# \#unicycler **URL:** https://help.galaxyproject.org/tag/unicycler/76.md [Latest](https://help.galaxyproject.org/latest.md) · [Categories](https://help.galaxyproject.org/categories.md) · [Tags](https://help.galaxyproject.org/tags.md) --- ## [Unicycler: long runtime? Allow the job to complete to get results!](https://help.galaxyproject.org/t/unicycler-long-runtime-allow-the-job-to-complete-to-get-results/10592)
**Author:** [@Alan](https://help.galaxyproject.org/u/Alan)\ **Replies:** 8\ **Last updated:** [August 17, 2023, 2:19pm UTC](https://help.galaxyproject.org/t/unicycler-long-runtime-allow-the-job-to-complete-to-get-results/10592 "2023-08-17T14:19:00Z")
Hi everyone! I started a unicycler run two days ago (07/08/2023) on a set of 87 paired reads. Everything went fine (80 ok, 4 with errors) until yesterday morning when I noticed two jobs were running and 1 was waiting fo… --- ## [Unicycler hybrid assembly fail (personal and tutorial data)](https://help.galaxyproject.org/t/unicycler-hybrid-assembly-fail-personal-and-tutorial-data/9763)
**Author:** [@Joanna\_Colovas](https://help.galaxyproject.org/u/Joanna_Colovas)\ **Replies:** 3\ **Last updated:** [March 31, 2023, 5:41pm UTC](https://help.galaxyproject.org/t/unicycler-hybrid-assembly-fail-personal-and-tutorial-data/9763 "2023-03-31T17:41:07Z")
Hi all, I have been trying to work through the training tutorial for hybrid assembly using unicycler, and the tool continues to fail using both the tutorial data and personal data: Unicycler Assembly The error(s) displ… --- ## [SPAdes/Unicycler assembly failures -- Resolved](https://help.galaxyproject.org/t/spades-unicycler-assembly-failures-resolved/263)
**Author:** [@dmack33](https://help.galaxyproject.org/u/dmack33)\ **Replies:** 13\ **Last updated:** [February 10, 2023, 8:19pm UTC](https://help.galaxyproject.org/t/spades-unicycler-assembly-failures-resolved/263 "2023-02-10T20:19:05Z")
Hi, this is my first time reporting an issue, so I apologize if I overlook info, can’t format code correctly in this flavor of markdown, etc. I’ve submitted a bug report via the Galaxy server, but, at the risk of redund… --- ## [Problem with Uniclycler](https://help.galaxyproject.org/t/problem-with-uniclycler/8858)
**Author:** [@mlopezm](https://help.galaxyproject.org/u/mlopezm)\ **Replies:** 7\ **Last updated:** [February 10, 2023, 8:09pm UTC](https://help.galaxyproject.org/t/problem-with-uniclycler/8858 "2023-02-10T20:09:38Z")
I have tried to assemble paired reads (Illumina) with nanopore reads but I always obtain the same error: An error occurred with this dataset: format fasta database \[?\] cannot find ‘lr’ Could anyone help me with this? … --- ## [Unicycler is not working](https://help.galaxyproject.org/t/unicycler-is-not-working/8829)
**Author:** [@alanelena](https://help.galaxyproject.org/u/alanelena)\ **Replies:** 2\ **Last updated:** [February 10, 2023, 8:08pm UTC](https://help.galaxyproject.org/t/unicycler-is-not-working/8829 "2023-02-10T20:08:11Z")
Dear galaxy project members, I have been having a lot of problems running unicycler since at least a month now. I have reported every different bug that came across and I have exchanged a few emails with people from the… --- ## [SPAdes, Unicycler, and Trinity have transitioned to run on the new Bridges-2 supercomputer](https://help.galaxyproject.org/t/spades-unicycler-and-trinity-have-transitioned-to-run-on-the-new-bridges-2-supercomputer/5411)
**Author:** [@nate](https://help.galaxyproject.org/u/nate)\ **Replies:** 0\ **Last updated:** [February 17, 2021, 8:27pm UTC](https://help.galaxyproject.org/t/spades-unicycler-and-trinity-have-transitioned-to-run-on-the-new-bridges-2-supercomputer/5411 "2021-02-17T20:27:42Z")
The Bridges-2 Supercomputer at the Pittsburgh Supercomputing Center has recently transitioned into production status and replaced the older Bridges-1 supercomputer where Galaxy’s SPAdes, Unicycler, and Trinity tools prev… --- ## [Unicycler job not running](https://help.galaxyproject.org/t/unicycler-job-not-running/5257)
**Author:** [@mharpole](https://help.galaxyproject.org/u/mharpole)\ **Replies:** 4\ **Last updated:** [January 25, 2021, 4:32pm UTC](https://help.galaxyproject.org/t/unicycler-job-not-running/5257 "2021-01-25T16:32:28Z")
Hello, I submitted a job to unicycler over 24 hours ago to the main USA galaxy server and it is still grayed out waiting to run. How long does this typically take? I am prepping for a course I am teaching and I was goi… --- ## ["these should be of equal length" when inputting collections to Unicycler](https://help.galaxyproject.org/t/these-should-be-of-equal-length-when-inputting-collections-to-unicycler/5190)
**Author:** [@TKlingstrom](https://help.galaxyproject.org/u/TKlingstrom)\ **Replies:** 2\ **Last updated:** [January 15, 2021, 8:43pm UTC](https://help.galaxyproject.org/t/these-should-be-of-equal-length-when-inputting-collections-to-unicycler/5190 "2021-01-15T20:43:44Z")
I am running Unicycler and getting the message when I try to run a job where I got 9 paired files for my pair ended reads and 3 files with Pacbio data. “The server could not complete the request. Please contact the Gala… --- ## [My Unicycler is still waiting to run after three days](https://help.galaxyproject.org/t/my-unicycler-is-still-waiting-to-run-after-three-days/4975)
**Author:** [@Wan\_Adibah\_Zakaria](https://help.galaxyproject.org/u/Wan_Adibah_Zakaria)\ **Replies:** 1\ **Last updated:** [December 7, 2020, 10:25am UTC](https://help.galaxyproject.org/t/my-unicycler-is-still-waiting-to-run-after-three-days/4975 "2020-12-07T10:25:49Z")
Hi I run Unicycler analysis with my data since two days ago, but it is still in grey and waiting to run. I run bowtie analysis before and i did not remember it took this long in a queue. I am afraid if there is any prob… --- ## [How to generate Nanopore fastq collection files for Unicycler?](https://help.galaxyproject.org/t/how-to-generate-nanopore-fastq-collection-files-for-unicycler/2662)
**Author:** [@isrulik1](https://help.galaxyproject.org/u/isrulik1)\ **Replies:** 2\ **Last updated:** [December 20, 2019, 12:08pm UTC](https://help.galaxyproject.org/t/how-to-generate-nanopore-fastq-collection-files-for-unicycler/2662 "2019-12-20T12:08:11Z")
I was notice that collection files that were recognized by FastQC (for example) are not recognized by Unicycler. Thanks! Israel --- ## [Unicycler launched but still queued after 2 days](https://help.galaxyproject.org/t/unicycler-launched-but-still-queued-after-2-days/2641)
**Author:** [@vanina.guernier](https://help.galaxyproject.org/u/vanina.guernier)\ **Replies:** 5\ **Last updated:** [December 13, 2019, 5:48pm UTC](https://help.galaxyproject.org/t/unicycler-launched-but-still-queued-after-2-days/2641 "2019-12-13T17:48:45Z")
Hi, I launched a few assembly analyses with Unicycler on Monday and they are still queued (in grey). The ones I did last week took no more than 2 hours, so I’m starting to wonder if there is an issue here or a maintenan… --- ## [Unicycler and PCS Bridges cluster service on usegalaxy.org](https://help.galaxyproject.org/t/unicycler-and-pcs-bridges-cluster-service-on-usegalaxy-org/2342)
**Author:** [@agmcarthur](https://help.galaxyproject.org/u/agmcarthur)\ **Replies:** 2\ **Last updated:** [October 24, 2019, 12:41am UTC](https://help.galaxyproject.org/t/unicycler-and-pcs-bridges-cluster-service-on-usegalaxy-org/2342 "2019-10-24T00:41:56Z")
Hello, my Unicycler jobs at usegalaxy.org are stalled at “This job is waiting to run” for 12 hours. Looking through past issues, this may be a PCS Bridges issue. Any advice on getting these to run? admin-edit: Remove en… --- ## [Unicycler - hybrid assembly failure](https://help.galaxyproject.org/t/unicycler-hybrid-assembly-failure/1366)
**Author:** [@piotr-piotr-majewski](https://help.galaxyproject.org/u/piotr-piotr-majewski)\ **Replies:** 1\ **Last updated:** [May 25, 2019, 1:23am UTC](https://help.galaxyproject.org/t/unicycler-hybrid-assembly-failure/1366 "2019-05-25T01:23:41Z")
Dear All, I’ve recently encountered some issues with Unicycler assembly. I’ve tried to perform hybrid assembly with use of trimmed Illumina reads R1 (0.17 Gb) + R2 (0.16 Gb); format: fastqsanger.gz nanopore reads …