error running shhh.flows-writing/reading unknown VMA

mothur bugs
1

Not sure if this is an os error (Ubuntu 12.04, running gnome classic) or a mothur error. I’m running a bunch of files through shhh.flows using command line mothur. Some of the files (~15%) are causing mothur to crash giving either a writing unknown VMA or reading unknown VMA error.

My commands so far-the sff files that I received were already separated by barcode (one sff per barcode) so my oligos only contains the F primer

for n in .sff; do mothur “#sff.info(file=$n, flow=T)”; done
for n in B.flow; do mothur “#trim.flows(flow=$n, oligos=B.oligos, pdiffs=2)”; done
for n in E*.flow; do mothur “#trim.flows(flow=$n, oligos=E.oligos, pdiffs=2)”; done
for n in *.flow; do mothur “#shhh.flows(flow=$n, processors=2)”; done

2

here’s the SegvAnalysis (not sure if this helps)

Segfault happened at :0xaa912b: movw $0x0, (%rdi, %rdx, 1)
PC(0x00aa912b) ok
source “$0x0” ok
destination “(%rdi,%rdx,1)” (0xffffffffc57cc060) not located in a known VMA region (needed writable region)

3

still having this issue, any ideas?

4

Have you tried running the files that fail without a script?

Don’t you want the last line to look for *.files instead of *.flow so you don’t try to process the *.scrap.flow files?

for n in .sff; do mothur “#sff.info(file=$n, flow=T)”; done
for n in B.flow; do mothur “#trim.flows(flow=$n, oligos=B.oligos, pdiffs=2)”; done
for n in E*.flow; do mothur “#trim.flows(flow=$n, oligos=E.oligos, pdiffs=2)”; done
for n in *.files; do mothur “#shhh.flows(file=$n, processors=2)”; done

5

oh, I thought running shhh.flows on files required the oligos file? These sff are already separated by barcode by the sequencing facility. The .scrap.flow files don’t seem to be taking much time. I have one of the files that failed running now to see if I get the same error.

6

So my *flow.files were created with sff.info but they are empty-possibly because I didn’t have any barcodes in my oligos since my files are already split?

I ran one of the files that gave the VMA error by itself and it ran fine