I’m new to Mothur and to coding in Unix using the Linux system. I had help from a colleague to move the newest version of Mothur (v1.32) into my directory and unzip the file into a new folder in the directory. When I now call mothur, the latest version appears. However, when I put in the first line of command (e.g. summary.seqs(fasta=nodC.fasta, processors=2), I get the message of “Illegal instructions” and then I get kicked out of mothur and back to my current directory and have to call mothur again. Could this be related to mothur, the installation/unzipping, or both? Any help? Thanks.
Welcome to the mothur community! I’d like to help you get started. Did you download our executable version? Can you post the commands you ran in terminal?
Yep, got the 32 bit executable version of Mothur 1.32.0. I also double-checked the file type (using ls -l) and it shows that it is an executable file (file type: drwxr-xr-x).
I’m running one of the first lines of command, which is:
Mothur seems to be processing for two seconds and then it tells me that there is an illegal instruction and then it kicks me out of Mothur and gets me back to my directory. However, if I run the trim.seqs command, without first running a summary.seqs on the fasta file, the command works and gives me three output files. When I try to run a summary.seqs(fasta=current), again, I get the illegal instruction message and get kicked out. Any help would be greatly appreciated. Thanks.
I uploaded a fresh copy of our 32bit version. Can you try downloading it again?
Were you able to solve this issue? I’m having the same problem with the 64 bit version (1.32.1) run on a linux server. I’ve tested multiple files (alined and unaligned), which run perfectly well for other commands in mothur, so I don’t think it’s a formatting issue.
It just occurred to me that the names of the sequences in my files are not the same as the sequence names generated by the MiSeq, since we did our own contig formation and assignment to samples based on index reads. Since the summary looks at tile information, could this be why the summary is not generated? It looks like the output file containing info for each sequence is still generated, even though it kicks you out of mothur.
I’m having the same problem. I have your executable version of Mothur installed on a 64-bit version of Red Hat. I downloaded the file on 1/13/2014. An older version (1.27.0) seems to be working just fine.
I’m having the same problem with v.1.32.1 (64 bit linux binary). The exact same files work like a charm on my Mac (again, v1.32.1, 64 bit binary downloaded at the same time as the linux version)
I rebuilt and uploaded a new 64bit Linux version. Can you give it a try?
Was this problem ever resolved? I am having the same problem trying to run things for the first time on a remote server. Sysadmin has made version 1.32.1 as an available module. Is there anyway to tell if it is 32 or 64 bit? It appears (using uname) that the server is running 64 bit linux. Mothur loads and can, for example, do help() , but the first time I try to analyze any data I get the illegal instruction…
It should be resolved. We’re actually now up to v.1.33. Can you upgrade to that version and see if you still have the problem?
Thanks Pat! I got sysadmin to install 1.33 and it seems to be working (though I’m struggling with MPI, but that’s an issue for a different thread!).