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mrmckain / Fast-Plast

Automated de novo assembly of whole chloroplast genomes.
MIT License
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no result found. #58

Open karthickbrlab opened 1 year ago

karthickbrlab commented 1 year ago

I used 2GB data of illumina reads.

the assembly resulted in all folders. but mapping is only completed, spades and fininshed assembly folders are empty.

Sample: deru Fast-Plast Version: Fast-Plast v.1.2.9 Total Cleaned Pair-End Reads: 22038830 Total Cleaned Single End Reads: 873034 Total Concordantly Mapped Reads: 19034802 Total Non-concordantly Mapped Reads: 790019

mrmckain commented 1 year ago

Please provide more information. There are log, error, and output files that help to describe what is going on. If you can send those along, it should help diagnose the problem.

Best, Michael

karthickbrlab commented 1 year ago

hi

HERE I ATTACH THE ERROR.LOG FILES AND PROGRESS.LOG FILES de_ru_Fast-Plast_Progress.log

de_ru_results_error.log

de_ru_results_out.log

karthickbrlab commented 1 year ago

hi michael. any updates?

mrmckain commented 1 year ago

From what I can see, there is an error with SPAdes.

1) Are your mapped reads files empty or are there reads?

2) Try running your SPAdes installation alone to see if it works. If you look at the output files, you can see that SPAdes is not able to find a component. I am wondering if it that SPAdes was is not properly installed. Perhaps your system is missing a module/requirement for SPAdes.

Best, Michael

RachelxGray commented 7 months ago

Hi, I am having the same issues as reported here and my log files report the same issues, where there are 0 contigs produced. Was there a solution to this? Thanks for your help.

mrmckain commented 7 months ago

Hi Rachel,

Can you send the log and error files? I will take a look.

Best, Michael

RachelxGray commented 7 months ago

Thank you - these are the errors. CHLORO_ILLUMINA_Fast-Plast_Progress.log CHLORO_ILLUMINA_results_error.log CHLORO_ILLUMINA_results_out.log

mrmckain commented 7 months ago

What version of Python are you running?

RachelxGray commented 7 months ago

the python version is python 3.10.13!

mrmckain commented 7 months ago

I just updated the SPAdes version in the installer. There was a SPAdes error at some point that looked a lot like that problem. You could either do a clean Fast-Plast install or install the new SPAdes directly (https://github.com/ablab/spades/releases/download/v3.15.5/SPAdes-3.15.5-Linux.tar.gz) and change the path to SPAdes at the beginning of the fast-plast.pl script.

Let me know if this works.

Best, Michael

RachelxGray commented 7 months ago

Thank you for your help Michael, updating spades has worked!

Thanks again, Rachel

mrmckain commented 7 months ago

Glad to hear that!

Best, Michael