[maker-devel] questions on master_datastore_index.log file

[Carson Holt]

That’s the stack trace. The error is going to be a few lines further back. It would be best to get a few hundred lines right around the area you are showing.

—Carson

> On Jan 4, 2018, at 2:36 PM, Qihua Liang <qlian003 at ucr.edu> wrote:
> 
> Hi Ence,
> 
> When I searched for “E/error” in the output file, here is what first showed up:
> Process::MpiChunk::__ANON__() called at /24-2/home/qliang/0.soft/maker/bin/../lib/Error.pm line 415
>         eval {...} called at /24-2/home/qliang/0.soft/maker/bin/../lib/Error.pm line 407
>         Error::subs::try(CODE(0x502bbb0), HASH(0x5007788)) called at /24-2/home/qliang/0.soft/maker/bin/../lib/Process/MpiChunk.pm line 4269
>         Process::MpiChunk::_go(Process::MpiChunk=HASH(0x50a1a18), "flow", HASH(0x50ad0f0), 2, 0) called at /24-2/home/qliang/0.soft/maker/bin/../lib/Process/MpiChunk.pm line 378
>         Process::MpiChunk::_flow(Process::MpiChunk=HASH(0x50a1a18), HASH(0x50ad0f0), 2, 0, Process::MpiTiers=HASH(0x4fb3350)) called at /24-2/home/qliang/0.soft/maker/bin/../lib/Process/MpiTiers.pm line 318
>         Process::MpiTiers::__ANON__() called at /24-2/home/qliang/0.soft/maker/bin/../lib/Error.pm line 415
>         eval {...} called at /24-2/home/qliang/0.soft/maker/bin/../lib/Error.pm line 407
>         Error::subs::try(CODE(0x50a9348), HASH(0x4ff0ec0)) called at /24-2/home/qliang/0.soft/maker/bin/../lib/Process/MpiTiers.pm line 338
>         Process::MpiTiers::_next_level(Process::MpiTiers=HASH(0x4fb3350)) called at /24-2/home/qliang/0.soft/maker/bin/../lib/Process/MpiTiers.pm line 179
> 
> Is this what you may need?
> 
> Qihua
> 
>> On Jan 4, 2018, at 6:16 AM, Ence,daniel <d.ence at ufl.edu <mailto:d.ence at ufl.edu>> wrote:
>> 
>> Hi, Before we can give any help to debug it, we need the error messages. These should be in the same file that the “maker is finished” message is in. Look for the first error message (the one closest to the top of the file) and send that to the mailing list. 
>> 
>> Thanks,
>> Daniel 
>> 
>> 
>>> On Jan 3, 2018, at 8:52 PM, Qihua Liang <qlian003 at ucr.edu <mailto:qlian003 at ucr.edu>> wrote:
>>> 
>>> Dear Maker Develop Team,
>>> 
>>> I have successfully run Maker for several times before. But I came across a strange thing days ago when I ran Maker again on a different assembly with the same input files and settings.
>>> 
>>> I saw the message of "Maker is now finished!!!” but got empty GFF3 and no fasta files. And then I checked the master_datastore_index.log and realized that there are a lot of “failed”s and “retry”s and “failed” again. What does this mean? Since I used same inputs as previous successful runs, could you provide some instructions on how to debug and solve it?
>>> 
>>> Thank you so much
>>> Qihua
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at box290.bluehost.com <mailto:maker-devel at box290.bluehost.com>
>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__box290.bluehost.com_mailman_listinfo_maker-2Ddevel-5Fyandell-2Dlab.org&d=DwIGaQ&c=pZJPUDQ3SB9JplYbifm4nt2lEVG5pWx2KikqINpWlZM&r=12jzlNvGVD0AlPJ4E7cTlw1Dvu6n9cb4kMCobJ28XPs&m=nUDCP_0kFOhDYlTHgOpWtf_zdL77aQFeQwYOGIQwP8c&s=9Z4T1hdtxOyIjpn6f70qhrQRuGsZxXdV-oLSJF1zGkY&e= 
>> 
> 
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20180105/00f9d2b3/attachment-0002.html>