ThrowNullPointerException()

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ThrowNullPointerException()

Marcus Naymik

I have maker running with MPI and I get this error over and over again for every contig. Any Ideas?


MAKER WARNING: All old files will be erased before continuing

#---------------------------------------------------------------------

Now starting the contig!!

SeqID: 5239

Length: 1395

#---------------------------------------------------------------------



Error: NCBI C++ Exception:

    "/packages/BUILDS/ncbi-blast-2.2.28+-src/c++/src/corelib/ncbiobj.cpp", line 925: Criti



This electronic message is intended to be for the use only of the named recipient, and may contain information that is confidential or privileged, including patient health information. If you are not the intended recipient, you are hereby notified that any disclosure, copying, distribution or use of the contents of this message is strictly prohibited. If you have received this message in error or are not the named recipient, please notify us immediately by contacting the sender at the electronic mail address noted above, and delete and destroy all copies of this message. Thank you.


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Re: ThrowNullPointerException()

Carson Holt-2
Try reinstalling blast, or upgrade to a newer version of blast.

—Carson


On Mar 2, 2017, at 1:05 PM, Marcus Naymik <[hidden email]> wrote:


I have maker running with MPI and I get this error over and over again for every contig. Any Ideas?


MAKER WARNING: All old files will be erased before continuing

#---------------------------------------------------------------------

Now starting the contig!!

SeqID: 5239

Length: 1395

#---------------------------------------------------------------------



Error: NCBI C++ Exception:

    "/packages/BUILDS/ncbi-blast-2.2.28+-src/c++/src/corelib/ncbiobj.cpp", line 925: Criti




This electronic message is intended to be for the use only of the named recipient, and may contain information that is confidential or privileged, including patient health information. If you are not the intended recipient, you are hereby notified that any disclosure, copying, distribution or use of the contents of this message is strictly prohibited. If you have received this message in error or are not the named recipient, please notify us immediately by contacting the sender at the electronic mail address noted above, and delete and destroy all copies of this message. Thank you.

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Re: ThrowNullPointerException()

Marcus Naymik
I have now tried with multiple versions of blast (2.6 and 2.28 binaries and built from source) and get the same error:

setting up GFF3 output and fasta chunks

doing blastn of ESTs

running  blast search.

#--------- command -------------#

Widget::blastn:

/home/mnaymik/TOOLS/ncbi-blast-2.2.28+/bin/blastn -db /scratch/mnaymik/maker/tmp/maker_cah

#-------------------------------#

Error: NCBI C++ Exception:

    "/home/mnaymik/TOOLS/ncbi-blast-2.2.28+-src/c++/src/corelib/ncbiobj.cpp", line 925: Cr


Error: NCBI C++ Exception:

    "/home/mnaymik/TOOLS/ncbi-blast-2.2.28+-src/c++/src/corelib/ncbiobj.cpp", line 925: Cr


examining contents of the fasta file and run log

ERROR: BLASTN failed

--> rank=87, hostname=pnap-pe7-s09

ERROR: Failed while doing blastn of ESTs

ERROR: Chunk failed at level:0, tier_type:3

FAILED CONTIG:6537645


ERROR: BLASTN failed

--> rank=88, hostname=pnap-pe7-s09

ERROR: Failed while doing blastn of ESTs

ERROR: Chunk failed at level:0, tier_type:3

FAILED CONTIG:6537659


ERROR: Chunk failed at level:4, tier_type:0

FAILED CONTIG:6537645


ERROR: Chunk failed at level:4, tier_type:0

FAILED CONTIG:6537659



On Thu, Mar 2, 2017 at 1:25 PM, Carson Holt <[hidden email]> wrote:
Try reinstalling blast, or upgrade to a newer version of blast.

—Carson


On Mar 2, 2017, at 1:05 PM, Marcus Naymik <[hidden email]> wrote:


I have maker running with MPI and I get this error over and over again for every contig. Any Ideas?


MAKER WARNING: All old files will be erased before continuing

#---------------------------------------------------------------------

Now starting the contig!!

SeqID: 5239

Length: 1395

#---------------------------------------------------------------------



Error: NCBI C++ Exception:

    "/packages/BUILDS/ncbi-blast-2.2.28+-src/c++/src/corelib/ncbiobj.cpp", line 925: Criti




This electronic message is intended to be for the use only of the named recipient, and may contain information that is confidential or privileged, including patient health information. If you are not the intended recipient, you are hereby notified that any disclosure, copying, distribution or use of the contents of this message is strictly prohibited. If you have received this message in error or are not the named recipient, please notify us immediately by contacting the sender at the electronic mail address noted above, and delete and destroy all copies of this message. Thank you.

_______________________________________________
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[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org



This electronic message is intended to be for the use only of the named recipient, and may contain information that is confidential or privileged, including patient health information. If you are not the intended recipient, you are hereby notified that any disclosure, copying, distribution or use of the contents of this message is strictly prohibited. If you have received this message in error or are not the named recipient, please notify us immediately by contacting the sender at the electronic mail address noted above, and delete and destroy all copies of this message. Thank you.


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Re: ThrowNullPointerException()

Carson Holt-2
The error itself is coming from BLAST. MAKER does provide the command used, so you can try it outside of MAKER. You can submit the files used as well as command used to the BLAST developers for them to test with.

MAKER deletes files on failure, but if you edit the …/maker/lib/GI.pm, you can stop it from deleting files.

Edit line 58 by setting CLEANUP => 0

Then you should be able to grab whatever files maker used to run blast, and copy the blast command used from STDERR.

—Carson



On Mar 14, 2017, at 11:29 AM, Marcus Naymik <[hidden email]> wrote:

I have now tried with multiple versions of blast (2.6 and 2.28 binaries and built from source) and get the same error:

setting up GFF3 output and fasta chunks

doing blastn of ESTs

running  blast search.

#--------- command -------------#

Widget::blastn:

/home/mnaymik/TOOLS/ncbi-blast-2.2.28+/bin/blastn -db /scratch/mnaymik/maker/tmp/maker_cah

#-------------------------------#

Error: NCBI C++ Exception:

    "/home/mnaymik/TOOLS/ncbi-blast-2.2.28+-src/c++/src/corelib/ncbiobj.cpp", line 925: Cr


Error: NCBI C++ Exception:

    "/home/mnaymik/TOOLS/ncbi-blast-2.2.28+-src/c++/src/corelib/ncbiobj.cpp", line 925: Cr


examining contents of the fasta file and run log

ERROR: BLASTN failed

--> rank=87, hostname=pnap-pe7-s09

ERROR: Failed while doing blastn of ESTs

ERROR: Chunk failed at level:0, tier_type:3

FAILED CONTIG:6537645


ERROR: BLASTN failed

--> rank=88, hostname=pnap-pe7-s09

ERROR: Failed while doing blastn of ESTs

ERROR: Chunk failed at level:0, tier_type:3

FAILED CONTIG:6537659


ERROR: Chunk failed at level:4, tier_type:0

FAILED CONTIG:6537645


ERROR: Chunk failed at level:4, tier_type:0

FAILED CONTIG:6537659



On Thu, Mar 2, 2017 at 1:25 PM, Carson Holt <[hidden email]> wrote:
Try reinstalling blast, or upgrade to a newer version of blast.

—Carson


On Mar 2, 2017, at 1:05 PM, Marcus Naymik <[hidden email]> wrote:


I have maker running with MPI and I get this error over and over again for every contig. Any Ideas?


MAKER WARNING: All old files will be erased before continuing

#---------------------------------------------------------------------

Now starting the contig!!

SeqID: 5239

Length: 1395

#---------------------------------------------------------------------



Error: NCBI C++ Exception:

    "/packages/BUILDS/ncbi-blast-2.2.28+-src/c++/src/corelib/ncbiobj.cpp", line 925: Criti




This electronic message is intended to be for the use only of the named recipient, and may contain information that is confidential or privileged, including patient health information. If you are not the intended recipient, you are hereby notified that any disclosure, copying, distribution or use of the contents of this message is strictly prohibited. If you have received this message in error or are not the named recipient, please notify us immediately by contacting the sender at the electronic mail address noted above, and delete and destroy all copies of this message. Thank you.

_______________________________________________
maker-devel mailing list
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org



This electronic message is intended to be for the use only of the named recipient, and may contain information that is confidential or privileged, including patient health information. If you are not the intended recipient, you are hereby notified that any disclosure, copying, distribution or use of the contents of this message is strictly prohibited. If you have received this message in error or are not the named recipient, please notify us immediately by contacting the sender at the electronic mail address noted above, and delete and destroy all copies of this message. Thank you.



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Re: ThrowNullPointerException()

Marcus Naymik
Thanks, you're right. I had to recompile blast from src with this flag: -std=c++0x 

On Tue, Mar 14, 2017 at 10:36 AM, Carson Holt <[hidden email]> wrote:
The error itself is coming from BLAST. MAKER does provide the command used, so you can try it outside of MAKER. You can submit the files used as well as command used to the BLAST developers for them to test with.

MAKER deletes files on failure, but if you edit the …/maker/lib/GI.pm, you can stop it from deleting files.

Edit line 58 by setting CLEANUP => 0

Then you should be able to grab whatever files maker used to run blast, and copy the blast command used from STDERR.

—Carson



On Mar 14, 2017, at 11:29 AM, Marcus Naymik <[hidden email]> wrote:

I have now tried with multiple versions of blast (2.6 and 2.28 binaries and built from source) and get the same error:

setting up GFF3 output and fasta chunks

doing blastn of ESTs

running  blast search.

#--------- command -------------#

Widget::blastn:

/home/mnaymik/TOOLS/ncbi-blast-2.2.28+/bin/blastn -db /scratch/mnaymik/maker/tmp/maker_cah

#-------------------------------#

Error: NCBI C++ Exception:

    "/home/mnaymik/TOOLS/ncbi-blast-2.2.28+-src/c++/src/corelib/ncbiobj.cpp", line 925: Cr


Error: NCBI C++ Exception:

    "/home/mnaymik/TOOLS/ncbi-blast-2.2.28+-src/c++/src/corelib/ncbiobj.cpp", line 925: Cr


examining contents of the fasta file and run log

ERROR: BLASTN failed

--> rank=87, hostname=pnap-pe7-s09

ERROR: Failed while doing blastn of ESTs

ERROR: Chunk failed at level:0, tier_type:3

FAILED CONTIG:6537645


ERROR: BLASTN failed

--> rank=88, hostname=pnap-pe7-s09

ERROR: Failed while doing blastn of ESTs

ERROR: Chunk failed at level:0, tier_type:3

FAILED CONTIG:6537659


ERROR: Chunk failed at level:4, tier_type:0

FAILED CONTIG:6537645


ERROR: Chunk failed at level:4, tier_type:0

FAILED CONTIG:6537659



On Thu, Mar 2, 2017 at 1:25 PM, Carson Holt <[hidden email]> wrote:
Try reinstalling blast, or upgrade to a newer version of blast.

—Carson


On Mar 2, 2017, at 1:05 PM, Marcus Naymik <[hidden email]> wrote:


I have maker running with MPI and I get this error over and over again for every contig. Any Ideas?


MAKER WARNING: All old files will be erased before continuing

#---------------------------------------------------------------------

Now starting the contig!!

SeqID: 5239

Length: 1395

#---------------------------------------------------------------------



Error: NCBI C++ Exception:

    "/packages/BUILDS/ncbi-blast-2.2.28+-src/c++/src/corelib/ncbiobj.cpp", line 925: Criti




This electronic message is intended to be for the use only of the named recipient, and may contain information that is confidential or privileged, including patient health information. If you are not the intended recipient, you are hereby notified that any disclosure, copying, distribution or use of the contents of this message is strictly prohibited. If you have received this message in error or are not the named recipient, please notify us immediately by contacting the sender at the electronic mail address noted above, and delete and destroy all copies of this message. Thank you.

_______________________________________________
maker-devel mailing list
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org



This electronic message is intended to be for the use only of the named recipient, and may contain information that is confidential or privileged, including patient health information. If you are not the intended recipient, you are hereby notified that any disclosure, copying, distribution or use of the contents of this message is strictly prohibited. If you have received this message in error or are not the named recipient, please notify us immediately by contacting the sender at the electronic mail address noted above, and delete and destroy all copies of this message. Thank you.




This electronic message is intended to be for the use only of the named recipient, and may contain information that is confidential or privileged, including patient health information. If you are not the intended recipient, you are hereby notified that any disclosure, copying, distribution or use of the contents of this message is strictly prohibited. If you have received this message in error or are not the named recipient, please notify us immediately by contacting the sender at the electronic mail address noted above, and delete and destroy all copies of this message. Thank you.


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Re: ThrowNullPointerException()

Carson Holt-2
Glad I could help. Remember to switch back CLEANUP => 1 if you set it to 0 to debug. Otherwise you will have a lot of files left in /tmp after each MAKER run.

—Carson



On Mar 15, 2017, at 10:54 AM, Marcus Naymik <[hidden email]> wrote:

Thanks, you're right. I had to recompile blast from src with this flag: -std=c++0x 

On Tue, Mar 14, 2017 at 10:36 AM, Carson Holt <[hidden email]> wrote:
The error itself is coming from BLAST. MAKER does provide the command used, so you can try it outside of MAKER. You can submit the files used as well as command used to the BLAST developers for them to test with.

MAKER deletes files on failure, but if you edit the …/maker/lib/GI.pm, you can stop it from deleting files.

Edit line 58 by setting CLEANUP => 0

Then you should be able to grab whatever files maker used to run blast, and copy the blast command used from STDERR.

—Carson



On Mar 14, 2017, at 11:29 AM, Marcus Naymik <[hidden email]> wrote:

I have now tried with multiple versions of blast (2.6 and 2.28 binaries and built from source) and get the same error:

setting up GFF3 output and fasta chunks

doing blastn of ESTs

running  blast search.

#--------- command -------------#

Widget::blastn:

/home/mnaymik/TOOLS/ncbi-blast-2.2.28+/bin/blastn -db /scratch/mnaymik/maker/tmp/maker_cah

#-------------------------------#

Error: NCBI C++ Exception:

    "/home/mnaymik/TOOLS/ncbi-blast-2.2.28+-src/c++/src/corelib/ncbiobj.cpp", line 925: Cr


Error: NCBI C++ Exception:

    "/home/mnaymik/TOOLS/ncbi-blast-2.2.28+-src/c++/src/corelib/ncbiobj.cpp", line 925: Cr


examining contents of the fasta file and run log

ERROR: BLASTN failed

--> rank=87, hostname=pnap-pe7-s09

ERROR: Failed while doing blastn of ESTs

ERROR: Chunk failed at level:0, tier_type:3

FAILED CONTIG:6537645


ERROR: BLASTN failed

--> rank=88, hostname=pnap-pe7-s09

ERROR: Failed while doing blastn of ESTs

ERROR: Chunk failed at level:0, tier_type:3

FAILED CONTIG:6537659


ERROR: Chunk failed at level:4, tier_type:0

FAILED CONTIG:6537645


ERROR: Chunk failed at level:4, tier_type:0

FAILED CONTIG:6537659



On Thu, Mar 2, 2017 at 1:25 PM, Carson Holt <[hidden email]> wrote:
Try reinstalling blast, or upgrade to a newer version of blast.

—Carson


On Mar 2, 2017, at 1:05 PM, Marcus Naymik <[hidden email]> wrote:


I have maker running with MPI and I get this error over and over again for every contig. Any Ideas?


MAKER WARNING: All old files will be erased before continuing

#---------------------------------------------------------------------

Now starting the contig!!

SeqID: 5239

Length: 1395

#---------------------------------------------------------------------



Error: NCBI C++ Exception:

    "/packages/BUILDS/ncbi-blast-2.2.28+-src/c++/src/corelib/ncbiobj.cpp", line 925: Criti




This electronic message is intended to be for the use only of the named recipient, and may contain information that is confidential or privileged, including patient health information. If you are not the intended recipient, you are hereby notified that any disclosure, copying, distribution or use of the contents of this message is strictly prohibited. If you have received this message in error or are not the named recipient, please notify us immediately by contacting the sender at the electronic mail address noted above, and delete and destroy all copies of this message. Thank you.

_______________________________________________
maker-devel mailing list
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org



This electronic message is intended to be for the use only of the named recipient, and may contain information that is confidential or privileged, including patient health information. If you are not the intended recipient, you are hereby notified that any disclosure, copying, distribution or use of the contents of this message is strictly prohibited. If you have received this message in error or are not the named recipient, please notify us immediately by contacting the sender at the electronic mail address noted above, and delete and destroy all copies of this message. Thank you.




This electronic message is intended to be for the use only of the named recipient, and may contain information that is confidential or privileged, including patient health information. If you are not the intended recipient, you are hereby notified that any disclosure, copying, distribution or use of the contents of this message is strictly prohibited. If you have received this message in error or are not the named recipient, please notify us immediately by contacting the sender at the electronic mail address noted above, and delete and destroy all copies of this message. Thank you.



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