moabs
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Automatically exported from code.google.com/p/moabs
moabs
What steps will reproduce the problem?
1. Using most recent Rcpp/RInside will lead an error;
2. Comping mcomp and ExactNumCI module;
3. Linux/Mac OS, clang version 3.5.0/gcc-4.6.2
What is the expected output? What do you see instead?
Compile failure.
What version of the product are you using? On what operating system?
moabs-v1.2.4
Please provide any additional information below.
1.
There is a bug in mcomp.cpp: Change line 54 into
RInside R2;
and replace all “R.” into “R2.”, in VIM you could do
:so%/R\./R2\./g
The reason is Rcpp/RInside already uses
RInside R;
2.
in ./moabs-v1.2.4/src/ExactNumCI/stats.cpp a header file
#include <iostream>
is needed.
3.
Current version (v1.4) of samtools doesn't seem to have any lib/include folder
unless one chooses to use a pre-build version provided by Linux distribution.
May be a script is needed to create them.
Original issue reported on code.google.com by [email protected]
on 12 Sep 2014 at 3:47
What steps will reproduce the problem?
When I run
moabs -cf mytestrun.cfg
the bsmap steps seem to work fine. when it moves to mcall though, I get
/srv/gs1/software/moabs/moabs-v1.3.0/bin/moabs: Start to execute
[/srv/gs1/software/moabs/moabs-v1.3.0//bin/mcall -m OX.bam -p 4 -r
/srv/gs1/projects/snyder/yxl/db/hu_genome37.58/Homo_sapiens_lambda.GRCh37.58.dna
.fa --sampleName OX > moabs.mcall.OX.log]
Tue May 19 19:35:32 PDT 2015
/srv/gs1/software/moabs/moabs-v1.3.0/bin/moabs: Start to execute
[/srv/gs1/software/moabs/moabs-v1.3.0//bin/mcall -m BS.bam -p 4 -r
/srv/gs1/projects/snyder/yxl/db/hu_genome37.58/Homo_sapiens_lambda.GRCh37.58.dna
.fa --sampleName BS > moabs.mcall.BS.log]
XR:Z or ZR:Z:, or ZS:Z: field not found, please enable -R option in bsmap
XR:Z or ZR:Z:, or ZS:Z: field not found, please enable -R option in bsmap
terminate called recursively
terminate called recursively
terminate called recursively
terminate called recursively
terminate called after throwing an instance of 'std::out_of_range'
sh: line 1: 20661 Aborted
/srv/gs1/software/moabs/moabs-v1.3.0//bin/mcall -m OX.bam -p 4 -r
/srv/gs1/projects/snyder/yxl/db/hu_genome37.58/Homo_sapiens_lambda.GRCh37.58.dna
.fa --sampleName OX > moabs.mcall.OX.log
sh: line 1: 20665 Aborted
/srv/gs1/software/moabs/moabs-v1.3.0//bin/mcall -m BS.bam -p 4 -r
/srv/gs1/projects/snyder/yxl/db/hu_genome37.58/Homo_sapiens_lambda.GRCh37.58.dna
.fa --sampleName BS > moabs.mcall.BS.log
/srv/gs1/software/moabs/moabs-v1.3.0/bin/moabs: Failed executing
[/srv/gs1/software/moabs/moabs-v1.3.0//bin/mcall -m BS.bam -p 4 -r
/srv/gs1/projects/snyder/yxl/db/hu_genome37.58/Homo_sapiens_lambda.GRCh37.58.dna
.fa --sampleName BS > moabs.mcall.BS.log] with doSys exit code 34304
/srv/gs1/software/moabs/moabs-v1.3.0/bin/moabs: Failed executing
[/srv/gs1/software/moabs/moabs-v1.3.0//bin/mcall -m OX.bam -p 4 -r
/srv/gs1/projects/snyder/yxl/db/hu_genome37.58/Homo_sapiens_lambda.GRCh37.58.dna
.fa --sampleName OX > moabs.mcall.OX.log] with doSys exit code 34304
Tue May 19 19:52:21 PDT 2015
Tue May 19 19:52:21 PDT 2015
Perl exited with active threads:
1 running and unjoined
0 finished and unjoined
0 running and detached
What is the expected output? What do you see instead?
I don't expect an error.
What version of the product are you using? On what operating system?
moabs-v1.3.0
Red Hat Enterprise Linux Server release 6.3 (Santiago)
Please provide any additional information below.
Original issue reported on code.google.com by [email protected]
on 20 May 2015 at 3:36
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