to-mr error

[Leone Sophia Hopkins]

Hello, 

I'm experiencing an error for one of my files, but the other ran fine. The error is:

terminate called after throwing an instance of 'std::length_error'

  what():  basic_string::_S_create

Is there a way to change the bam file so that the to-mr script will run? 

Thanks

[Meng Zhou]

Hi Leone,

Is is possible to make a minimum subset of your input file so that we can reproduce the error?

Best regards,
Meng

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[Leone Sophia Hopkins]

Hi Meng,

The file only contains the lambda genome, so it isn't too large to begin with. I've run it twice and gotten the same error. Would you like me to send you the file? 

Thanks,

Leone

[Meng Zhou]

Yes, please send to my gmail: mzho...@gmail.com

Best regards,
Meng

[Gina Turco]

Hi I am getting a similar error running to-mr on a bismark output

terminate called after throwing an instance of 'std::out_of_range'

  what():  basic_string::substr  

the command is

to-mr -m bismark -o test.mr test

Can I send a subset as well?

[Meng Zhou]

Sure.

Best regards,
Meng

[Meng Zhou]

Hi Gina and other users who had this specific "terminate ... what():  basic_string::substr" error,

This error is caused by the input file name. Currently to-mr determines whether the input file is SAM or BAM based on the file name extension. So please make sure your files are named properly ending with either ".sam" or ".bam". If your input file does not have a dot in the file name, this error occurs. It is a funny error and we will make sure to-mr is "smarter" in later updates.

BTW Gina, it seems that the test file you sent to me is not generated by Bismark, because I saw a "bsmap" in the file. But for now I recommend you not to use -m bsmap because this option has not been fully tested. Please use -m general instead.

To Leone, the error you have seen might be something else, but please also check your command, and send me a test file when you are ready. Thanks.

Best regards,
Meng

On Mon, Jun 2, 2014 at 3:24 PM, Gina Turco <gtur...@gmail.com> wrote:

[Gina Turco]

thanks works great!

Gina

Graduate Student 

Brady Lab 

UC Davis BMCDB

https://twitter.com/sudogenes

[Peter Hill]

Hi Meng,

I'm getting the same error:

terminate called after throwing an instance of 'std::length_error'

  what():  basic_string::_S_create

my files seem properly named:

to-mr -o E10_deduplicated.mr -m bismark E10_deduplicated.bam

Why would this be?

Thanks!

Peter.

[Meng Zhou]

Hi Peter,

Could you please provide a small testing BAM file so that I can reproduce the error?

Best regards,
Meng

[Peter Hill]

Hi Meng,

I've sent you the data through a file exchange.

Thanks!

Peter.

[Meng Zhou]

Hi Peter,

I found that you are using an older version of bismark (v0.7.8), which uses unconventional SAM flag for bisulfite pair-end reads. This incompatible error only exists for bismark version before 0.8.3. I think your data is huge, so re-mapping them might not be a good option. I'll send you some source code files to fix this.

Best regards,
Meng

[Meng Zhou]

Please replace the file in src/smithlab_cpp/SAM.cpp with the attached file.

Best regards,
Meng

[Peter Hill]

Hi Meng,

I replaced the SAM.cpp file, but now I'm now getting the error: 

Fail to open SAM/BAM file E10_deduplicated.bam

When I run to-mr -o E10.mr -m bismark E10_deduplicated.bam ...

Samtools/0.1.19 is in my PATH so that's not the problem. Thoughts?

Peter.

to-mr -o E10.mr -m bismark E10_deduplicated.bam

[Meng Zhou]

Hi Peter,

That looked weird; I couldn't reproduce this error. Could you please try the following commands in methpipe directory and run to-mr again?

make clean
make install

Best regards,
Meng

[Peter Hill]

looks like that solved the problem. Thanks!

Peter.