# HISAT2 - Could not display BAM file **URL:** \ **Category:** Uncategorized\ **Tags:** fastq-format\ **Created:** [October 18, 2019, 10:20am UTC](https://help.galaxyproject.org/t/hisat2-could-not-display-bam-file/2303 "2019-10-18T10:20:01Z")\ **Posts on this page:** 7\ **Page:** 1
**Author:** ![artem](https://avatars.discourse-cdn.com/v4/letter/a/f0a364/32.png) [@artem](https://help.galaxyproject.org/u/artem)\ **Post date:** [October 18, 2019, 10:20am UTC](https://help.galaxyproject.org/t/hisat2-could-not-display-bam-file/2303/1 "2019-10-18T10:20:02Z")
Hello! I have local Galaxy installed. Also I used Data Manager for creating indexes. - Galaxy - 19.05 - HISAT2 - 2.1.0+galaxy5 I have just tried to run Hisat2 on [usegalaxy.org](http://usegalaxy.org) with one of my files and it run successfully. I uploaded this file to galaxy: > [http://212.150.245.226/~mali/Galaxy/RNA\_seq/a1.fastq](http://212.150.245.226/~mali/Galaxy/RNA_seq/a1.fastq) Then I run HISAT2 using this file as input (single end) fastq and hg38 as index , that’s all, very simple In [usegalaxy.org](http://usegalaxy.org) it works, in local galaxy it runs forever… I don’t have any error, just eternal job. This only one thing that I can found this message: > Could not display BAM file, error was: > file has no sequences defined (mode=‘rb’) - is it SAM/BAM format? Consider opening with check\_sq=False Also I try the same run in console and notice the same behavior. ---
**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:** [October 18, 2019, 8:07pm UTC](https://help.galaxyproject.org/t/hisat2-could-not-display-bam-file/2303/2 "2019-10-18T20:07:17Z")
Welcome @artem It seems that your computer is running out of resources when running the mapping job locally. Tools use about the same resources whether run line-command or in Galaxy. The `hg38` database is very large, and your input fastq data may be large, too. Make sure that you set up your local properly to work with large data. Instructions/tutorials for configuration can be found at: - [https://getgalaxy.org](https://getgalaxy.org) – then follow the links to the basics [https://galaxyproject.org/admin/get-galaxy/#configure-for-production](https://galaxyproject.org/admin/get-galaxy/#configure-for-production) - [https://github.com/galaxyproject/dagobah-training](https://github.com/galaxyproject/dagobah-training) – largest/current overview tutorials, but there are other current branches (gcc-2019) [https://github.com/galaxyproject/dagobah-training/tree/2019-pennstate](https://github.com/galaxyproject/dagobah-training/tree/2019-pennstate) I’ll also ping the developers at Gitter to see if they can tell what else might be going wrong. Feel free to join in the conversation. They may reply here or there: [https://gitter.im/galaxyproject/Lobby?at=5daa1be5e3646f24c74d65ea](https://gitter.im/galaxyproject/Lobby?at=5daa1be5e3646f24c74d65ea) Thanks! ---
**Author:** ![artem](https://avatars.discourse-cdn.com/v4/letter/a/f0a364/32.png) [@artem](https://help.galaxyproject.org/u/artem)\ **Post date:** [October 20, 2019, 4:29pm UTC](https://help.galaxyproject.org/t/hisat2-could-not-display-bam-file/2303/3 "2019-10-20T16:29:37Z")
@jennaj Thanks for your answer! Right now I use AWS instance t3.2xlarge (8 CPU and 32Gb RAM), HISAT2 job has been started more then 4 hours ago, but any result. Also don’t see any errors or etc. Maybe I missed something, I’m a technical specialist, and unfortunately I do not understand the intricacies of Galaxy. Thanks! ---
**Author:** ![artem](https://avatars.discourse-cdn.com/v4/letter/a/f0a364/32.png) [@artem](https://help.galaxyproject.org/u/artem)\ **Post date:** [October 21, 2019, 1:03pm UTC](https://help.galaxyproject.org/t/hisat2-could-not-display-bam-file/2303/4 "2019-10-21T13:03:28Z")
I have modified file “ **job\_conf.xml** ”, add “local\_slots” option. And noticing, that hisat2 running with “ **-p 8** ” option, but only one processor is utilizing and not use RAM. I have waiting 24h, but HISAT2 job not finished. ---
**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:** [October 21, 2019, 4:16pm UTC](https://help.galaxyproject.org/t/hisat2-could-not-display-bam-file/2303/5 "2019-10-21T16:16:01Z")
Thanks for the clarification about your Galaxy, @artem So you have tested in both a GVL cloud Galaxy instance and a `19.05` local version of Galaxy, same problem (job errors)? But the same job works at the public Galaxy server [https://usegalaxy.org](https://usegalaxy.org)? One of these could be going wrong: 1. The genome was not fully indexed. Any genome should have Data Managers run in this order: [Indexing reference genomes with Data Managers: Resources, tutorials, troubleshooting](https://help.galaxyproject.org/t/indexing-reference-genomes-with-data-managers-resources-tutorials-troubleshooting/1223/2). The cloud version of Galaxy would have this genome already indexed. In a local Galaxy, you’ll need to do the indexing. 2. Your data is in `fastqsanger` format and the first read has an exact human genome match (hg19, hg38), so the problem doesn’t seem to be with either of those – unless you manually assigned the datatype to be `fastqsanger.gz` (compressed fastq). When the assigned datatype is a mismatch for the actual data content, errors are produced. FAQs: [https://galaxyproject.org/support/](https://galaxyproject.org/support/) - [How to format fastq data for tools that require .fastqsanger format?](https://galaxyproject.org/support/fastqsanger/) - [Understanding compressed fastq data (fastq.gz)](https://galaxyproject.org/support/compressed-fastq/) - [Common datatypes explained](https://galaxyproject.org/learn/datatypes/) Thanks! ---
**Author:** ![artem](https://avatars.discourse-cdn.com/v4/letter/a/f0a364/32.png) [@artem](https://help.galaxyproject.org/u/artem)\ **Post date:** [October 21, 2019, 5:21pm UTC](https://help.galaxyproject.org/t/hisat2-could-not-display-bam-file/2303/6 "2019-10-21T17:21:08Z")
Thanks for the answer! Indeed, I checked the hisat2 index files, and noticed that there were not enough files, although the Hisat2 index was successful (via Data Manager). I recreated the index and it worked, thanks !!! ---
**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:** [October 24, 2019, 12:09am UTC](https://help.galaxyproject.org/t/hisat2-could-not-display-bam-file/2303/7 "2019-10-24T00:09:03Z")
Super, glad this is working for you now, and appreciate the feedback 🙂