I am using m1 mac, and the STAR 2.7.11b I compiled has always been usable。
But yesterday I upgraded the computer system to mac os sonama14.5. When I used STAR again, this problem occurred - Transcriptome.cpp:18: Transcriptome: exiting because of INPUT FILE error: could not open input file /geneInfo.tab,
so I followed @developer-ss28's approach and made the following modifications to the ParametersGenome.cpp file,
// before
transform.outYes = transform.outSAM = transform.outSJ = false;
//after
transform.outYes = transform.outSAM = transform.outSJ = transform.outQuant = false;
but the prompt Transcriptome.cpp:18:Transcriptome: exiting because of INPUT FILE error: could not open input file /geneInfo.tab still appears.
My solution is to download the preview version of Alex https://github.com/dobinlab/STAR_pre_releases/releases/tag/2.7.11b_alpha_2024-02-09, and then compile it.
During the compilation process, the following error will appear, SharedMemory. cpp: In member function 'void SharedMemory::CreateAndInitSharedObject(size_t)':
SharedMemory.cpp:109:59: error: 'SHM_NORESERVE' was not declared in this scope; did you mean 'MAP_NORESERVE'?
109 | _shmID=shmget(_key, toReserve, IPC_CREAT | IPC_EXCL | SHM_NORESERVE | 0666); // _shmID = shmget(shmKey, shmSize, IPC_CREAT | SHM_NORESERVE | SHM_HUGETLB | 0666);
| ^~~~~
| MAP_NORESERVE
SharedMemory.cpp: In member function 'void SharedMemory::EnsureCounter()':
SharedMemory.cpp:254:72: error: 'SHM_NORESERVE' was not declared in this scope; did you mean 'MAP_NORESERVE'?
254 | _sharedCounterID=shmget(_counterKey, 1, IPC_CREAT | IPC_EXCL | SHM_NORESERVE | 0666);
| ^~~~~
| MAP_NORESERVE
make: *** [SharedMemory.o] Error 1
Therefore, I changed SHM_NORESERVE on lines 109 and 254 of the SharedMemory.cpp file to MAP_NORESERVE, and the compilation was successful. After running the new STAR again, Transcriptome.cpp:18:Transcriptome: exiting because of INPUT FILE error: could not open input file /geneInfo.tab, this error did not appear again.
I am using m1 mac, and the STAR 2.7.11b I compiled has always been usable。
But yesterday I upgraded the computer system to mac os sonama14.5. When I used STAR again, this problem occurred - Transcriptome.cpp:18: Transcriptome: exiting because of INPUT FILE error: could not open input file /geneInfo.tab,
so I followed @developer-ss28's approach and made the following modifications to the ParametersGenome.cpp file, // before transform.outYes = transform.outSAM = transform.outSJ = false; //after transform.outYes = transform.outSAM = transform.outSJ = transform.outQuant = false; but the prompt Transcriptome.cpp:18:Transcriptome: exiting because of INPUT FILE error: could not open input file /geneInfo.tab still appears.
My solution is to download the preview version of Alex https://github.com/dobinlab/STAR_pre_releases/releases/tag/2.7.11b_alpha_2024-02-09, and then compile it. During the compilation process, the following error will appear, SharedMemory. cpp: In member function 'void SharedMemory::CreateAndInitSharedObject(size_t)': SharedMemory.cpp:109:59: error: 'SHM_NORESERVE' was not declared in this scope; did you mean 'MAP_NORESERVE'? 109 | _shmID=shmget(_key, toReserve, IPC_CREAT | IPC_EXCL | SHM_NORESERVE | 0666); // _shmID = shmget(shmKey, shmSize, IPC_CREAT | SHM_NORESERVE | SHM_HUGETLB | 0666); | ^
~~~~ | MAP_NORESERVE SharedMemory.cpp: In member function 'void SharedMemory::EnsureCounter()': SharedMemory.cpp:254:72: error: 'SHM_NORESERVE' was not declared in this scope; did you mean 'MAP_NORESERVE'? 254 | _sharedCounterID=shmget(_counterKey, 1, IPC_CREAT | IPC_EXCL | SHM_NORESERVE | 0666); | ^~~~~ | MAP_NORESERVE make: *** [SharedMemory.o] Error 1Therefore, I changed SHM_NORESERVE on lines 109 and 254 of the SharedMemory.cpp file to MAP_NORESERVE, and the compilation was successful. After running the new STAR again, Transcriptome.cpp:18:Transcriptome: exiting because of INPUT FILE error: could not open input file /geneInfo.tab, this error did not appear again.
I hope this helps some people