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The directories "half_mapped_reads", "mapped_reads" and "non_mapped_reads" are empty. Loks like a bug.
[mtop@albiorix raw_data_to_no-skeletonema-016536_2015_10_09]$ pwd
/nobackup/data5/Skeletonema_marinoi_genome_project/test/Anja_Kamps_data/mapping_to_016536/raw_data_to_no-skeletonema-016536_2015_10_09Reactions are currently unavailable