MaSuRCA does not find path when launched from container

Question

[RiccPicc]

Hi everyone.

I would like to have a container with the whole pipeline to assemble a genome. The first software I installed is MaSuRCA. I built the container using singularity. The problem is that when I launch MaSuRCA on the config file (external to the container, as the reads files) it comes out this error:

singularity exec assembly.tools.2.simg /home/MaSuRCA-3.4.0/bin/masurca /home/user/sandboxes/LbotWT180.config.txt 
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
    LANGUAGE = "en_US:en",
    LC_ALL = (unset),
    LC_TIME = "it_IT.UTF-8",
    LC_MONETARY = "it_IT.UTF-8",
    LC_ADDRESS = "it_IT.UTF-8",
    LC_TELEPHONE = "it_IT.UTF-8",
    LC_NAME = "it_IT.UTF-8",
    LC_MEASUREMENT = "it_IT.UTF-8",
    LC_IDENTIFICATION = "it_IT.UTF-8",
    LC_NUMERIC = "it_IT.UTF-8",
    LC_PAPER = "it_IT.UTF-8",
    LANG = "en_US.UTF-8"
    are supported and installed on your system.
perl: warning: Falling back to the standard locale ("C").
Error line 17 of configuration file '/home/user/sandboxes/LbotWT180.config.txt':
invalid forward file for PE library 'lb': '/media/user/HardDisk/WT180/140619_D00200_0194_AH9C1NADXX_1_TP-D7-005_TP-D5-006_1.sanfastq.gz' Bad file descriptor

While if I launch MaSuRCA installed on my pc using the same config file as input, it does build the assemble.sh as it should.

Can someone help me understand this problem?

[ATpoint]

invalid forward file for PE library 'lb': '/media/riccardo/HardDisk/WT180/140619_D00200_0194_AH9C1NADXX_1_TP-D7-005_TP-D5-006_1.sanfastq.gz' Bad file descriptor

.sanfastq.gz does not look like a typical suffix, is this correct?

[RiccPicc]

Yes it is true. I checked the files and they are in fastq format as well. Indeed local MaSuRCA works well.