# miRdeep 2 quantifier **URL:** \ **Category:** usegalaxy.org support\ **Tags:** troubleshooting\ **Created:** [September 25, 2023, 2:58pm UTC](https://help.galaxyproject.org/t/mirdeep-2-quantifier/10840 "2023-09-25T14:58:54Z")\ **Posts on this page:** 7\ **Page:** 1
**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 25, 2023, 2:58pm UTC](https://help.galaxyproject.org/t/mirdeep-2-quantifier/10840/1 "2023-09-25T14:58:54Z")
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 a screenshot of my files ![image](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/0/0c75c80623138bc1c8cb753aa0d3df690c15f642.png) ![image](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/f/fa8a6db7dfb5e7896f2278072ccc14b4225d2d50.png) ![image](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/1/17190cdc5817eb0f6cb872a4b33f8be6513f015c.png) Do I have to index these files 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, 4:17pm UTC](https://help.galaxyproject.org/t/mirdeep-2-quantifier/10840/2 "2023-09-25T16:17:51Z")
Hi @Sabrina_Napoletano Would you please share the data within the context of your Galaxy history? That will capture details of the run that will usually matter when troubleshooting. Meaning: the data, server, tool/version, parameters, command-string, logs. All of the related details about how all of those inputs were consumed by the tool at runtime with context leads to the best actionable help. How-to: [Troubleshooting errors](https://training.galaxyproject.org/training-material/faqs/galaxy/analysis_troubleshooting.html) ---
**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 26, 2023, 2:00pm UTC](https://help.galaxyproject.org/t/mirdeep-2-quantifier/10840/3 "2023-09-26T14:00:40Z")
Hi jennaj thank you for your reply, this is the output of my run ![image](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/5/5bd2fe23305aa96387709a1671431abf08183b32.png) these are the strings of the files I used for the history reads.fa ![image](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/0/0c75c80623138bc1c8cb753aa0d3df690c15f642.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/1/17190cdc5817eb0f6cb872a4b33f8be6513f015c.png) ---
**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 26, 2023, 4:53pm UTC](https://help.galaxyproject.org/t/mirdeep-2-quantifier/10840/4 "2023-09-26T16:53:30Z")
> [@Sabrina\_Napoletano](#): > > the run ends with an error which apparently lacks any suggestions on where the error is Your example doesn’t look like an error. Am I misunderstanding? ---
**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 27, 2023, 9:30am UTC](https://help.galaxyproject.org/t/mirdeep-2-quantifier/10840/5 "2023-09-27T09:30:52Z")
Hi, thank you for your reply, in other blogs I read that it could be there were mismatches between fasta identifiers in the provided miRNAs (precursors, star and mature) However they don’t suggest how solve this problem Do you have any suggestion? Thank you very much ---
**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 27, 2023, 4:43pm UTC](https://help.galaxyproject.org/t/mirdeep-2-quantifier/10840/6 "2023-09-27T16:43:37Z")
Hi @Sabrina_Napoletano You could still share your history, and we’ll help with a more detailed review. > [@jennaj](#): > > Would you please share the data within the context of your Galaxy history? That will capture details of the run that will usually matter when troubleshooting. Meaning: the data, server, tool/version, parameters, command-string, logs. All of the related details about how all of those inputs were consumed by the tool at runtime with context leads to the best actionable help. > > How-to: [Troubleshooting errors](https://training.galaxyproject.org/training-material/faqs/galaxy/analysis_troubleshooting.html) ---
**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:** [August 14, 2026, 7:28pm UTC](https://help.galaxyproject.org/t/mirdeep-2-quantifier/10840/7 "2026-08-14T19:28:23Z")
Closed on August 14, 2026, 7:28pm UTC