mothur

Make.contigs command killed

The command make.contigs always killed, the process was not finished. What is the problem?

I have 98 samples.

I am really grateful if anyone can help me figure the issue out.

Lixue

I’d be happy to help. Could you tell me more about the issue?

  1. What version of mothur are you running? On what operating system?

  2. What commands did you run in mothur?

  3. What is the error message you are receiving?

Dear Westcott,

Thanks for your help.

  1. The version of mothur is 1.44, it is running on the Ubuntu virtual machine.

  2. I would like to run the make .contigs command to process 98 samples including 196 fq.gz files.

  3. The command just killed suddenly without any warning information.

I split the 98 samples into 57 and 41 samples respectively, and then run the make.contigs command. It works. The computer has 8G RAM, 512G SSD and the cpu is 10 th i5 with 64-bit OS.

Lixue

Thanks for the additional information. Here are some things to try:

Version 1.44.3 includes a bug fix for the make.contigs command. Could you upgrade to version 1.44.3? Release Version 1.44.3 · mothur/mothur · GitHub

If you upgrade and mothur is still unable to complete the command, it may be due to the RAM. Can you try allocating more RAM to the virtual machine?

If you are still unable to run the make.contigs command, could you send your input files and log files to mothur.bugs@gmail.com?

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