# Nanopore data assembly with CANU **URL:** \ **Category:** usegalaxy.eu support\ **Tags:** galaxy-local, assembly\ **Created:** [March 26, 2019, 1:02pm UTC](https://help.galaxyproject.org/t/nanopore-data-assembly-with-canu/921 "2019-03-26T13:02:31Z")\ **Posts on this page:** 5\ **Page:** 1
**Author:** ![VLeducq](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/vleducq/32/685_2.png) [@VLeducq](https://help.galaxyproject.org/u/VLeducq)\ **Post date:** [March 26, 2019, 1:02pm UTC](https://help.galaxyproject.org/t/nanopore-data-assembly-with-canu/921/1 "2019-03-26T13:02:31Z")
Hello, I’m trying to run an assembly on Nanopore raw reads (fastq) with the Canu 1.7.1 assembler. I tried on different servers, with my data and with public nanopore data from EMBL-EBI. I’m getting an error message from the tool every time : “Fatal error: Exit code 1 ()”. Can someone tell me if the tool works or if it’s coming from me. Thank you ---
**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:** [April 19, 2019, 8:43pm UTC](https://help.galaxyproject.org/t/nanopore-data-assembly-with-canu/921/2 "2019-04-19T20:43:31Z")
Hi - Not sure if you worked the usage out or not yet, but I just tested the tool with some sample data from the tool author and everything processed fine at Galaxy EU [https://usegalaxy.eu](https://usegalaxy.eu). Shared history: [https://usegalaxy.eu/u/jenj/h/test-canu-nanopore-fastq](https://usegalaxy.eu/u/jenj/h/test-canu-nanopore-fastq) Expand the history annotation to see where I got the datasets and example command-line options. For the test jobs, I mapped over the command-line options to the tool form options without any other changes. Hope that helps! _Admin edit 7/6/2019: Corrected shared history link name URL “name” (active URL was ok) but did need to reset history share status._ ---
**Author:** ![michele.dellab](https://avatars.discourse-cdn.com/v4/letter/m/7ab992/32.png) [@michele.dellab](https://help.galaxyproject.org/u/michele.dellab)\ **Post date:** [July 5, 2019, 5:06pm UTC](https://help.galaxyproject.org/t/nanopore-data-assembly-with-canu/921/3 "2019-07-05T17:06:39Z")
Hello, I recently tried to run an assembly with CANU on Minion trimmed reads (trimmed with Porechop). I had three different dataset, 1 small dataset (~30.000 reads) and two bigger datasets. The small dataset ran successfully. For the second dataset I got an error after about 30 hours “Fatal error: Exit code 1 ()” The third dataset is still running, after 1 week… ---
**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:** [July 6, 2019, 1:54am UTC](https://help.galaxyproject.org/t/nanopore-data-assembly-with-canu/921/4 "2019-07-06T01:54:04Z")
Pinging the administrators of the Galaxy EU server. Please be patient for a reply as they are hosting the annual [GCC conference](https://galaxyproject.org/events/gcc2019/) right now. @hexylena @bjoern.gruening Also, I reset the share status for the history in my original reply, although I do not think it will help for your specific problem given the error description. ---
**Author:** ![bjoern.gruening](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/bjoern.gruening/32/10_2.png) [@bjoern.gruening](https://help.galaxyproject.org/u/bjoern.gruening)\ **Post date:** [July 11, 2019, 12:09pm UTC](https://help.galaxyproject.org/t/nanopore-data-assembly-with-canu/921/5 "2019-07-11T12:09:59Z")
@michele.dellab can you send me an error report from Galaxy on the [usgalaxy.eu](http://usgalaxy.eu) instance. I need more information to debug this. Thanks!