/usr/local/bin/gcc-4.8 -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Wed 28 Jan 2015 12:09:11 EST :/Users/workspace/STAR-STAR_2.4.0i/source"' bam_cat.c
cc1: warning: command line option '-std=c++11' is valid for C++/ObjC++ but not for C [enabled by default]
bam_cat.c:54:19: fatal error: cstring: No such file or directory
#include <cstring>
^
compilation terminated.
make: *** [bam_cat.o] Error 1
I use Mac OS X version 10.9.5
Thanks
bash-3.2$ bin/star --genomeDir data/GRCh38/star_indices_overhang100/ --runThreadN 4 --readFilesIn data/GRCh38/sequence/Homo_sapiens.GRCh38.dna.chromosome.1.fa --outFileNamePrefix data/GRCh38/results/chr1
Jul 14 11:30:07 ..... Started STAR run
Jul 14 11:30:07 ..... Loading genome
Jul 14 11:34:14 ..... Started mapping
Segmentation fault: 11
I used readFilesCommand gzip -c for *.fa.gz and also got problem:
bin/star --genomeDir data/GRCh38/star_indices_overhang100/ --runThreadN 4 --readFilesIn data/GRCh38/sequence/Homo_sapiens.GRCh38.dna.chromosome.10.fa.gz --readFilesCommand gzip -c --outFileNamePrefix data/GRCh38/results/chr10
Jul 15 14:17:21 ..... Started STAR run
Jul 15 14:17:21 ..... Loading genome
Jul 15 14:21:21 ..... Started mapping
ReadAlignChunk_processChunks.cpp:115:processChunks EXITING because of FATAL ERROR in input reads: unknown file format: the read ID should start with @ or >
However, I successfully passed the step1 to construct indices using the same DNA reads.
You may be right, that is, the reads have problem.
But I need your help.
Thank you again.
Yuande