make.contigs/16S Microbial Analysis with Mothur

hello, I have loaded my sequences in galaxy because I want to do 16S Microbial Analysis with Mothur, and in the step of make.contings, the files are not created, a message that says “This job is currently running” appears, many hours have passed but Many, I do not know if I’m doing something wrong or it’s normal, could you help me please?

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Which Galaxy server are you using? In general bioinformatic tools can run a long long time, even days. This is dependent on the tool in question, the size of the input data size and how busy the server is. So I wouldn’t worry and wait a little bit longer.

You also might want to have a look at our training material about 16S analysis with Mothur.

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Hello,

I have the same problem as you. When I’m starting make.contings, it takes a long time (hours). I have 40 samples in total. Did you solve the issue ? Should I wait more, or should I change some parameters ? Thank you :slight_smile:

Thank you very much for your answer

Marion R

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Hi @mregnier

Allow the job to process unless you notice there is an obvious input problem and need to rerun it.

Tools execute as resources become available. Some queue longer than others and some execute longer than others. Rerunning the same exact job again will only place it back at the end of the job queue, further extending wait time.

FAQ: Datasets and how jobs execute

Thanks!

Thank you very much for your kind reply. It worked well after many hours :wink:

Now, I have another issue in the Following steps

When I use the tool “Unique.seqs”, the following error message appairs : "Fatal error 1 () with the message “TERM environment variable not set”. When I look to the previous step (Screen.seqs), the contigs.report and the align.report are contain 0 lines. Does someone already had this issue and know how to fix it ? Thank you very much :slight_smile:

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Moved to a new topic: ERROR : "TERM environment variable not set"

Closing this topic to keep the conversation in one place.