I want extracting my plasmid sequences from my WGS data. But it always ends with an error. please help me for it
Hi @Ghazal_Aziz
Please explain a bit more about the error and the server URL of where you are working. Sharing your history is one choice if you are not sure what is relevant.
here is the link for the history.
please see and suggest the issues in failed jobs
Hi @Ghazal_Aziz
Try to start troubleshooting by adjusting the tool form options to match your reads (pacbio).
How to find that view directly in the application is included in the first FAQ I linked. It includes all the inputs, parameters, and logs in a summary format. Sometimes easier to review than the tool rerun form.
These trainings will also help for your use case:
- Search GTN Materials query=quality
- Search GTN Materials query=assembly
no this one is not resolved yet.
note: this history is separate from the other one for which I have get results with no display. I have been facing both issues with different histories and data
OK, then you’ll need to share data about the problems, or we cannot offer advice.
Meaning, share both histories, note the datasets involved in each, along with your specific question for each.
You can do that in this topic since it seems to involve similar data/tools.
If you are following a tutorial for either, or have any insights about the data, include that too.
The more context you can provide the more other people can help. The FAQs I listed originally explain the kind of information generally needed for troubleshooting.
This is the history for the pacBio WGS sequence of E. faecium.
the plasmidSpades was successfully run in this history but with no results to display.
for the time being I am not following any tutorial but aimed to have plasmid sequence.
This is the history where i get failed for the plasmidSpades job
This data is a pacBio data for WGS of Clostridium. but in another database the sequence was seems to be E. faecium.
I’m reviewing both today, please leave these shared and avoid posting in other topics or creating new topics about these same issues until resolved here.
any update?
For both of the plasmidSpades jobs (both histories), the inputs are not of the correct type for the tool. Meaning, the long reads were input where the short reads are input.
You have only input pacbio reads. SPAdes claims to be able to assemble that data alone. Try inputting the data into the correct place on the form, and try again.
Keep in mind that using all default parameters is unlikely to produce great scientific results. The tool form links out to resources, or you can browse publications and related online resources for how others have used the tools.
You could also consider different tools. Unicycler is one choice I can think of off hand, but please don’t limit to that, instead please see https://training.galaxyproject.org/
Quote from the tool form:
Input
SPAdes takes as input paired-end reads, mate-pairs and single (unpaired) reads in FASTA and FASTQ. For IonTorrent data SPAdes also supports unpaired reads in unmapped BAM format (like the one produced by Torrent Server). However, in order to run read error correction, reads should be in FASTQ or BAM format. Sanger, Oxford Nanopore and PacBio CLR reads can be provided in both formats since SPAdes does not run error correction for these types of data.
To run SPAdes 3.15.3 you need at least one library of the following types:
- Illumina paired-end/high-quality mate-pairs/unpaired reads
- IonTorrent paired-end/high-quality mate-pairs/unpaired reads
- PacBio CCS reads
- Illumina and IonTorrent libraries should not be assembled together. All other types of input data are compatible. SPAdes should not be used if only PacBio CLR, Oxford Nanopore, Sanger reads or additional contigs are available.