your frg files into one if you have many
OTHER=/FULL_PATH/file.frg
END

and I get

perl: warning: Setting locale failed. perl: warning: Please check that your locale settings: LANGUAGE = "en_US:en", LC_ALL = (unset), LC_CTYPE = "UTF-8", LANG = "en_US.UTF-8" are supported and installed on your system. perl: warning: Falling back to a fallback locale ("en_US.UTF-8"). Error line 17 of configuration file 'sr_config_DLK2.txt': invalid forward file for PE library 'pe': '~/projects/miseq/pant_bact/DLK2/frag_1.fastq' Bad file descriptor

I checked the path and the file and they seem ok... I am stuck here.. Any help? Thanks, Chiara

Answer 1

[shelkmike]

Try to replace "~" with a full path to the reads

Answer 2

[mariachiaracascarano]

oh my god thanks, I was getting crazy for such small thing.... it worked :)