# paired-end histogram failure **URL:** \ **Category:** usegalaxy.org support\ **Tags:** custom-genome, igv, dropbox, picard\_markduplicates\ **Created:** [December 11, 2023, 2:26am UTC](https://help.galaxyproject.org/t/paired-end-histogram-failure/11293 "2023-12-11T02:26:08Z")\ **Posts on this page:** 5\ **Page:** 1
**Author:** ![michele\_palermo](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/michele_palermo/32/4753_2.png) [@michele\_palermo](https://help.galaxyproject.org/u/michele_palermo)\ **Post date:** [December 11, 2023, 2:26am UTC](https://help.galaxyproject.org/t/paired-end-histogram-failure/11293/1 "2023-12-11T02:26:08Z")
I have a project due for class and keep getting an error at the paired-end histogram step. I have asked the professor but he does not know what is wrong or how to help. Any ideas of what the error means and how I can fix it ? This is the instructions - Mapp the cutadapt output to the reference genome using **Bowtie2** - The genome and gene annotations are in the “_Sp5.0 Mapping Test_” History that I already shared with you, and also posted in the shared DropBox folder IGV\_Sp5\_Genome\_links.txt - If you mapped to the whole genome, great! Otherwise, Map the reads to **Sp5.0\_Chromosome\_NW\_022145615.1.fa** as if it was the entire genome. The chromosome and its corresponding index are also located in the DropBox folder. - Filter duplicate reads with **MarkDuplicates** - _ **Visualize and analyze** _ the distribution of read lengths with the tool **Paired-end histogram\*\*\*\*Peak call and visualization of normalized data** This is the error An error occurred with this dataset: format tabular database [papHam1](https://usegalaxy.org/datasets/f9cad7b01a4721350088c59ca11ec297/preview#) Picked up \_JAVA\_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/054/233/54233597/tmp -Xmx2488m -Xms256m Exception in thread “main” htsjdk.samtools.SAMFormatException: SAM validation error: ERROR: Record 941707, Read name LH00401:11:GW231120000:5:1105:14959: ---
**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:** [December 11, 2023, 6:53pm UTC](https://help.galaxyproject.org/t/paired-end-histogram-failure/11293/2 "2023-12-11T18:53:59Z")
> [@michele\_palermo](#): > > **database papHam1** Hi @michele_palermo That part of the log is reporting the target reference genome. The Baboon genome is the default for runs that use a native index on the server. It sounds like you want to map against a custom reference genome instead. To do that, adjust the settings for the target genome then select your fasta from the history. Or, if you actually want to use a native index, you’ll need to choose the correct option on the form. Hope that helps! ---
**Author:** ![michele\_palermo](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/michele_palermo/32/4753_2.png) [@michele\_palermo](https://help.galaxyproject.org/u/michele_palermo)\ **Post date:** [December 12, 2023, 2:26am UTC](https://help.galaxyproject.org/t/paired-end-histogram-failure/11293/3 "2023-12-12T02:26:20Z")
I just looked but paired-end histogram does not give you the option to pick a genome reference this is for urchin. It only allows you to put an upper and lower bp limit. ![aya](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/3/34a2651c5c1ec62892692a45ac3c62a8fce7a419.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:** [December 12, 2023, 5:54pm UTC](https://help.galaxyproject.org/t/paired-end-histogram-failure/11293/4 "2023-12-12T17:54:25Z")
Hi @michele_palermo I was probably unclear … but what you want to do is back up to the prior mapping step. It looks like you mapped against the wrong genome. To review what was done: click on the “i” icon for the BAM output of Bowtie2 and you’ll likely spot the problem in the summary table. ---
**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:** [March 17, 2026, 5:55am UTC](https://help.galaxyproject.org/t/paired-end-histogram-failure/11293/5 "2026-03-17T05:55:30Z")