align.seqs Error

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aivelo
Posts: 2
Joined: Tue Jun 06, 2017 9:33 am

align.seqs Error

Post by aivelo » Tue Jun 06, 2017 10:39 am

Hi,

I'm running mothur on Ubuntu server and the batch file seems to run like a dream until it gets to align.seqs. Then happens this error:

mothur > align.seqs(fasta=mb.trim.contigs.good.unique.fasta, reference=silva.bacteria.pcr.fasta)\

Using 16 processors.

Reading in the silva.bacteria.pcr.fasta template sequences... DONE.
It took 13 to read 13683 sequences.
Aligning sequences from mb.trim.contigs.good.unique.fasta ...
*** Error in `mothur': double free or corruption (out): 0x0000000023e69e00 ***
*** Error in `mothur': munmap_chunk(): invalid pointer: 0x0000000023e6ac90 ***
*** Error in `mothur': free(): invalid size: 0x0000000023e6ac90 ***
*** Error in `mothur': munmap_chunk(): invalid pointer: 0x0000000023e6ac90 ***
*** Error in `mothur': munmap_chunk(): invalid pointer: 0x0000000023e6ac90 ***
*** Error in `mothur': munmap_chunk(): invalid pointer: 0x0000000023e6ac90 ***
*** Error in `mothur': free(): invalid size: 0x0000000023e6ac90 ***
*** Error in `mothur': munmap_chunk(): invalid pointer: 0x0000000023e6ac90 ***
*** Error in `mothur': double free or corruption (out): 0x0000000023e6ac90 ***
*** Error in `mothur': free(): invalid size: 0x0000000023e6ac90 ***
*** Error in `mothur': munmap_chunk(): invalid pointer: 0x0000000023e6ac90 ***
*** Error in `mothur': munmap_chunk(): invalid pointer: 0x0000000023e6ac90 ***
*** Error in `mothur': munmap_chunk(): invalid pointer: 0x0000000023e6ac90 ***
*** Error in `mothur': munmap_chunk(): invalid pointer: 0x0000000023e69c60 ***
*** Error in `mothur': munmap_chunk(): invalid pointer: 0x0000000023e6ac90 ***
Aborted (core dumped)

Any idea what causes this / how this can be prevented?

aivelo
Posts: 2
Joined: Tue Jun 06, 2017 9:33 am

Re: align.seqs Error

Post by aivelo » Wed Jun 07, 2017 4:33 am

...and I resolved the problem by just redoing the reference file. The alignment works nicely with new reference file (though it should contain the same sequences).

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