masurca invalid forward file for PE library
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2.7 years ago

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

assembly masurca illumina Tool • 1.2k views
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2.7 years ago
shelkmike ▴ 540

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

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2.7 years ago

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

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