# Error quantifier module of MirDeep2 **URL:** \ **Category:** usegalaxy.eu support\ **Tags:** troubleshooting\ **Created:** [June 24, 2020, 8:00am UTC](https://help.galaxyproject.org/t/error-quantifier-module-of-mirdeep2/3973 "2020-06-24T08:00:16Z")\ **Posts on this page:** 7\ **Page:** 1
**Author:** ![luca](https://avatars.discourse-cdn.com/v4/letter/l/51bf81/32.png) [@luca](https://help.galaxyproject.org/u/luca)\ **Post date:** [June 24, 2020, 8:00am UTC](https://help.galaxyproject.org/t/error-quantifier-module-of-mirdeep2/3973/1 "2020-06-24T08:00:16Z")
Hi there, I am trying to run the second step of quantification (i.e. quantifier) following the mapper module of mirDeep2. In the mapping step everything is fine and I get the _collapsed reads_ to be given to the quantifier module. Then, when trying to run the quantifier module, providing mature, precursor and star sequences, the run ends with an error which apparently lacks any suggestions on where the error is. Here the error: > Fatal error: Exit code 1 () > Tool generated the following standard error: > > getting samples and corresponding read numbers > > Converting input files > building bowtie index > mapping mature sequences against index > mapping read sequences against index > Mapping statistics > > #desc total mapped unmapped %mapped %unmapped > total: 12382657 343630 12039027 0.028 0.972 > seq: 12382657 343630 12039027 0.028 0.972 > mapping star sequences against index > analyzing data > Expressed miRNAs are written to expression\_analyses/expression\_analyses\_galaxy/miRNA\_expressed.csv > not expressed miRNAs are written to expression\_analyses/expression\_analyses\_galaxy/miRNA\_not\_expressed.csv > > Creating miRBase.mrd file > > make\_html2.pl -q expression\_analyses/expression\_analyses\_galaxy/miRBase.mrd -k dataset\_21574970.dat -y galaxy -o -i expression\_analyses/expression\_analyses\_galaxy/dataset\_21574970.dat\_mapped.arf -j expression\_analyses/expression\_analyses\_galaxy/dataset\_21574968.dat\_mapped.arf -l -M miRNAs\_expressed\_all\_samples\_galaxy.csv > miRNAs\_expressed\_all\_samples\_galaxy.csv file with miRNA expression values > parsing miRBase.mrd file finished > creating PDF files Any clues on what’s going on here? I see a lot of unmapped sequences but this is somewhat expected from a biological point of view as the miRNA fraction is not usually the most abundant in the tissue I am investigating (zebrafish gonads) Thanks Luca ---
**Author:** ![luca](https://avatars.discourse-cdn.com/v4/letter/l/51bf81/32.png) [@luca](https://help.galaxyproject.org/u/luca)\ **Post date:** [June 26, 2020, 9:58am UTC](https://help.galaxyproject.org/t/error-quantifier-module-of-mirdeep2/3973/2 "2020-06-26T09:58:32Z")
Found out, there were mismatches between fasta identifiers in the provided miRNAs (precursors, star and mature) ---
**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\ **Post date:** [June 26, 2020, 4:12pm UTC](https://help.galaxyproject.org/t/error-quantifier-module-of-mirdeep2/3973/3 "2020-06-26T16:12:14Z")
Thanks for posting back @luca and very glad you found the problem 🙂 FAQ for others that may run into the same root issue (across tools). [Mismatched Chromosome identifiers (and how to avoid them)](https://galaxyproject.org/support/chrom-identifiers/) There are many ways to compare data to ensure consistent identifier naming across inputs, but some hints to get started often help. Tools can error in various ways with mismatched inputs – or sometimes not error at all and just produce odd results. ---
**Author:** ![Bisma\_Ishtiaq](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/bisma_ishtiaq/32/4002_2.png) [@Bisma\_Ishtiaq](https://help.galaxyproject.org/u/Bisma_Ishtiaq)\ **Post date:** [February 13, 2023, 8:11am UTC](https://help.galaxyproject.org/t/error-quantifier-module-of-mirdeep2/3973/4 "2023-02-13T08:11:58Z")
Hey can you tell how did you found about the mismatches and how did you resolved the issue ---
**Author:** ![Sabrina\_Napoletano](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/sabrina_napoletano/32/4724_2.png) [@Sabrina\_Napoletano](https://help.galaxyproject.org/u/Sabrina_Napoletano)\ **Post date:** [September 23, 2023, 12:27pm UTC](https://help.galaxyproject.org/t/error-quantifier-module-of-mirdeep2/3973/5 "2023-09-23T12:27:36Z")
Hi, I have this same problem with quantifier but I can’t solve it. Could you help me how index the following files reads.fa ![image](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/7/717b45cc28aa755aa2e3a3cb36f40e3783e50cf4.png) hairpin.fa ![image](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/f/fa8a6db7dfb5e7896f2278072ccc14b4225d2d50.png) mature.fa ![image](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/3/3f6261d74a45d6fd11b6f95deaf0b7720bfda200.png) Do I have to index these ile in bowtie? I hope you can help me ---
**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\ **Post date:** [September 25, 2023, 4:07pm UTC](https://help.galaxyproject.org/t/error-quantifier-module-of-mirdeep2/3973/6 "2023-09-25T16:07:40Z")
Let’s keep your new question in the other thread, and close this old topic out. Thanks! [miRdeep 2 quantifier](https://help.galaxyproject.org/t/mirdeep-2-quantifier/10840) ---
**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\ **Post date:** [September 25, 2023, 4:07pm UTC](https://help.galaxyproject.org/t/error-quantifier-module-of-mirdeep2/3973/7 "2023-09-25T16:07:47Z")
Closed on September 25, 2023, 4:07pm UTC