# bowtie2 fatal error message **URL:** \ **Category:** usegalaxy.org support\ **Tags:** fastq-format\ **Created:** [September 11, 2019, 2:34pm UTC](https://help.galaxyproject.org/t/bowtie2-fatal-error-message/2091 "2019-09-11T14:34:44Z")\ **Posts on this page:** 5\ **Page:** 1
**Author:** ![Michel](https://avatars.discourse-cdn.com/v4/letter/m/ea666f/32.png) [@Michel](https://help.galaxyproject.org/u/Michel)\ **Post date:** [September 11, 2019, 2:34pm UTC](https://help.galaxyproject.org/t/bowtie2-fatal-error-message/2091/1 "2019-09-11T14:34:44Z")
Good morning, I am running a ChIP-Seq (pair-end) analysis for the first time and managed to find a good pipeline to follow. The pipeline is described in the following way FASTQC - TRIMMOMATIC - FASTQC - BOWTIE2 - MACS2 callpeak - MACS2 bdgdiff - HOMER Peak annotation and motif discovery My have managed to analyze my data with no problems up to the TRIMMOMATIC and the following FASTQC. However, when i run the BOWTIE2 (pair-end) with my data from the trimmomatic, the analysis is interrupted and gives me the folloring error message: ## Dataset Error An error occurred while running the tool **toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.2**. ### Error Details Execution resulted in the following messages: Fatal error: Exit code 1 () As i am new to this, i don’t really know where the problem lies. I have tried to search for help on Biostars but couldn’t find anything conclusive for my analysis. Would anyone have a possible solution/advice on how to solve this problem? Thank you very much in advance for all time and effort invested in my request Michel ---
**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 12, 2019, 2:33pm UTC](https://help.galaxyproject.org/t/bowtie2-fatal-error-message/2091/2 "2019-09-12T14:33:31Z")
Hi @Michel This error usually means that there is some problem with the fastq inputs. This prior Q&A includes links that can help (is here at Galaxy Help): [Fatal error: exit code 1 () using bowtie2](https://help.galaxyproject.org/t/fatal-error-exit-code-1-using-bowtie2/267) Please review your data/work for format issues first, then let us know if you need more help. Thanks, Jen ---
**Author:** ![Michel](https://avatars.discourse-cdn.com/v4/letter/m/ea666f/32.png) [@Michel](https://help.galaxyproject.org/u/Michel)\ **Post date:** [September 12, 2019, 6:16pm UTC](https://help.galaxyproject.org/t/bowtie2-fatal-error-message/2091/3 "2019-09-12T18:16:15Z")
Hello Jen, Thank you very much for your reply. I checked the initial files and ran bowtie2 on those (so not trimmed). The bowtie2 worked and gave me the following results: 86172044 reads; of these: 86172044 (100.00%) were paired; of these: 53820433 (62.46%) aligned concordantly 0 times 24592530 (28.54%) aligned concordantly exactly 1 time 7759081 (9.00%) aligned concordantly \>1 times ---- 53820433 pairs aligned concordantly 0 times; of these: 70903 (0.13%) aligned discordantly 1 time ---- 53749530 pairs aligned 0 times concordantly or discordantly; of these: 107499060 mates make up the pairs; of these: 106304905 (98.89%) aligned 0 times 628764 (0.58%) aligned exactly 1 time 565391 (0.53%) aligned \>1 times 38.32% overall alignment rate The overall alignment rates are quite low. Maybe because the data is not trimmed though. However, when i run bowtie 2 on the trimmed data i get again the same error report as previously reported. How do i verify proper formatting during the trimming so that bowtie would work on the trimmed dataset. Thank you very much for your help Michel ---
**Author:** ![Michel](https://avatars.discourse-cdn.com/v4/letter/m/ea666f/32.png) [@Michel](https://help.galaxyproject.org/u/Michel)\ **Post date:** [September 12, 2019, 6:16pm UTC](https://help.galaxyproject.org/t/bowtie2-fatal-error-message/2091/4 "2019-09-12T18:16:58Z")
Hello Jen, Thank you very much for your reply. I checked the initial files and ran bowtie2 on those (so not trimmed). The bowtie2 worked and gave me the following results: ## 86172044 reads; of these: 86172044 (100.00%) were paired; of these: 53820433 (62.46%) aligned concordantly 0 times 24592530 (28.54%) aligned concordantly exactly 1 time 7759081 (9.00%) aligned concordantly \>1 times ## 53820433 pairs aligned concordantly 0 times; of these: 70903 (0.13%) aligned discordantly 1 time 53749530 pairs aligned 0 times concordantly or discordantly; of these: 107499060 mates make up the pairs; of these: 106304905 (98.89%) aligned 0 times 628764 (0.58%) aligned exactly 1 time 565391 (0.53%) aligned \>1 times 38.32% overall alignment rate The overall alignment rates are quite low. Maybe because the data is not trimmed though. However, when i run bowtie 2 on the trimmed data i get again the same error report as previously reported. How do i verify proper formatting during the trimming so that bowtie would on the trimmed dataset. Thank you very much for your help Michel ---
**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 12, 2019, 6:38pm UTC](https://help.galaxyproject.org/t/bowtie2-fatal-error-message/2091/5 "2019-09-12T18:38:32Z")
Hi @Michel You are working at Galaxy Main [https://usegalaxy.org](https://usegalaxy.org), correct? If so, please send in a bug report from the `Bowtie2` error dataset and include in the comments a link to this Galaxy Help post so we can associate the two. Please be sure to leave all input datasets for the complete analysis _undeleted_. If you are using a workflow, create a share link to that and also include it in the comments of your bug report submission. We can follow up directly via email about the specifics of your analysis, then post anything that would be of general use to others back to the forum (but nothing that would include your actual data – that will remain private). Whenever this error comes up, there is almost always some input problem/mixup. It could be the how the data was entered on the tool form, the reads themselves (content or format), or a custom genome content/format issue, or a problem with some other incorporated input (example: mismatched reference annotation). Reviewing your work will help to isolate and offer advice to fix whatever is going wrong. Thanks and I’ll watch for your bug submission (click on the green “bug” icon in the expanded red error dataset, enter comments, and submit). Some tools create multiple outputs, but you can send in the bug report from any of those (just one is enough).