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?