Re: [AMOS-help] Segmentation Fault Error (AMOScmp)

[Adam P. <aph...@gm...>]

Hi Jeri,
Can you run this again, just like you did, and keep an eye on the memory
usage while step 50 runs? Perhaps the consensus program is running out of
memory?

-Adam


On Fri, May 25, 2012 at 11:57 AM, Jeri Dilts <jd...@ai...> wrote:

>  I’m getting  a weird segmentation fault error at step-50 when I run
> AMOScmp. It’s a vague error and I’m not sure how to handle it.  Is this
> something that somebody else has run into?****
>
> ** **
>
> Thanks****
>
> Jeri****
>
> ** **
>
> !!! 2012-05-25 11:32:12  Doing step 40:  Running layout****
>
> !!! 2012-05-25 11:32:12  Running:
> /usr/local/bin/amos-3.1.0-rc1/bin/casm-layout -r -S -t 10 -o 5 -m 50 -U
> R_2012_05_15_17_14_35_user_15May2012_clinical-test_Auto_15May2012_clinical-test_11.layout
> -C
> R_2012_05_15_17_14_35_user_15May2012_clinical-test_Auto_15May2012_clinical-test_11.conflict
> -b
> R_2012_05_15_17_14_35_user_15May2012_clinical-test_Auto_15May2012_clinical-test_11.bnk
> R_2012_05_15_17_14_35_user_15May2012_clinical-test_Auto_15May2012_clinical-test_11.delta
> ****
>
> INPUT****
>
> reads****
>
> lis****
>
> mates****
>
> WARNING: Could not open bank file,
> R_2012_05_15_17_14_35_user_15May2012_clinical-test_Auto_15May2012_clinical-test_11.bnk/FRG.ifo,
> No such file or directory****
>
>   could not retrieve mate-pair information****
>
> PLACEMENT****
>
> CONFLICT****
>
> ASSEMBLY****
>
> OUTPUT****
>
> !!! 2012-05-25 11:32:17  Done! Elapsed time:0d 0h 0m 5s****
>
> ** **
>
> !!! 2012-05-25 11:32:17  Doing step 50:  Running consensus****
>
> !!! 2012-05-25 11:32:17  Running:
> /usr/local/bin/amos-3.1.0-rc1/bin/make-consensus -B -b
> R_2012_05_15_17_14_35_user_15May2012_clinical-test_Auto_15May2012_clinical-test_11.bnk
> -e 0.06 -w 2 -x
> R_2012_05_15_17_14_35_user_15May2012_clinical-test_Auto_15May2012_clinical-test_11.exclude.seqs
> ****
>
> Starting on Fri May 25 11:32:17 2012****
>
> ** **
>
> Expelled reads listed in file
> R_2012_05_15_17_14_35_user_15May2012_clinical-test_Auto_15May2012_clinical-test_11.exclude.seqs
> ****
>
> Read bank is
> R_2012_05_15_17_14_35_user_15May2012_clinical-test_Auto_15May2012_clinical-test_11.bnk
> ****
>
> Alignment error rate is 0.06****
>
> Minimum overlap bases is 5****
>
> Output will be written to the bank****
>
> Input is being read from the bank ****
>
> Segmentation fault (core dumped)****
>
> !!! 2012-05-25 11:32:17  Command:
> /usr/local/bin/amos-3.1.0-rc1/bin/make-consensus -B -b
> R_2012_05_15_17_14_35_user_15May2012_clinical-test_Auto_15May2012_clinical-test_11.bnk
> -e 0.06 -w 2 -x
> R_2012_05_15_17_14_35_user_15May2012_clinical-test_Auto_15May2012_clinical-test_11.exclude.seqs
> exited with status: 139****
>
> !!! END - Elapsed time: 0d 0h 0m 10s****
>
>
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