An issue with application of SPAdes genome assembly in Galaxy

1

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

2

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

Regards

3

Thanks I sent an email about the error report

4

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.

Regards

5

Hi 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>:‬

6

Also rnaSPADES can fit your requirements: rnaSPADES.

Regards