negative repeat count does nothing at quantifier.pl line 1312, <in> line 5603.

[erickfabian0]

Hi @Drmirdeep , I also have this problem but in different line, and whit quantifier.pl in line 1312. One of such lines is below: negative repeat count does nothing at quantifier.pl line 1312, line 5603.

Line 1312 of my miRDeep2_core_algorithm is: my $mat = $hash{$k1}{$k2}{'mature'};;

could you please look into it? thanks!

I’m working on a server (Alliance Canada), and I need to install miRDeep2 using the second method, which doesn't require Perl, because I don't have sudo access on the server. I followed the tutorial, and it worked fine, but for my database, I need to change the format of the identifiers, replacing spaces with underscores ("_").

First, I align the reference genome with a miRBase database using Bowtie, and then I use the mapper tool to obtain the reads_collapsed.fa and reads_collapsed_vs_genome.fa files. Finally, I execute the miRDeep2 command using a mature comparison with the Pan paniscus mature sequence (ppa).

here is an example of the head of every fiel i used:

• reference genome: >dna:chromosome:GRCh38:1:1:248956422:1_REF NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

• reads.fa (G010_04011_clean_total.fa/After delete the spaces: output.fa ) : >A00253_627_HMLMGDRXY_1_2101_4128_1000_1_N_0_CACCATAC GGCTGGTCCGATGGTAGTGGGTTATCAGAACT

  A00253_627_HMLMGDRXY_1_2101_5195_1000_1_N_0_CACCTAAC GGCTGGTCCGATGGTAGTGGGTTATCAGAACT A00253_627_HMLMGDRXY_1_2101_7310_1000_1_N_0_CACCTTAC GGCTGGTCCGATGGTAGTGGGTTATCAGAACTTATTA A00253_627_HMLMGDRXY_1_2101_7618_1000_1_N_0_CACCTTAC GGCTGGTCCGATGGTAGTGGGTTATCAGAACT A00253_627_HMLMGDRXY_1_2101_8486_1000_1_N_0_CACCTTAC GGCTGGTCCGATGGTAGTGGGTTATCAGAAC A00253_627_HMLMGDRXY_1_2101_9299_1000_1_N_0_CACCTTAC GGCTGGTCCGATGGTAGTGGGTTATCAGAAC

• mature_fi_clean.fa: >hsa-let-7a-5p_MIMAT0000062_Homo_sapiens_let-7a-5p UGAGGUAGUAGGUUGUAUAGUU

  hsa-let-7a-3p_MIMAT0004481_Homo_sapiens_let-7a-3p CUAUACAAUCUACUGUCUUUC hsa-let-7a-2-3p_MIMAT0010195_Homo_sapiens_let-7a-2-3p CUGUACAGCCUCCUAGCUUUCC hsa-let-7b-5p_MIMAT0000063_Homo_sapiens_let-7b-5p UGAGGUAGUAGGUUGUGUGGUU hsa-let-7b-3p_MIMAT0004482_Homo_sapiens_let-7b-3p CUAUACAACCUACUGCCUUCCC hsa-let-7c-5p_MIMAT0000064_Homo_sapiens_let-7c-5p UGAGGUAGUAGGUUGUAUGGUU

• hairpin_fi_clean.fa : GNU nano 7.2 hairpin_fi_clean.fa >hsa-let-7a-1_MI0000060_Homo_sapiens_let-7a-1_stem-loop UGGGAUGAGGUAGUAGGUUGUAUAGUUUUAGGGUCACACCCACCACUGGGAGAUAACUAU

  hsa-let-7a-2_MI0000061_Homo_sapiens_let-7a-2_stem-loop AGGUUGAGGUAGUAGGUUGUAUAGUUUAGAAUUACAUCAAGGGAGAUAACUGUACAGCCU hsa-let-7a-3_MI0000062_Homo_sapiens_let-7a-3_stem-loop GGGUGAGGUAGUAGGUUGUAUAGUUUGGGGCUCUGCCCUGCUAUGGGAUAACUAUACAAU hsa-let-7b_MI0000063_Homo_sapiens_let-7b_stem-loop CGGGGUGAGGUAGUAGGUUGUGUGGUUUCAGGGCAGUGAUGUUGCCCCUCGGAAGAUAAC hsa-let-7c_MI0000064_Homo_sapiens_let-7c_stem-loop GCAUCCGGGUUGAGGUAGUAGGUUGUAUGGUUUAGAGUUACACCCUGGGAGUUAACUGUA hsa-let-7d_MI0000065_Homo_sapiens_let-7d_stem-loop CCUAGGAAGAGGUAGUAGGUUGCAUAGUUUUAGGGCAGGGAUUUUGCCCACAAGGAGGUA

• mature_pp_fi.fa : >ppa-mir-141_MI0002490 UGGCCGGCCCUGGGUCCAUCUUCCAGUACAGUGUUGGAUGGUCUAAUUGUGAAGCUCCUAACACUGUCUGGUAAAGAUGGCCCCCGGGUGGGUUC

  ppa-mir-15b_MI0002493 UUGAGGCCUUAAAGUACUGUAGCAGCACAUCAUGGUUUACAUGCUACAGUCAAGAUGCGAAUCAUUAUUUGCUGCUCUAGAAAUUUAAGGAAAUUCAU ppa-mir-23b_MI0002501 CUCAGGUGCUCUGGCUGCUUGGGUUCCUGGCAUGCUGAUUUGUGACUUAAGAUUAAAAUCACAUUGCCAGGGAUUACCACGCAACCACGACCUUGGC ppa-mir-30b_MI0002508 ACCAAGUUUCAGUUCAUGUAAACAUCCUACACUCAGCUGUAAUACAUGGAUUGGCUGGGAGGUGGAUGUUUACUUCAGCUGACUUGGA ppa-mir-125b_MI0002511 UGCGCUCCUCUCAGUCCCUGAGACCCUAACUUGUGAUGUUUACCGUUUAAAUCCACGGGUUAGGCUCUUGGGAGCUGCGAGUCGU ppa-mir-128_MI0002523 UGAGCUGUUGGAUUCGGGGCCGUAGCACUGUCUGAGAGGUUUACAUUUCUCACAGUGAACCGGUCUCUUUUUCAGCUGCUUC ppa-mir-130a_MI0002527 UGCUGCUGGCCAGAGCUCUUUUCACAUUGUGCUACUGUCUGCACCUGUCACUAGCAGUGCAAUGUUAAAAGGGCAUUGGCCGUGUAGUG ppa-mir-133a_MI0002530 ACAAUGCUUUGCUAGAGCUGGUAAAAUGGAACCAAAUCGCCUCUUCAAUGGAUUUGGUCCCCUUCAACCAGCUGUAGCUAUGCAUUGA ppa-mir-135-1_MI0002539 AGGCCUCGCUGUUCUCUAUGGCUUUUUAUUCCUAUGUGAUUCUACUGCUCACUCAUAUAGGGAUUGGAGCCGUGGCGCACGGCGGGGACG

[likhitha-surapaneni]

Hi @erickfabian0, hope you are having a good day. Is there a related problem with running or using VEP in particular?

[likhitha-surapaneni]

Hi @erickfabian0 , I am closing this issue for now. Please feel free to open a new issue if you are facing any issues.

Thank you.