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  • Tlexander
    Member
    • Aug 2010
    • 14
    #1

    Bismark Bug v0.14.4 --remove_spaces in bismark_methylation_extractor.

    I think there is some bugs in the option of --remove_spaces in bismark_methylation_extractor.



    bismark_methylation_extractor --single-end --bedGraph --counts --ignore 3 --buffer_size 10G --remove_spaces --zero_based --comprehensive --output ../methyfreq ../bam/ENCFF000LWO_trimmed.fq_bismark_bt2.bam



    The error is as the following:

    Changed directory to /media/LTS_33T/SG_LTS33T/monod/haib/methyfreq/
    Now replacing whitespaces in the sequence ID field of the Bismark methylation extractor output /media/LTS_33T/SG_LTS33T/monod/haib/methyfreq/CpG_context_ENCFF000LWP_trimmed.fq_bismark_bt2.txt prior to bedGraph conversion

    Couldn't write to file /media/LTS_33T/SG_LTS33T/monod/haib/methyfreq/CpG_context_ENCFF000LWP_trimmed.fq_bismark_bt2.txt.spaces_removed.txt: No such file or directory
    Finished BedGraph conversion ...
    Tags: None
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