running error

[ghost]

Hi.

I want to running bayesembler with my data, but the program show me this error. I don't know what problem is. Please tell me how I can solve this error .

$ bayesembler -b Atcol0.bam -p 64
You are using the Bayesembler v1.1.1. For more information go to bayesembler.binf.ku.dk

[17/12/2014 10:01:09] Removing duplicate reads
[17/12/2014 10:22:08] Removed duplicates from 19745500 mapped read pairs
[17/12/2014 10:22:08] Wrote 17018947 read pairs used for splice-graph construction

[17/12/2014 10:22:08] Spawning graph construction thread
[17/12/2014 10:22:08] Generating splice-graphs from Atcol0_nd_unstranded.bam using cem
bayesembler: /opt/bayesembler/src/assembler.cpp:687: void Assembler::graphConstructorCallback(std::string, std::list<GraphInfo>*, std::string, boost::mutex*, int*, int*): Assertion `system(instance_system_string.c_str()) == 0' failed.
Aborted (core dumped)

[lassemaretty]

Hi,

Thanks for reporting your problem. The error you have encountered indicates that the call to processsam, a program that we use for constructing the splice-graph, was not successful. If you have not done so already, try setting the CEM_PROCESSSAM_PATH environment variable to the full path of processsam:

export CEM_PROCESSSAM_PATH=<path/to/processsam>

Note that if you downloaded the binary you already have processsam in your installation directory. If you installed from source, you need to download it from here. Please let us know if it solved your problem.

/Lasse

[ghost]

Hi,

Thank you for your answer. You were right about error that I described above mentioned. I solved it but other things attacked me.

$ bayesembler -b Atcol0.bam -p 10

You are using the Bayesembler v1.1.1. For more information go to bayesembler.binf.ku.dk

[19/12/2014 10:20:10] Removing duplicate reads
[19/12/2014 10:41:13] Removed duplicates from 19745500 mapped read pairs
[19/12/2014 10:41:13] Wrote 17018947 read pairs used for splice-graph construction

[19/12/2014 10:41:13] Spawning graph construction thread
[19/12/2014 10:41:13] Generating splice-graphs from Atcol0_nd_unstranded.bam using cem
bayesembler: /opt/bayesembler/src/assembler.cpp:894: void Assembler::graphConstructorCallback(std::string, std::list<GraphInfo>*, std::string, boost::mutex*, int*, int*): Assertion `current_ref_strand == "."' failed.
Aborted (core dumped)

I found a same problem in another issue. But I don't understand how to solve this problem. So Please explain me easily how this problem are solved.

PS. These are result files that bayesembler meet the problem.

$ ls -l
total 2.1G
-rwxrwxrwx 1 jc jc   64 Dec 17 10:00 Atcol0.bam
-rw-r--r-- 1 jc jc 2.1G Dec 19 10:40 Atcol0_nd_unstranded.bam
-rw-r--r-- 1 jc jc 2.7M Dec 19 10:41 Atcol0_nd_unstranded.bam.bai
-rw-r--r-- 1 jc jc  33M Dec 19 10:53 Atcol0_nd_unstranded.instance
-rw-r--r-- 1 jc jc 7.9M Dec 19 10:53 Atcol0_nd_unstranded_instance_log.txt

[lassemaretty]

Hi,

Im happy that the first fix worked. Sorry that you are still experiencing problems. Would it be possible for you to give us access to the bam-file and the .instance-file? That would make debugging a lot easier.

/Lasse