# An issue with application of SPAdes genome assembly in Galaxy

**URL:** <https://help.galaxyproject.org/t/an-issue-with-application-of-spades-genome-assembly-in-galaxy/7049>\
**Category:** Uncategorized\
**Tags:** rnaspades\
**Created:** [November 18, 2021, 8:41pm UTC](https://help.galaxyproject.org/t/an-issue-with-application-of-spades-genome-assembly-in-galaxy/7049 "2021-11-18T20:41:04Z")\
**Posts on this page:** 6\
**Page:** 1

<div class="post-metadata">

**Author:** ![Adnan](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/adnan/32/653_2.png) [@Adnan](https://help.galaxyproject.org/u/Adnan)\
**Post date:** [November 18, 2021, 8:41pm UTC](https://help.galaxyproject.org/t/an-issue-with-application-of-spades-genome-assembly-in-galaxy/7049/1 "2021-11-18T20:41:04Z")

</div>

Dear Colleagues, I would like to let you know that I am a new user in the Galaxy Platform. I have tried several time to operate the SPAdes genome assembly. However, I have kept facing an error ( _SPAdes on data 8 and data 7: contig stats Command line: /ocean/projects/mcb140028p/xcgalaxy/conda/envs/\_\_spades@3.12.0/bin/spades.py -o /ocean/projects/mcb140028p/xcgalaxy/main/staging/39113298/working --disable-gzip-output --careful -t 24 -m 62 -k 117,121,127 --pe1-fr --pe1-1 fastq.gz:/ocean/pr An error occurred with this dataset Command line: /ocean/projects/mcb140028p/xcgalaxy/conda/envs/\_\_spades@3.12.0/bin/spades.py -o /ocean/projects/mcb140028p/xcgalaxy/main/staging/39113298/working --disable-gzip-output --careful -t 24 -m 62 -k 117,121,127 --pe1-fr --pe1-1 fastq.gz:/ocean/pr_). Please any help to overcome this issue. Adnan

---

<div class="post-metadata">

**Author:** ![gallardoalba](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/gallardoalba/32/1903_2.png) [@gallardoalba](https://help.galaxyproject.org/u/gallardoalba)\
**Post date:** [November 19, 2021, 10:20am UTC](https://help.galaxyproject.org/t/an-issue-with-application-of-spades-genome-assembly-in-galaxy/7049/2 "2021-11-19T10:20:49Z")

</div>

Hi @Adnan,  
could you send an error report? You can do it by clicking in the bug icon.

Regards

---

<div class="post-metadata">

**Author:** ![Adnan](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/adnan/32/653_2.png) [@Adnan](https://help.galaxyproject.org/u/Adnan)\
**Post date:** [November 19, 2021, 7:13pm UTC](https://help.galaxyproject.org/t/an-issue-with-application-of-spades-genome-assembly-in-galaxy/7049/3 "2021-11-19T19:13:34Z")

</div>

> [@Adnan](#):
>
> Dear Colleagues, I would like to let you know that I am a new user in the Galaxy Platform. I have tried several time to operate the SPAdes genome assembly. However, I have kept facing an error

Thanks I sent an email about the error report

---

<div class="post-metadata">

**Author:** ![gallardoalba](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/gallardoalba/32/1903_2.png) [@gallardoalba](https://help.galaxyproject.org/u/gallardoalba)\
**Post date:** [November 22, 2021, 10:51am UTC](https://help.galaxyproject.org/t/an-issue-with-application-of-spades-genome-assembly-in-galaxy/7049/4 "2021-11-22T10:51:58Z")

</div>

Hi @Adnan,  
I reviewed your report; according to that, your datasets correspond to RNA-seq data, isn’t it? So probably this tool doesn’t fit with your analysis. If you are trying to assembly the transcriptome, I suggest you use [Trinity](https://usegalaxy.org/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/trinity/trinity/2.9.1+galaxy1).

Regards

---

<div class="post-metadata">

**Author:** ![Adnan](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/adnan/32/653_2.png) [@Adnan](https://help.galaxyproject.org/u/Adnan)\
**Post date:** [November 22, 2021, 6:45pm UTC](https://help.galaxyproject.org/t/an-issue-with-application-of-spades-genome-assembly-in-galaxy/7049/5 "2021-11-22T18:45:25Z")

</div>

Hi [gallardoalba](https://help.galaxyproject.org/u/gallardoalba),  
Thanks for your response and indeed the data is RNA seq. Thans for your suggestion.  
Regards

‫في الاثنين، 22 نوفمبر 2021 في 2:17 م تمت كتابة ما يلي بواسطة ‪Cristóbal Gallardo via Galaxy Community Help‬‏ \<‪[galaxy@discoursemail.com](mailto:galaxy@discoursemail.com)‬‏\>:‬

---

<div class="post-metadata">

**Author:** ![gallardoalba](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/gallardoalba/32/1903_2.png) [@gallardoalba](https://help.galaxyproject.org/u/gallardoalba)\
**Post date:** [November 22, 2021, 9:36pm UTC](https://help.galaxyproject.org/t/an-issue-with-application-of-spades-genome-assembly-in-galaxy/7049/6 "2021-11-22T21:36:43Z")

</div>

Also rnaSPADES can fit your requirements: [rnaSPADES](https://usegalaxy.org/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/rnaspades/rnaspades/3.9.0.2).

Regards