Hi, I am trying to remove the adapters from my sequences by performing Cutadapt paired-end but it doesn’t work anymore. In the past for similar files it did. I think it’s the problem with fastqsanger.gz format, but when I edit my dataset and in Datatypes I set up a new data type for fastq.gz, which is recommended for cutadapt, it doesn’t work anyway. Some suggestions for another way to change the input format? Or any clues what else can be the reason that it doesn’t work?
Thanks,
That doesn’t sound good for sure!
Have you submitted a bug report to the Galaxy Europe bug tracker yet?
Or in case there’s no job error, can you share the link to a history so that we can investigate?
Hi @EsteraJ , hi @wm75
I successfully completed Cutadapter job on PE data in Europe.
@EsteraJ, are you sure the files are compressed? Have you changed datatype for the input files? What is the log files say? To see the log files, click at info (i icon) and check the standard output and the standard error log files in the middle window.
Kind regards,
Igor
Hi,
@igor : So it shows me Fatal error: compression level should be between 0 and 3, but I have compressed reads. Additionally, yesterday I tried from curosity run the job on Galaxy.org, and there with exactly same samples and command it worked immediately…
@wm75 I just reported an error as you suggested
Now I think I will simply continue with my samples on Galaxy.org, I don’t know why it doesn’t work for me on Galaxy.eu…
Thanks you both for your help!
Best,
Estera
@EsteraJ thanks for submitting the bug report.
That compression level complaint is rather clear indeed.
The problem is that you have run version 4.0+galaxy1 of the tool on Galaxy Europe. If I rerun the exact same job with the latest version it also just works fine.
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