#4 Problem in ISq compilation

[Gabriel da Luz Wallau]

Dear Abhishek,

I'm trying to compile the ISquest code following you manual with the comand make after unzip the code but after the processing that seems ok (follow the output below) I can't find the Isq executable..

wallau@wallau[isquest] sudo -s make [ 9:53]
g++ -g -c nwaln.cpp
g++ -g -c swaln.cpp
gcc -g -c gbfp.c
gbfp.c: In function ‘parseGBFF’:
gbfp.c:724:9: warning: passing argument 2 of ‘_parseGBFF’ from incompatible pointer type [enabled by default]
(pptGBDatas + iGBFSeqPos) = _parseGBFF(FSeqFile,&sTempLine);
^
gbfp.c:644:17: note: expected ‘char ’ but argument is of type ‘char ()[65536]’
static gb_data _parseGBFF(FILE FSeqFile, char sTempLine) {
^
g++ -g -c gbfpTest.cpp
g++ -g -c -lpthread gtest/gtest-all.cc
mv gtest-all.o gtest

Can you tell me if I'm doing something wrong?

Best Regards.

Gabriel Wallau

[Abhishek Biswas]

Hi,

No you are not doing anything wrong. I fixed the make file. It should work now.

Thanks,
Abhishek

[Gabriel da Luz Wallau]

Hi Abiswas,

Now I'm having another problem... I'm having this kind of error. It seems to happens when Isquest get the transposases an try to blast it against the reads... It always happens when this file "transHitsBLASTResult.txt" reach 6MB of space, I'm not sure why...

Building a new DB, current time: 08/21/2015 15:01:49
New DB name: transHits
New DB title: transHits
Sequence type: Nucleotide
Keep Linkouts: T
Keep MBits: T
Maximum file size: 1000000000B
Adding sequences from FASTA; added 44 sequences in 0.068665 seconds.
Iteration 0 BLAST complete...
terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc
zsh: abort ./isq param.conf contigs_1.fa all.fasta acineto

Do you know how can I solve this?

Best Regards.
Gabriel Wallau

[Abhishek Biswas]

Try the command unlimit.