I am having trouble using miRDeep2 package. It looks like I am running mapper.pl using a config.txt file which contains multiple samples correctly. However, when I try to run miRDeep2.pl I get the following error. If I run quantifer.pl it runs smoothly though. Any ideas?
Error: problem with processed_reads.fa Use of uninitialized value in split at /usr/biosoft/packages/miRDeep2/mirdeep2_0_0_8/bin/sanity_check_reads_ready_file.pl line 179, <IN> line 11334728. Use of uninitialized value in length at /usr/biosoft/packages/miRDeep2/mirdeep2_0_0_8/bin/sanity_check_reads_ready_file.pl line 185, <IN> line 11334728. Error in line 5.667.364: The sequence AACCCGTAGATCCGAACTTGT occures at least twice in your reads file. At first it occured at line Please make sure that your reads file only contains unique sequences.