MaSuRCA does not find path when launched from container
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17 months ago
RiccPicc ▴ 10

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?

singularity MaSuRCA assembly • 375 views
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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?

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

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