fmaguire / bridger_assembler Goto Github PK

Hello.

I tried your assembler on test data and on real data. The install was successful, and assembly was ok for test data. However, I got a core dump while trying to assemble real data, here's the issue:

### Splicing Graphs Reconstruction ###

CMD: /Home/aechchik/software/Bridger_r2014-12-01/src/Assemble --reads both.fa -k 25  --pair_end --double_stranded_mode 2>Assemble.log
sh: line 1: 17303 Aborted                 (core dumped) /Home/aechchik/software/Bridger_r2014-12-01/src/Assemble --reads both.fa -k 25 --pair_end --double_stranded_mode 2> Assemble.log
Error, cmd: /Home/aechchik/software/Bridger_r2014-12-01/src/Assemble --reads both.fa -k 25  --pair_end --double_stranded_mode 2>Assemble.log died with ret 34304 !

The log reads:

vim Assemble.log

terminate called after throwing an instance of 'std::runtime_error'
  what():  locale::facet::_S_create_c_locale name not valid

I installed Bridger version Bridger_r2014-12-01.tar.gz on Linux server Linux 2.6.32-642.11.1.el6.x86_64 x86_64 GNU/Linux

Hi everybody,

I have a problem when I try to make Bridger. The configure steps works fine but the make step crashes. First I have a problem at the beginnign when it can't find some files:
./common.h:12:10: fatal error: 'bits/types.h' file not found
./common.h:12:10: fatal error: 'bits/typesizes.h' file not found
Because I'm working on a OSX machine i just turned off the calling to these two files using "//" but later on I have an issue that I don't how to fix:
./lemon/bits/base_extender.h:362:11: error: use of undeclared identifier 'aNode'
./lemon/bits/base_extender.h:362:11: error: use of undeclared identifier 'bNode'

I'm stuck here and do not know how to fix these issues... Any ideas, anyones knows ?

thank you in advance for your answers !

Hello,

I wanted to perform assembly on paired-end RNAseq data.

Here is the command I used:
perl ~/software/Bridger_r2014-12-01/Bridger.pl --seqType fq --left Sample1_R1_fastq.gz --right Sample1_R2_fastq.gz --CPU 4 --SS_lib_type FR --output bridger_out

But I am getting following error:

Splicing Graphs Reconstruction

CMD: ~/software/Bridger_r2014-12-01/src/Assemble --reads both.fa -k 25 --pair_end --fr_strand 2 2>Assemble.log
Error, cmd: ~/software/Bridger_r2014-12-01/src/Assemble --reads both.fa -k 25 --pair_end --fr_strand 2 2>Assemble.log died with ret 256 !

Assemble.log:
[Error] Cannot create directory ./RawGraphs/ !

Any idea why I am getting this error. I tried with changing the permission of output folder but still getting this error.

Many thanks.

I Installed boostlib and exported LIB path in .bashrc and configured Bridger_r2014-12-01 with boost lib it went well. make pops up an error. How do I rectify this?
./configure --with-boost=/home/softwares/boost_1_72_0
make
Error

make[2]: Leaving directory '/home/softwares/Bridger_r2014-12-01/plugins/fastool'
Making all in ./plugins/rsem/
make[2]: Entering directory '/home/softwares/Bridger_r2014-12-01/plugins/rsem'
g++ -Wall -O3 extractRef.cpp -o rsem-extract-reference-transcripts
extractRef.cpp: In function ‘int main(int, char**)’:
extractRef.cpp:273:25: error: cannot convert ‘std::basic_istream’ to ‘void*’ in assignment
pt = getline(fin, line);
^
extractRef.cpp:279:36: error: cannot convert ‘std::basic_istream’ to ‘void*’ in assignment
while((pt = getline(fin, line)) && line[0] != '>') {
^
makefile:16: recipe for target 'rsem-extract-reference-transcripts' failed
make[2]: *** [rsem-extract-reference-transcripts] Error 1
make[2]: Leaving directory '/home/softwares/Bridger_r2014-12-01/plugins/rsem'
Makefile:316: recipe for target 'all-recursive' failed
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory '/home/softwares/Bridger_r2014-12-01'
Makefile:245: recipe for target 'all' failed
make: *** [all] Error 2

Hello,

I am getting the following errors while trying to assemble a new dataset on a system with 64 CPUs and 250 GB memory:

Error, command: /home/user/Bridger_r2014-12-01/src/PathSearch -i comp48 -k 25 --pair_end --double_stranded_mode >/data/user/rna-seq/trimmed/rna-seq_all/transcripts/comp48.transcripts.fasta died with ret 35072 Killed Error, command: /home/user/Bridger_r2014-12-01/src/PathSearch -i comp9396 -k 25 --pair_end --double_stranded_mode >/data/user/rna-seq/trimmed/rna-seq_all/transcripts/comp9396.transcripts.fasta died with ret 35072 terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc Aborted (core dumped)

The installation of Bridger works fine with other datasets but is failing across 3 different datasets for this particular organism.

There are some errors during my deployment of Bridger.
1. assign errors like:
***** pt=getline *****
Reason and solution: see https://stackoverflow.com/a/38659160
solution 2 : simply modify the codes like this:
while (getline(fin, line) && line[0] == '>') {
I have tested this solution and it worked.
2. return errors like:
***** return (in>>sid>>pos) ******
Reason and solution: same with above, change the codes like
return (bool)(in>>sid>>pos);
3. RawGraphs directory error like:
***** died with ret 256 *****
Reason: Acctually you can find the real reason in /bridger_out_dir/Assemble.log:
Cannot create directory /RawGraphs/
I don't know why it throw a exception while the directory is in fact created successfully, so just skip the error test by
editing src/assemble.cpp : comment out the line
//(errAbort(const_cast<char*>("Cannot create directory % !\n"), out_dir.c_str()))

Then run the sample test, it will work.

Does any one know what the following error my represent, and how do i fixt it? i'm using the latest version of Boost, and trying to run Bridger in a Ubuntu server 13.10.

./lemon/topology.h:1215:34: warning: typedef 'Edge' locally defined but not used [-Wunused-local-typedefs]
     typedef typename Graph::Edge Edge;
                                  ^
./lemon/topology.h: In function 'bool lemon::bipartite(const UGraph&)':
./lemon/topology.h:1470:37: warning: typedef 'EdgeIt' locally defined but not used [-Wunused-local-typedefs]
     typedef typename UGraph::EdgeIt EdgeIt;
                                     ^
./lemon/topology.h: In function 'bool lemon::bipartitePartitions(const UGraph&, NodeMap&)':
./lemon/topology.h:1514:35: warning: typedef 'Node' locally defined but not used [-Wunused-local-typedefs]
     typedef typename UGraph::Node Node;
                                   ^
./lemon/topology.h:1516:37: warning: typedef 'EdgeIt' locally defined but not used [-Wunused-local-typedefs]
     typedef typename UGraph::EdgeIt EdgeIt;
                                     ^
In file included from reachability_bp_graph.h:45:0,
                 from reachability_bp_graph.cpp:13:
transitive_closure.h: In function 'void get_transitive_closure(const Graph&, GraphTC&, G_to_TC_VertexMap, VertexIndexMap)':
transitive_closure.h:76:60: warning: typedef 'edge' locally defined but not used [-Wunused-local-typedefs]
   typedef typename graph_traits < Graph >::edge_descriptor edge;
                                                            ^
transitive_closure.h:194:64: warning: typedef 'tc_vertex' locally defined but not used [-Wunused-local-typedefs]
   typedef typename graph_traits < GraphTC >::vertex_descriptor tc_vertex;
                                                                ^
transitive_closure.h: In function 'void warshall_transitive_closure(G&)':
transitive_closure.h:281:58: warning: typedef 'vertex' locally defined but not used [-Wunused-local-typedefs]
   typedef typename graph_traits < G >::vertex_descriptor vertex;
                                                          ^
transitive_closure.h: In function 'void warren_transitive_closure(G&)':
transitive_closure.h:304:58: warning: typedef 'vertex' locally defined but not used [-Wunused-local-typedefs]
   typedef typename graph_traits < G >::vertex_descriptor vertex;
                                                          ^
In file included from ./lemon/list_graph.h:26:0,
                 from ./lemon/dfs.h:26,
                 from ./lemon/topology.h:22,
                 from reachability_bp_graph.h:22,
                 from reachability_bp_graph.cpp:13:
./lemon/bits/base_extender.h: In instantiation of 'lemon::BidirBpUGraphExtender<Base>::Node lemon::BidirBpUGraphExtender<Base>::source(const UEdge&) const [with Base = lemon::SmartBpUGraphBase; lemon::BidirBpUGraphExtender<Base>::Node = lemon::SmartBpUGraphBase::Node; lemon::BidirBpUGraphExtender<Base>::UEdge = lemon::SmartBpUGraphBase::UEdge]':
reachability_bp_graph.cpp:81:70:   required from here
./lemon/bits/base_extender.h:362:21: error: 'aNode' was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive]
    return aNode(edge);
                     ^
./lemon/bits/base_extender.h:362:21: note: declarations in dependent base 'lemon::SmartBpUGraphBase' are not found by unqualified lookup
./lemon/bits/base_extender.h:362:21: note: use 'this->aNode' instead
./lemon/bits/base_extender.h: In instantiation of 'lemon::BidirBpUGraphExtender<Base>::Node lemon::BidirBpUGraphExtender<Base>::target(const UEdge&) const [with Base = lemon::SmartBpUGraphBase; lemon::BidirBpUGraphExtender<Base>::Node = lemon::SmartBpUGraphBase::Node; lemon::BidirBpUGraphExtender<Base>::UEdge = lemon::SmartBpUGraphBase::UEdge]':
reachability_bp_graph.cpp:82:70:   required from here
./lemon/bits/base_extender.h:365:21: error: 'bNode' was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive]
    return bNode(edge);
                     ^
./lemon/bits/base_extender.h:365:21: note: declarations in dependent base 'lemon::SmartBpUGraphBase' are not found by unqualified lookup
./lemon/bits/base_extender.h:365:21: note: use 'this->bNode' instead
make[2]: *** [PathSearch-reachability_bp_graph.o] Error 1
make[2]: Leaving directory `/home/cdtec/Frederico/programas/Bridger_r2014-11-05/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/cdtec/Frederico/programas/Bridger_r2014-11-05'
make: *** [all] Error 2

Hi,
I tried running Bridger on the sample data provided for testing but get a seg fault. Here's the log:

Begin loading reads ...
10546 reads have been loaded !
Beginning kmer hash ...
Kmer hash finished, get 73443 kmers! (elapsed time: 0 s)
remove erroneous kmers...
Done! (elapsed time: 0 s)
kmer count after errors deletion: 71772
Sorting kmers ...
Done sorting. (elapsed time: 0 s)
Segmentation fault (core dumped)

Any thoughts why this might be happening? Thank you.

kseq.h:220:2: note: in expansion of macro ‘__KSEQ_BASIC’
__KSEQ_BASIC(type_t)
^~~~~~~~~~~~
fastool.c:19:1: note: in expansion of macro ‘KSEQ_INIT’
KSEQ_INIT(gzFile, gzread)
^~~~~~~~~
fastool.c: In function ‘main’:
fastool.c:151:18: warning: passing argument 1 of ‘process_input’ from incompatible pointer type [-Wincompatible-pointer-types]
process_input(fp,reverse_complement, string_to_append, to_fasta, illumina_trinity);
^~
fastool.c:39:5: note: expected ‘FILE * {aka struct _IO_FILE *}’ but argument is of type ‘gzFile {aka struct gzFile_s *}’
int process_input(FILE *stream, int rev_comp, char *string, int to_fa, int ilmn_trin) {
^~~~~~~~~~~~~
fastool.c:158:22: warning: implicit declaration of function ‘fileno’; did you mean ‘mblen’? [-Wimplicit-function-declaration]
fp_stdin = gzdopen(fileno(stdin), "rb");
^~~~~~
mblen
fastool.c:159:17: warning: passing argument 1 of ‘process_input’ from incompatible pointer type [-Wincompatible-pointer-types]
process_input(fp_stdin, reverse_complement, string_to_append, to_fasta, illumina_trinity);
^~~~~~~~
fastool.c:39:5: note: expected ‘FILE * {aka struct _IO_FILE }’ but argument is of type ‘gzFile {aka struct gzFile_s }’
int process_input(FILE stream, int rev_comp, char string, int to_fa, int ilmn_trin) {
^~~~~~~~~~~~~
make[2]: Leaving directory /home/jjlee/program/Bridger_r2014-12-01/plugins/fastool' Making all in ./plugins/rsem/ make[2]: Entering directory /home/jjlee/program/Bridger_r2014-12-01/plugins/rsem'
g++ -Wall -O3 extractRef.cpp -o rsem-extract-reference-transcripts
extractRef.cpp: In function ‘int main(int, char)’:
extractRef.cpp:273:25: error: cannot convert ‘std::basic_istream’ to ‘void’ in assignment
pt = getline(fin, line);
^
extractRef.cpp:279:36: error: cannot convert ‘std::basic_istream’ to ‘void’ in assignment
while((pt = getline(fin, line)) && line[0] != '>') {
^
make[2]: *** [rsem-extract-reference-transcripts] Error 1
make[2]: Leaving directory /home/jjlee/program/Bridger_r2014-12-01/plugins/rsem' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory /home/jjlee/program/Bridger_r2014-12-01'
make: *** [all] Error 2

does anyone know this type of errors? I used the latest boost(v.1.8.0), python 3.8.5 and centos 7.
I tried to figure out this problem on a couple of weeks by changing boost version and python environment.
But every efforts goes wrong.
I think B2 boost builder works well but i got some error messages about MPI like that

warning: Graph library does not contain MPI-based parallel components.
note: to enable them, add "using mpi ;" to your user-config.jam.
note: to suppress this message, pass "--without-graph_parallel" to bjam.

./configure works appropriately and send any corruption messages.
How can I fix this problem?
bless

So I am trying to compile the program with GCC 5 on a Fedora 23 workstation.

I think the error commes from the fact that the config file or some other sub file if searching for gcc 4.8.

One error line that stands out is
"checking for the toolset name used by Boost for g++... configure: WARNING: could not figure out which toolset name to use for g++"

Is there a possible fix?

Thanks

After initiating a Bridger assembly with Bridger.pl --cpu 64, Assemble runs on a single thread for an extreme duration. Is there any way to run Assemble multi-threaded?

I've installed an updated BOOST; I get an error message that says 'error: cannot find the flags to link with Boost system'