1:BUILD_BY[name] student5 1:BUILD_ENVIRONMENT[operating system 32 vs 64] 1:END_BUILD_ENVIRONMENT 1:DEPENDENCIES[list of dependencies with where to get them] 1. gcc 1:END_DEPENDENCIES 1:NOTES[notes on attempted build] make command returns an error: student@ubuntu:~/Downloads/builds/tods37/LiPT12/wham$ sudo make [sudo] password for student: g++ -c -O3 -Wno-write-strings hash.cpp hash.cpp: In member function ‘int HashTable::preProcessEnd()’: hash.cpp:193:27: internal compiler error: Aborted Please submit a full bug report, with preprocessed source if appropriate. See for instructions. Preprocessed source stored into /tmp/ccFq1gSg.out file, please attach this to your bugreport. make: *** [hash.o] Error 1 1:END_NOTES 2:BUILD_BY[name] student4 2:BUILD_ENVIRONMENT[operating system 32 vs 64] >>>> lsb_release -a No LSB modules are available. Distributor ID: Ubuntu Description: Ubuntu 12.04.4 LTS Release: 12.04 Codename: precise >>>> uname -a Linux student-VPCSE13FX 3.2.0-60-generic #91-Ubuntu SMP Wed Feb 19 03:54:44 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux >>>> lscpu Architecture: x86_64 CPU op-mode(s): 32-bit, 64-bit Byte Order: Little Endian CPU(s): 4 On-line CPU(s) list: 0-3 Thread(s) per core: 2 Core(s) per socket: 2 Socket(s): 1 NUMA node(s): 1 Vendor ID: GenuineIntel CPU family: 6 Model: 42 Stepping: 7 CPU MHz: 800.000 BogoMIPS: 4789.10 Virtualization: VT-x L1d cache: 32K L1i cache: 32K L2 cache: 256K L3 cache: 3072K NUMA node0 CPU(s): 0-3 >>>> javac -version javac 1.7.0_51 >>>> gcc --version gcc (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3 2:END_BUILD_ENVIRONMENT 2:DEPENDENCIES[list of dependencies with where to get them] 2:END_DEPENDENCIES 2:NOTES[notes on attempted build] Using the MANUAL > make ... ... main.cpp:(.text+0x1af8): undefined reference to `pthread_create' main.cpp:(.text+0x1bf8): undefined reference to `pthread_join' collect2: ld returned 1 exit status make: *** [wham] Error 1 Change: LDLIBS=-lpthread to LDLIBS=-pthread And now it compiles. For running the test, as in MANUAL: student@student-VPCSE13FX:~/temp/repro/wham$ ./wham-build -l 60 -v 2 --mask sequences/chr1_100k.fa indexes/idx length: 60, #mismatch: 2, #partition: 0 loading reference sequences... Preprocessing reference sequences... preprocessing sequences/chr1_100k.fa... loading reference sequences... [########################################] 100% saving the reference sequences... optimizer chooses 3 fragments building WHAM index... preprocessing... [########################################] 100% building... [########################################] 100% saving... building time: 0.021407 sec Complete. student@student-VPCSE13FX:~/temp/repro/wham$ ./wham reads/sample.fq indexes/idx output loading short reads... loading WHAM indexes... loading time: 0 sec align reads using indexes... [########################################] 100% *************************** Total Align Time: 0.000709 sec Valid Reads: 3/5=60.00% Valid Alignments: 3 *************************** see output for all valid alignments. 2:END_NOTES