an issue when running gcap.workflow

[Bao110110]

l am running this commend:

gcap.workflow(tumourseqfile = "/home/baorx/test1/gcap/bam/M9-T_bwa.bam", 
                   normalseqfile = "/home/baorx/test1/gcap/bam/M9-N_bwa.bam",
                   tumourname = "M7-T", normalname = "M7-B", jobname = "M7", 
                   genome_build = "hg38", model = "XGB11", outdir = "/home/baorx/test1/gcap/gcap", 
                   result_file_prefix = "GCAP_BMM7", allelecounter_exe = "~/miniconda3/envs/cancerit/bin/alleleCounter", 
                   g1000allelesprefix = file.path("/home/baorx/miniconda3/envs/cancerit/ref/G1000_allelesAll_hg38",
                                                  "G1000_alleles_hg38_chr"),
                   g1000lociprefix = file.path("/home/baorx/miniconda3/envs/cancerit/ref/G1000_lociAll_hg38",
                                               "G1000_loci_hg38_chr"), 
                   GCcontentfile = "/home/baorx/miniconda3/envs/cancerit/ref/GC_G1000_hg38.txt", 
                   replictimingfile = "/home/baorx/miniconda3/envs/cancerit/ref/RT_G1000_hg38.txt")

but facing errors

7ffd15efd000-7ffd15eff000 r-xp 00000000 00:00 0                          [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0                  [vsyscall]
[E::sam_itr_next] Null iterator
[ERROR] (src/bam_access.c: bam_access_get_multi_position_base_counts:379 errno: None) Error detected (-2) when trying to iterate through region.
[ERROR] (./src/alleleCounter.c: main:432 errno: None) Error scanning through bam file for loci list with dense snps.
*** Error in `/home/baorx/miniconda3/envs/cancerit/bin/alleleCounter': munmap_chunk(): invalid pointer: 0x00007ffc51171457 ***
======= Backtrace: =========
/lib64/libc.so.6(+0x7f5e4)[0x7fea62b375e4]
/home/baorx/miniconda3/envs/cancerit/bin/alleleCounter(main+0x144)[0x55dcc75a6454]
/lib64/libc.so.6(__libc_start_main+0xf5)[0x7fea62ada445]
/home/baorx/miniconda3/envs/cancerit/bin/alleleCounter(+0x2aa1)[0x55dcc75a6aa1]
======= Memory map: ========
55dcc75a4000-55dcc75a6000 r--p 00000000 00:2b 6384932095811731369        /home/baorx/miniconda3/envs/cancerit/bin/alleleCounter
55dcc75a6000-55dcc75aa000 r-xp 00002000 00:2b 6384932095811731369        /home/baorx/miniconda3/envs/cancerit/bin/alleleCounter
55dcc75aa000-55dcc75ac000 r--p 00006000 00:2b 6384932095811731369        /home/baorx/miniconda3/envs/cancerit/bin/alleleCounter
55dcc75ac000-55dcc75ad000 r--p 00008000 00:2b 6384932095811731369        /home/baorx/miniconda3/envs/cancerit/bin/alleleCounter
55dcc75ad000-55dcc75ae000 rw-p 00009000 00:2b 6384932095811731369        /home/baorx/miniconda3/envs/cancerit/bin/alleleCounter
55dcc764b000-55dd4433b000 rw-p 00000000 00:00 0                          [heap]
7fea628b0000-7fea628b7000 r-xp 00000000 fd:00 11016382                   /usr/lib64/librt-2.17.so
7fea628b7000-7fea62ab6000 ---p 00007000 fd:00 11016382                   /usr/lib64/librt-2.17.so
7fea62ab6000-7fea62ab7000 r--p 00006000 fd:00 11016382                   /usr/lib64/librt-2.17.so
7fea62ab7000-7fea62ab8000 rw-p 00007000 fd:00 11016382                   /usr/lib64/librt-2.17.so
7fea62ab8000-7fea62c7b000 r-xp 00000000 fd:00 11016352                   /usr/lib64/libc-2.17.so
7fea62c7b000-7fea62e7a000 ---p 001c3000 fd:00 11016352                   /usr/lib64/libc-2.17.so
7fea62e7a000-7fea62e7e000 r--p 001c2000 fd:00 11016352                   /usr/lib64/libc-2.17.so
7fea62e7e000-7fea62e80000 rw-p 001c6000 fd:00 11016352                   /usr/lib64/libc-2.17.so
7fea62e80000-7fea62e85000 rw-p 00000000 00:00 0 
7fea62e85000-7fea62e87000 r-xp 00000000 fd:00 11016358                   /usr/lib64/libdl-2.17.so
7fea62e87000-7fea63087000 ---p 00002000 fd:00 11016358                   /usr/lib64/libdl-2.17.so
7fea63087000-7fea63088000 r--p 00002000 fd:00 11016358                   /usr/lib64/libdl-2.17.so
7fea63088000-7fea63089000 rw-p 00003000 fd:00 11016358                   /usr/lib64/libdl-2.17.so
7fea63089000-7fea6318a000 r-xp 00000000 fd:00 11016360                   /usr/lib64/libm-2.17.so
7fea6318a000-7fea63389000 ---p 00101000 fd:00 11016360                   /usr/lib64/libm-2.17.so
7fea63389000-7fea6338a000 r--p 00100000 fd:00 11016360                   /usr/lib64/libm-2.17.so
7fea6338a000-7fea6338b000 rw-p 00101000 fd:00 11016360                   /usr/lib64/libm-2.17.so
7fea6338b000-7fea633a2000 r-xp 00000000 fd:00 11016378                   /usr/lib64/libpthread-2.17.so
7fea633a2000-7fea635a1000 ---p 00017000 fd:00 11016378                   /usr/lib64/libpthread-2.17.so
7fea635a1000-7fea635a2000 r--p 00016000 fd:00 11016378                   /usr/lib64/libpthread-2.17.so
7fea635a2000-7fea635a3000 rw-p 00017000 fd:00 11016378                   /usr/lib64/libpthread-2.17.so
7fea635a3000-7fea635a7000 rw-p 00000000 00:00 0 
7fea635a7000-7fea635c9000 r-xp 00000000 fd:00 11016345                   /usr/lib64/ld-2.17.so
7fea6360f000-7fea63613000 r--p 00000000 00:2b 12547459619057434142       /home/baorx/miniconda3/envs/cancerit/lib/libgcc_s.so.1
7fea63613000-7fea63628000 r-xp 00004000 00:2b 12547459619057434142       /home/baorx/miniconda3/envs/cancerit/lib/libgcc_s.so.1
7fea63628000-7fea6362c000 r--p 00019000 00:2b 12547459619057434142       /home/baorx/miniconda3/envs/cancerit/lib/libgcc_s.so.1
7fea6362c000-7fea6362d000 r--p 0001c000 00:2b 12547459619057434142       /home/baorx/miniconda3/envs/cancerit/lib/libgcc_s.so.1
7fea6362d000-7fea6362e000 rw-p 0001d000 00:2b 12547459619057434142       /home/baorx/miniconda3/envs/cancerit/lib/libgcc_s.so.1
7fea6362e000-7fea63632000 rw-p 00000000 00:00 0 
7fea63632000-7fea63633000 r--p 00000000 00:2b 4384565586930135332        /home/baorx/miniconda3/envs/cancerit/lib/libdeflate.so.0
7fea63633000-7fea63642000 r-xp 00001000 00:2b 4384565586930135332        /home/baorx/miniconda3/envs/cancerit/lib/libdeflate.so.0
7fea63642000-7fea63647000 r--p 00010000 00:2b 4384565586930135332        /home/baorx/miniconda3/envs/cancerit/lib/libdeflate.so.0
7fea63647000-7fea63648000 r--p 00014000 00:2b 4384565586930135332        /home/baorx/miniconda3/envs/cancerit/lib/libdeflate.so.0
7fea63648000-7fea63649000 rw-p 00015000 00:2b 4384565586930135332        /home/baorx/miniconda3/envs/cancerit/lib/libdeflate.so.0
7fea63649000-7fea6364a000 rw-p 00000000 00:00 0 
7fea6364a000-7fea6364e000 r--p 00000000 00:2b 14885991866705956940       /home/baorx/miniconda3/envs/cancerit/lib/liblzma.so.5.2.6
7fea6364e000-7fea63665000 r-xp 00004000 00:2b 14885991866705956940       /home/baorx/miniconda3/envs/cancerit/lib/liblzma.so.5.2.6
7fea63665000-7fea63670000 r--p 0001b000 00:2b 14885991866705956940       /home/baorx/miniconda3/envs/cancerit/lib/liblzma.so.5.2.6
7fea63670000-7fea63671000 ---p 00026000 00:2b 14885991866705956940       /home/baorx/miniconda3/envs/cancerit/lib/liblzma.so.5.2.6
7fea63671000-7fea63672000 r--p 00026000 00:2b 14885991866705956940       /home/baorx/miniconda3/envs/cancerit/lib/liblzma.so.5.2.6
7fea63672000-7fea63673000 rw-p 00027000 00:2b 14885991866705956940       /home/baorx/miniconda3/envs/cancerit/lib/liblzma.so.5.2.6
7fea63673000-7fea63674000 rw-p 00000000 00:00 0 
7fea63674000-7fea63676000 r--p 00000000 00:2b 2988501068377944316        /home/baorx/miniconda3/envs/cancerit/lib/libbz2.so.1.0.8
7fea63676000-7fea63684000 r-xp 00002000 00:2b 2988501068377944316        /home/baorx/miniconda3/envs/cancerit/lib/libbz2.so.1.0.8
7fea63684000-7fea63686000 r--p 00010000 00:2b 2988501068377944316        /home/baorx/miniconda3/envs/cancerit/lib/libbz2.so.1.0.8
7fea63686000-7fea63687000 r--p 00011000 00:2b 2988501068377944316        /home/baorx/miniconda3/envs/cancerit/lib/libbz2.so.1.0.8
7fea63687000-7fea63688000 rw-p 00012000 00:2b 2988501068377944316        /home/baorx/miniconda3/envs/cancerit/lib/libbz2.so.1.0.8
7fea63688000-7fea6368b000 r--p 00000000 00:2b 11235798539474949561       /home/baorx/miniconda3/envs/cancerit/lib/libz.so.1.3.1
7fea6368b000-7fea6369a000 r-xp 00003000 00:2b 11235798539474949561       /home/baorx/miniconda3/envs/cancerit/lib/libz.so.1.3.1
7fea6369a000-7fea636a1000 r--p 00012000 00:2b 11235798539474949561       /home/baorx/miniconda3/envs/cancerit/lib/libz.so.1.3.1
7fea636a1000-7fea636a2000 r--p 00018000 00:2b 11235798539474949561       /home/baorx/miniconda3/envs/cancerit/lib/libz.so.1.3.1
7fea636a2000-7fea636a3000 rw-p 00019000 00:2b 11235798539474949561       /home/baorx/miniconda3/envs/cancerit/lib/libz.so.1.3.1
7fea636a3000-7fea636a4000 rw-p 00000000 00:00 0 
7fea636ba000-7fea636bb000 rw-p 00000000 00:00 0 
7fea636bb000-7fea636ca000 r--p 00000000 00:2b 10940355597678270174       /home/baorx/miniconda3/envs/cancerit/lib/libhts.so.1.21
7fea636ca000-7fea6379c000 r-xp 0000f000 00:2b 10940355597678270174       /home/baorx/miniconda3/envs/cancerit/lib/libhts.so.1.21
7fea6379c000-7fea637bf000 r--p 000e1000 00:2b 10940355597678270174       /home/baorx/miniconda3/envs/cancerit/lib/libhts.so.1.21
7fea637bf000-7fea637c1000 r--p 00103000 00:2b 10940355597678270174       /home/baorx/miniconda3/envs/cancerit/lib/libhts.so.1.21
7fea637c1000-7fea637c6000 rw-p 00105000 00:2b 10940355597678270174       /home/baorx/miniconda3/envs/cancerit/lib/libhts.so.1.21
7fea637c6000-7fea637c8000 rw-p 00000000 00:00 0 
7fea637c8000-7fea637c9000 r--p 00021000 fd:00 11016345                   /usr/lib64/ld-2.17.so
7fea637c9000-7fea637ca000 rw-p 00022000 fd:00 11016345                   /usr/lib64/ld-2.17.so
7fea637ca000-7fea637cb000 rw-p 00000000 00:00 0 
7fff31c4a000-7fff31c6b000 rw-p 00000000 00:00 0                          [stack]
7fff31c6c000-7fff31c6e000 r-xp 00000000 00:00 0                          [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0                  [vsyscall]
======= Backtrace: =========
/lib64/libc.so.6(+0x7f5e4)[0x7f5a22fae5e4]
/home/baorx/miniconda3/envs/cancerit/bin/alleleCounter(main+0x144)[0x55cf4acca454]
/lib64/libc.so.6(__libc_start_main+0xf5)[0x7f5a22f51445]
/home/baorx/miniconda3/envs/cancerit/bin/alleleCounter(+0x2aa1)[0x55cf4accaaa1]
======= Memory map: ========
55cf4acc8000-55cf4acca000 r--p 00000000 00:2b 6384932095811731369        /home/baorx/miniconda3/envs/cancerit/bin/alleleCounter
55cf4acca000-55cf4acce000 r-xp 00002000 00:2b 6384932095811731369        /home/baorx/miniconda3/envs/cancerit/bin/alleleCounter
55cf4acce000-55cf4acd0000 r--p 00006000 00:2b 6384932095811731369        /home/baorx/miniconda3/envs/cancerit/bin/alleleCounter
55cf4acd0000-55cf4acd1000 r--p 00008000 00:2b 6384932095811731369        /home/baorx/miniconda3/envs/cancerit/bin/alleleCounter
55cf4acd1000-55cf4acd2000 rw-p 00009000 00:2b 6384932095811731369        /home/baorx/miniconda3/envs/cancerit/bin/alleleCounter
55cf4b00e000-55cfbc2d8000 rw-p 00000000 00:00 0                          [heap]
7f5a22d27000-7f5a22d2e000 r-xp 00000000 fd:00 11016382                   /usr/lib64/librt-2.17.so
7f5a22d2e000-7f5a22f2d000 ---p 00007000 fd:00 11016382                   /usr/lib64/librt-2.17.so
7f5a22f2d000-7f5a22f2e000 r--p 00006000 fd:00 11016382                   /usr/lib64/librt-2.17.so
7f5a22f2e000-7f5a22f2f000 rw-p 00007000 fd:00 11016382                   /usr/lib64/librt-2.17.so
7f5a22f2f000-7f5a230f2000 r-xp 00000000 fd:00 11016352                   /usr/lib64/libc-2.17.so
7f5a230f2000-7f5a232f1000 ---p 001c3000 fd:00 11016352                   /usr/lib64/libc-2.17.so
7f5a232f1000-7f5a232f5000 r--p 001c2000 fd:00 11016352                   /usr/lib64/libc-2.17.so
7f5a232f5000-7f5a232f7000 rw-p 001c6000 fd:00 11016352                   /usr/lib64/libc-2.17.so
7f5a232f7000-7f5a232fc000 rw-p 00000000 00:00 0 
7f5a232fc000-7f5a232fe000 r-xp 00000000 fd:00 11016358                   /usr/lib64/libdl-2.17.so
7f5a232fe000-7f5a234fe000 ---p 00002000 fd:00 11016358                   /usr/lib64/libdl-2.17.so
7f5a234fe000-7f5a234ff000 r--p 00002000 fd:00 11016358                   /usr/lib64/libdl-2.17.so
7f5a234ff000-7f5a23500000 rw-p 00003000 fd:00 11016358                   /usr/lib64/libdl-2.17.so
7f5a23500000-7f5a23601000 r-xp 00000000 fd:00 11016360                   /usr/lib64/libm-2.17.so
7f5a23601000-7f5a23800000 ---p 00101000 fd:00 11016360                   /usr/lib64/libm-2.17.so
7f5a23800000-7f5a23801000 r--p 00100000 fd:00 11016360                   /usr/lib64/libm-2.17.so
7f5a23801000-7f5a23802000 rw-p 00101000 fd:00 11016360                   /usr/lib64/libm-2.17.so
7f5a23802000-7f5a23819000 r-xp 00000000 fd:00 11016378                   /usr/lib64/libpthread-2.17.so
7f5a23819000-7f5a23a18000 ---p 00017000 fd:00 11016378                   /usr/lib64/libpthread-2.17.so
7f5a23a18000-7f5a23a19000 r--p 00016000 fd:00 11016378                   /usr/lib64/libpthread-2.17.so
7f5a23a19000-7f5a23a1a000 rw-p 00017000 fd:00 11016378                   /usr/lib64/libpthread-2.17.so
7f5a23a1a000-7f5a23a1e000 rw-p 00000000 00:00 0 
7f5a23a1e000-7f5a23a40000 r-xp 00000000 fd:00 11016345                   /usr/lib64/ld-2.17.so
7f5a23a86000-7f5a23a8a000 r--p 00000000 00:2b 12547459619057434142       /home/baorx/miniconda3/envs/cancerit/lib/libgcc_s.so.1
7f5a23a8a000-7f5a23a9f000 r-xp 00004000 00:2b 12547459619057434142       /home/baorx/miniconda3/envs/cancerit/lib/libgcc_s.so.1
7f5a23a9f000-7f5a23aa3000 r--p 00019000 00:2b 12547459619057434142       /home/baorx/miniconda3/envs/cancerit/lib/libgcc_s.so.1
7f5a23aa3000-7f5a23aa4000 r--p 0001c000 00:2b 12547459619057434142       /home/baorx/miniconda3/envs/cancerit/lib/libgcc_s.so.1
7f5a23aa4000-7f5a23aa5000 rw-p 0001d000 00:2b 12547459619057434142       /home/baorx/miniconda3/envs/cancerit/lib/libgcc_s.so.1
7f5a23aa5000-7f5a23aa9000 rw-p 00000000 00:00 0 
7f5a23aa9000-7f5a23aaa000 r--p 00000000 00:2b 4384565586930135332        /home/baorx/miniconda3/envs/cancerit/lib/libdeflate.so.0
7f5a23aaa000-7f5a23ab9000 r-xp 00001000 00:2b 4384565586930135332        /home/baorx/miniconda3/envs/cancerit/lib/libdeflate.so.0
7f5a23ab9000-7f5a23abe000 r--p 00010000 00:2b 4384565586930135332        /home/baorx/miniconda3/envs/cancerit/lib/libdeflate.so.0
7f5a23abe000-7f5a23abf000 r--p 00014000 00:2b 4384565586930135332        /home/baorx/miniconda3/envs/cancerit/lib/libdeflate.so.0
7f5a23abf000-7f5a23ac0000 rw-p 00015000 00:2b 4384565586930135332        /home/baorx/miniconda3/envs/cancerit/lib/libdeflate.so.0
7f5a23ac0000-7f5a23ac1000 rw-p 00000000 00:00 0 
7f5a23ac1000-7f5a23ac5000 r--p 00000000 00:2b 14885991866705956940       /home/baorx/miniconda3/envs/cancerit/lib/liblzma.so.5.2.6
7f5a23ac5000-7f5a23adc000 r-xp 00004000 00:2b 14885991866705956940       /home/baorx/miniconda3/envs/cancerit/lib/liblzma.so.5.2.6
7f5a23adc000-7f5a23ae7000 r--p 0001b000 00:2b 14885991866705956940       /home/baorx/miniconda3/envs/cancerit/lib/liblzma.so.5.2.6
7f5a23ae7000-7f5a23ae8000 ---p 00026000 00:2b 14885991866705956940       /home/baorx/miniconda3/envs/cancerit/lib/liblzma.so.5.2.6
7f5a23ae8000-7f5a23ae9000 r--p 00026000 00:2b 14885991866705956940       /home/baorx/miniconda3/envs/cancerit/lib/liblzma.so.5.2.6
7f5a23ae9000-7f5a23aea000 rw-p 00027000 00:2b 14885991866705956940       /home/baorx/miniconda3/envs/cancerit/lib/liblzma.so.5.2.6
7f5a23aea000-7f5a23aeb000 rw-p 00000000 00:00 0 
7f5a23aeb000-7f5a23aed000 r--p 00000000 00:2b 2988501068377944316        /home/baorx/miniconda3/envs/cancerit/lib/libbz2.so.1.0.8
7f5a23aed000-7f5a23afb000 r-xp 00002000 00:2b 2988501068377944316        /home/baorx/miniconda3/envs/cancerit/lib/libbz2.so.1.0.8
7f5a23afb000-7f5a23afd000 r--p 00010000 00:2b 2988501068377944316        /home/baorx/miniconda3/envs/cancerit/lib/libbz2.so.1.0.8
7f5a23afd000-7f5a23afe000 r--p 00011000 00:2b 2988501068377944316        /home/baorx/miniconda3/envs/cancerit/lib/libbz2.so.1.0.8
7f5a23afe000-7f5a23aff000 rw-p 00012000 00:2b 2988501068377944316        /home/baorx/miniconda3/envs/cancerit/lib/libbz2.so.1.0.8
7f5a23aff000-7f5a23b02000 r--p 00000000 00:2b 11235798539474949561       /home/baorx/miniconda3/envs/cancerit/lib/libz.so.1.3.1
7f5a23b02000-7f5a23b11000 r-xp 00003000 00:2b 11235798539474949561       /home/baorx/miniconda3/envs/cancerit/lib/libz.so.1.3.1
7f5a23b11000-7f5a23b18000 r--p 00012000 00:2b 11235798539474949561       /home/baorx/miniconda3/envs/cancerit/lib/libz.so.1.3.1
7f5a23b18000-7f5a23b19000 r--p 00018000 00:2b 11235798539474949561       /home/baorx/miniconda3/envs/cancerit/lib/libz.so.1.3.1
7f5a23b19000-7f5a23b1a000 rw-p 00019000 00:2b 11235798539474949561       /home/baorx/miniconda3/envs/cancerit/lib/libz.so.1.3.1
7f5a23b1a000-7f5a23b1b000 rw-p 00000000 00:00 0 
7f5a23b31000-7f5a23b32000 rw-p 00000000 00:00 0 
7f5a23b32000-7f5a23b41000 r--p 00000000 00:2b 10940355597678270174       /home/baorx/miniconda3/envs/cancerit/lib/libhts.so.1.21
7f5a23b41000-7f5a23c13000 r-xp 0000f000 00:2b 10940355597678270174       /home/baorx/miniconda3/envs/cancerit/lib/libhts.so.1.21
7f5a23c13000-7f5a23c36000 r--p 000e1000 00:2b 10940355597678270174       /home/baorx/miniconda3/envs/cancerit/lib/libhts.so.1.21
7f5a23c36000-7f5a23c38000 r--p 00103000 00:2b 10940355597678270174       /home/baorx/miniconda3/envs/cancerit/lib/libhts.so.1.21
7f5a23c38000-7f5a23c3d000 rw-p 00105000 00:2b 10940355597678270174       /home/baorx/miniconda3/envs/cancerit/lib/libhts.so.1.21
7f5a23c3d000-7f5a23c3f000 rw-p 00000000 00:00 0 
7f5a23c3f000-7f5a23c40000 r--p 00021000 fd:00 11016345                   /usr/lib64/ld-2.17.so
7f5a23c40000-7f5a23c41000 rw-p 00022000 fd:00 11016345                   /usr/lib64/ld-2.17.so
7f5a23c41000-7f5a23c42000 rw-p 00000000 00:00 0 
7fff74a33000-7fff74a54000 rw-p 00000000 00:00 0                          [stack]
7fff74b02000-7fff74b04000 r-xp 00000000 00:00 0                          [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0                  [vsyscall]
[E::sam_itr_next] Null iterator
[ERROR] (src/bam_access.c: bam_access_get_multi_position_base_counts:379 errno: None) Error detected (-2) when trying to iterate through region.
[ERROR] (./src/alleleCounter.c: main:432 errno: None) Error scanning through bam file for loci list with dense snps.
======= Backtrace: =========
/lib64/libc.so.6(+0x7f5e4)[0x7f2e02da15e4]
/home/baorx/miniconda3/envs/cancerit/bin/alleleCounter(main+0x144)[0x55da8d189454]
/lib64/libc.so.6(__libc_start_main+0xf5)[0x7f2e02d44445]
/home/baorx/miniconda3/envs/cancerit/bin/alleleCounter(+0x2aa1)[0x55da8d189aa1]
======= Memory map: ========
55da8d187000-55da8d189000 r--p 00000000 00:2b 6384932095811731369        /home/baorx/miniconda3/envs/cancerit/bin/alleleCounter
55da8d189000-55da8d18d000 r-xp 00002000 00:2b 6384932095811731369        /home/baorx/miniconda3/envs/cancerit/bin/alleleCounter
55da8d18d000-55da8d18f000 r--p 00006000 00:2b 6384932095811731369        /home/baorx/miniconda3/envs/cancerit/bin/alleleCounter
55da8d18f000-55da8d190000 r--p 00008000 00:2b 6384932095811731369        /home/baorx/miniconda3/envs/cancerit/bin/alleleCounter
55da8d190000-55da8d191000 rw-p 00009000 00:2b 6384932095811731369        /home/baorx/miniconda3/envs/cancerit/bin/alleleCounter
55da8db0e000-55db3c7fb000 rw-p 00000000 00:00 0                          [heap]
7f2e02b1a000-7f2e02b21000 r-xp 00000000 fd:00 11016382                   /usr/lib64/librt-2.17.so
7f2e02b21000-7f2e02d20000 ---p 00007000 fd:00 11016382                   /usr/lib64/librt-2.17.so
7f2e02d20000-7f2e02d21000 r--p 00006000 fd:00 11016382                   /usr/lib64/librt-2.17.so
7f2e02d21000-7f2e02d22000 rw-p 00007000 fd:00 11016382                   /usr/lib64/librt-2.17.so
7f2e02d22000-7f2e02ee5000 r-xp 00000000 fd:00 11016352                   /usr/lib64/libc-2.17.so
7f2e02ee5000-7f2e030e4000 ---p 001c3000 fd:00 11016352                   /usr/lib64/libc-2.17.so
7f2e030e4000-7f2e030e8000 r--p 001c2000 fd:00 11016352                   /usr/lib64/libc-2.17.so
7f2e030e8000-7f2e030ea000 rw-p 001c6000 fd:00 11016352                   /usr/lib64/libc-2.17.so
7f2e030ea000-7f2e030ef000 rw-p 00000000 00:00 0 
7f2e030ef000-7f2e030f1000 r-xp 00000000 fd:00 11016358                   /usr/lib64/libdl-2.17.so
7f2e030f1000-7f2e032f1000 ---p 00002000 fd:00 11016358                   /usr/lib64/libdl-2.17.so
7f2e032f1000-7f2e032f2000 r--p 00002000 fd:00 11016358                   /usr/lib64/libdl-2.17.so
7f2e032f2000-7f2e032f3000 rw-p 00003000 fd:00 11016358                   /usr/lib64/libdl-2.17.so
7f2e032f3000-7f2e033f4000 r-xp 00000000 fd:00 11016360                   /usr/lib64/libm-2.17.so
7f2e033f4000-7f2e035f3000 ---p 00101000 fd:00 11016360                   /usr/lib64/libm-2.17.so
7f2e035f3000-7f2e035f4000 r--p 00100000 fd:00 11016360                   /usr/lib64/libm-2.17.so
7f2e035f4000-7f2e035f5000 rw-p 00101000 fd:00 11016360                   /usr/lib64/libm-2.17.so
7f2e035f5000-7f2e0360c000 r-xp 00000000 fd:00 11016378                   /usr/lib64/libpthread-2.17.so
7f2e0360c000-7f2e0380b000 ---p 00017000 fd:00 11016378                   /usr/lib64/libpthread-2.17.so
7f2e0380b000-7f2e0380c000 r--p 00016000 fd:00 11016378                   /usr/lib64/libpthread-2.17.so
7f2e0380c000-7f2e0380d000 rw-p 00017000 fd:00 11016378                   /usr/lib64/libpthread-2.17.so
7f2e0380d000-7f2e03811000 rw-p 00000000 00:00 0 
7f2e03811000-7f2e03833000 r-xp 00000000 fd:00 11016345                   /usr/lib64/ld-2.17.so
7f2e03879000-7f2e0387d000 r--p 00000000 00:2b 12547459619057434142       /home/baorx/miniconda3/envs/cancerit/lib/libgcc_s.so.1
7f2e0387d000-7f2e03892000 r-xp 00004000 00:2b 12547459619057434142       /home/baorx/miniconda3/envs/cancerit/lib/libgcc_s.so.1
7f2e03892000-7f2e03896000 r--p 00019000 00:2b 12547459619057434142       /home/baorx/miniconda3/envs/cancerit/lib/libgcc_s.so.1
7f2e03896000-7f2e03897000 r--p 0001c000 00:2b 12547459619057434142       /home/baorx/miniconda3/envs/cancerit/lib/libgcc_s.so.1
7f2e03897000-7f2e03898000 rw-p 0001d000 00:2b 12547459619057434142       /home/baorx/miniconda3/envs/cancerit/lib/libgcc_s.so.1
7f2e03898000-7f2e0389c000 rw-p 00000000 00:00 0 
7f2e0389c000-7f2e0389d000 r--p 00000000 00:2b 4384565586930135332        /home/baorx/miniconda3/envs/cancerit/lib/libdeflate.so.0
7f2e0389d000-7f2e038ac000 r-xp 00001000 00:2b 4384565586930135332        /home/baorx/miniconda3/envs/cancerit/lib/libdeflate.so.0
7f2e038ac000-7f2e038b1000 r--p 00010000 00:2b 4384565586930135332        /home/baorx/miniconda3/envs/cancerit/lib/libdeflate.so.0
7f2e038b1000-7f2e038b2000 r--p 00014000 00:2b 4384565586930135332        /home/baorx/miniconda3/envs/cancerit/lib/libdeflate.so.0
7f2e038b2000-7f2e038b3000 rw-p 00015000 00:2b 4384565586930135332        /home/baorx/miniconda3/envs/cancerit/lib/libdeflate.so.0
7f2e038b3000-7f2e038b4000 rw-p 00000000 00:00 0 
7f2e038b4000-7f2e038b8000 r--p 00000000 00:2b 14885991866705956940       /home/baorx/miniconda3/envs/cancerit/lib/liblzma.so.5.2.6
7f2e038b8000-7f2e038cf000 r-xp 00004000 00:2b 14885991866705956940       /home/baorx/miniconda3/envs/cancerit/lib/liblzma.so.5.2.6
7f2e038cf000-7f2e038da000 r--p 0001b000 00:2b 14885991866705956940       /home/baorx/miniconda3/envs/cancerit/lib/liblzma.so.5.2.6
7f2e038da000-7f2e038db000 ---p 00026000 00:2b 14885991866705956940       /home/baorx/miniconda3/envs/cancerit/lib/liblzma.so.5.2.6
7f2e038db000-7f2e038dc000 r--p 00026000 00:2b 14885991866705956940       /home/baorx/miniconda3/envs/cancerit/lib/liblzma.so.5.2.6
7f2e038dc000-7f2e038dd000 rw-p 00027000 00:2b 14885991866705956940       /home/baorx/miniconda3/envs/cancerit/lib/liblzma.so.5.2.6
7f2e038dd000-7f2e038de000 rw-p 00000000 00:00 0 
7f2e038de000-7f2e038e0000 r--p 00000000 00:2b 2988501068377944316        /home/baorx/miniconda3/envs/cancerit/lib/libbz2.so.1.0.8
7f2e038e0000-7f2e038ee000 r-xp 00002000 00:2b 2988501068377944316        /home/baorx/miniconda3/envs/cancerit/lib/libbz2.so.1.0.8
7f2e038ee000-7f2e038f0000 r--p 00010000 00:2b 2988501068377944316        /home/baorx/miniconda3/envs/cancerit/lib/libbz2.so.1.0.8
7f2e038f0000-7f2e038f1000 r--p 00011000 00:2b 2988501068377944316        /home/baorx/miniconda3/envs/cancerit/lib/libbz2.so.1.0.8
7f2e038f1000-7f2e038f2000 rw-p 00012000 00:2b 2988501068377944316        /home/baorx/miniconda3/envs/cancerit/lib/libbz2.so.1.0.8
7f2e038f2000-7f2e038f5000 r--p 00000000 00:2b 11235798539474949561       /home/baorx/miniconda3/envs/cancerit/lib/libz.so.1.3.1
7f2e038f5000-7f2e03904000 r-xp 00003000 00:2b 11235798539474949561       /home/baorx/miniconda3/envs/cancerit/lib/libz.so.1.3.1
7f2e03904000-7f2e0390b000 r--p 00012000 00:2b 11235798539474949561       /home/baorx/miniconda3/envs/cancerit/lib/libz.so.1.3.1
7f2e0390b000-7f2e0390c000 r--p 00018000 00:2b 11235798539474949561       /home/baorx/miniconda3/envs/cancerit/lib/libz.so.1.3.1
7f2e0390c000-7f2e0390d000 rw-p 00019000 00:2b 11235798539474949561       /home/baorx/miniconda3/envs/cancerit/lib/libz.so.1.3.1
7f2e0390d000-7f2e0390e000 rw-p 00000000 00:00 0 
7f2e03924000-7f2e03925000 rw-p 00000000 00:00 0 
7f2e03925000-7f2e03934000 r--p 00000000 00:2b 10940355597678270174       /home/baorx/miniconda3/envs/cancerit/lib/libhts.so.1.21
7f2e03934000-7f2e03a06000 r-xp 0000f000 00:2b 10940355597678270174       /home/baorx/miniconda3/envs/cancerit/lib/libhts.so.1.21
7f2e03a06000-7f2e03a29000 r--p 000e1000 00:2b 10940355597678270174       /home/baorx/miniconda3/envs/cancerit/lib/libhts.so.1.21
7f2e03a29000-7f2e03a2b000 r--p 00103000 00:2b 10940355597678270174       /home/baorx/miniconda3/envs/cancerit/lib/libhts.so.1.21
7f2e03a2b000-7f2e03a30000 rw-p 00105000 00:2b 10940355597678270174       /home/baorx/miniconda3/envs/cancerit/lib/libhts.so.1.21
7f2e03a30000-7f2e03a32000 rw-p 00000000 00:00 0 
7f2e03a32000-7f2e03a33000 r--p 00021000 fd:00 11016345                   /usr/lib64/ld-2.17.so
7f2e03a33000-7f2e03a34000 rw-p 00022000 fd:00 11016345                   /usr/lib64/ld-2.17.so
7f2e03a34000-7f2e03a35000 rw-p 00000000 00:00 0 
7ffd66f32000-7ffd66f53000 rw-p 00000000 00:00 0                          [stack]
7ffd66fb9000-7ffd66fbb000 r-xp 00000000 00:00 0                          [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0                  [vsyscall]
*** Error in `/home/baorx/miniconda3/envs/cancerit/bin/alleleCounter': munmap_chunk(): invalid pointer: 0x00007ffe29a81455 ***
Done reading locis
Multi pos start:
*** Error in `/home/baorx/miniconda3/envs/cancerit/bin/alleleCounter': munmap_chunk(): invalid pointer: 0x00007ffd564a4455 ***
======= Backtrace: =========
/lib64/libc.so.6(+0x7f5e4)[0x7fd11e4675e4]
/home/baorx/miniconda3/envs/cancerit/bin/alleleCounter(main+0x144)[0x55e6afa04454]
/lib64/libc.so.6(__libc_start_main+0xf5)[0x7fd11e40a445]
/home/baorx/miniconda3/envs/cancerit/bin/alleleCounter(+0x2aa1)[0x55e6afa04aa1]
======= Memory map: ========
55e6afa02000-55e6afa04000 r--p 00000000 00:2b 6384932095811731369        /home/baorx/miniconda3/envs/cancerit/bin/alleleCounter
55e6afa04000-55e6afa08000 r-xp 00002000 00:2b 6384932095811731369        /home/baorx/miniconda3/envs/cancerit/bin/alleleCounter
55e6afa08000-55e6afa0a000 r--p 00006000 00:2b 6384932095811731369        /home/baorx/miniconda3/envs/cancerit/bin/alleleCounter
55e6afa0a000-55e6afa0b000 r--p 00008000 00:2b 6384932095811731369        /home/baorx/miniconda3/envs/cancerit/bin/alleleCounter
55e6afa0b000-55e6afa0c000 rw-p 00009000 00:2b 6384932095811731369        /home/baorx/miniconda3/envs/cancerit/bin/alleleCounter
55e6b05b9000-55e7a8dbb000 rw-p 00000000 00:00 0                          [heap]
7fd11e1e0000-7fd11e1e7000 r-xp 00000000 fd:00 11016382                   /usr/lib64/librt-2.17.so
7fd11e1e7000-7fd11e3e6000 ---p 00007000 fd:00 11016382                   /usr/lib64/librt-2.17.so
7fd11e3e6000-7fd11e3e7000 r--p 00006000 fd:00 11016382                   /usr/lib64/librt-2.17.so
7fd11e3e7000-7fd11e3e8000 rw-p 00007000 fd:00 11016382                   /usr/lib64/librt-2.17.so
7fd11e3e8000-7fd11e5ab000 r-xp 00000000 fd:00 11016352                   /usr/lib64/libc-2.17.so
7fd11e5ab000-7fd11e7aa000 ---p 001c3000 fd:00 11016352                   /usr/lib64/libc-2.17.so
7fd11e7aa000-7fd11e7ae000 r--p 001c2000 fd:00 11016352                   /usr/lib64/libc-2.17.so
7fd11e7ae000-7fd11e7b0000 rw-p 001c6000 fd:00 11016352                   /usr/lib64/libc-2.17.so
7fd11e7b0000-7fd11e7b5000 rw-p 00000000 00:00 0 
7fd11e7b5000-7fd11e7b7000 r-xp 00000000 fd:00 11016358                   /usr/lib64/libdl-2.17.so
7fd11e7b7000-7fd11e9b7000 ---p 00002000 fd:00 11016358                   /usr/lib64/libdl-2.17.so
7fd11e9b7000-7fd11e9b8000 r--p 00002000 fd:00 11016358                   /usr/lib64/libdl-2.17.so
7fd11e9b8000-7fd11e9b9000 rw-p 00003000 fd:00 11016358                   /usr/lib64/libdl-2.17.so
7fd11e9b9000-7fd11eaba000 r-xp 00000000 fd:00 11016360                   /usr/lib64/libm-2.17.so
7fd11eaba000-7fd11ecb9000 ---p 00101000 fd:00 11016360                   /usr/lib64/libm-2.17.so
7fd11ecb9000-7fd11ecba000 r--p 00100000 fd:00 11016360                   /usr/lib64/libm-2.17.so
7fd11ecba000-7fd11ecbb000 rw-p 00101000 fd:00 11016360                   /usr/lib64/libm-2.17.so
7fd11ecbb000-7fd11ecd2000 r-xp 00000000 fd:00 11016378                   /usr/lib64/libpthread-2.17.so
7fd11ecd2000-7fd11eed1000 ---p 00017000 fd:00 11016378                   /usr/lib64/libpthread-2.17.so
7fd11eed1000-7fd11eed2000 r--p 00016000 fd:00 11016378                   /usr/lib64/libpthread-2.17.so
7fd11eed2000-7fd11eed3000 rw-p 00017000 fd:00 11016378                   /usr/lib64/libpthread-2.17.so
7fd11eed3000-7fd11eed7000 rw-p 00000000 00:00 0 
7fd11eed7000-7fd11eef9000 r-xp 00000000 fd:00 11016345                   /usr/lib64/ld-2.17.so
7fd11ef3f000-7fd11ef43000 r--p 00000000 00:2b 12547459619057434142       /home/baorx/miniconda3/envs/cancerit/lib/libgcc_s.so.1
7fd11ef43000-7fd11ef58000 r-xp 00004000 00:2b 12547459619057434142       /home/baorx/miniconda3/envs/cancerit/lib/libgcc_s.so.1
7fd11ef58000-7fd11ef5c000 r--p 00019000 00:2b 12547459619057434142       /home/baorx/miniconda3/envs/cancerit/lib/libgcc_s.so.1
7fd11ef5c000-7fd11ef5d000 r--p 0001c000 00:2b 12547459619057434142       /home/baorx/miniconda3/envs/cancerit/lib/libgcc_s.so.1
7fd11ef5d000-7fd11ef5e000 rw-p 0001d000 00:2b 12547459619057434142       /home/baorx/miniconda3/envs/cancerit/lib/libgcc_s.so.1
7fd11ef5e000-7fd11ef62000 rw-p 00000000 00:00 0 
7fd11ef62000-7fd11ef63000 r--p 00000000 00:2b 4384565586930135332        /home/baorx/miniconda3/envs/cancerit/lib/libdeflate.so.0
7fd11ef63000-7fd11ef72000 r-xp 00001000 00:2b 4384565586930135332        /home/baorx/miniconda3/envs/cancerit/lib/libdeflate.so.0
7fd11ef72000-7fd11ef77000 r--p 00010000 00:2b 4384565586930135332        /home/baorx/miniconda3/envs/cancerit/lib/libdeflate.so.0
7fd11ef77000-7fd11ef78000 r--p 00014000 00:2b 4384565586930135332        /home/baorx/miniconda3/envs/cancerit/lib/libdeflate.so.0
7fd11ef78000-7fd11ef79000 rw-p 00015000 00:2b 4384565586930135332        /home/baorx/miniconda3/envs/cancerit/lib/libdeflate.so.0
7fd11ef79000-7fd11ef7a000 rw-p 00000000 00:00 0 
7fd11ef7a000-7fd11ef7e000 r--p 00000000 00:2b 14885991866705956940       /home/baorx/miniconda3/envs/cancerit/lib/liblzma.so.5.2.6
7fd11ef7e000-7fd11ef95000 r-xp 00004000 00:2b 14885991866705956940       /home/baorx/miniconda3/envs/cancerit/lib/liblzma.so.5.2.6
7fd11ef95000-7fd11efa0000 r--p 0001b000 00:2b 14885991866705956940       /home/baorx/miniconda3/envs/cancerit/lib/liblzma.so.5.2.6
7fd11efa0000-7fd11efa1000 ---p 00026000 00:2b 14885991866705956940       /home/baorx/miniconda3/envs/cancerit/lib/liblzma.so.5.2.6
7fd11efa1000-7fd11efa2000 r--p 00026000 00:2b 14885991866705956940       /home/baorx/miniconda3/envs/cancerit/lib/liblzma.so.5.2.6
7fd11efa2000-7fd11efa3000 rw-p 00027000 00:2b 14885991866705956940       /home/baorx/miniconda3/envs/cancerit/lib/liblzma.so.5.2.6
7fd11efa3000-7fd11efa4000 rw-p 00000000 00:00 0 
7fd11efa4000-7fd11efa6000 r--p 00000000 00:2b 2988501068377944316        /home/baorx/miniconda3/envs/cancerit/lib/libbz2.so.1.0.8
7fd11efa6000-7fd11efb4000 r-xp 00002000 00:2b 2988501068377944316        /home/baorx/miniconda3/envs/cancerit/lib/libbz2.so.1.0.8
7fd11efb4000-7fd11efb6000 r--p 00010000 00:2b 2988501068377944316        /home/baorx/miniconda3/envs/cancerit/lib/libbz2.so.1.0.8
7fd11efb6000-7fd11efb7000 r--p 00011000 00:2b 2988501068377944316        /home/baorx/miniconda3/envs/cancerit/lib/libbz2.so.1.0.8
7fd11efb7000-7fd11efb8000 rw-p 00012000 00:2b 2988501068377944316        /home/baorx/miniconda3/envs/cancerit/lib/libbz2.so.1.0.8
7fd11efb8000-7fd11efbb000 r--p 00000000 00:2b 11235798539474949561       /home/baorx/miniconda3/envs/cancerit/lib/libz.so.1.3.1
7fd11efbb000-7fd11efca000 r-xp 00003000 00:2b 11235798539474949561       /home/baorx/miniconda3/envs/cancerit/lib/libz.so.1.3.1
7fd11efca000-7fd11efd1000 r--p 00012000 00:2b 11235798539474949561       /home/baorx/miniconda3/envs/cancerit/lib/libz.so.1.3.1
7fd11efd1000-7fd11efd2000 r--p 00018000 00:2b 11235798539474949561       /home/baorx/miniconda3/envs/cancerit/lib/libz.so.1.3.1
7fd11efd2000-7fd11efd3000 rw-p 00019000 00:2b 11235798539474949561       /home/baorx/miniconda3/envs/cancerit/lib/libz.so.1.3.1
7fd11efd3000-7fd11efd4000 rw-p 00000000 00:00 0 
7fd11efea000-7fd11efeb000 rw-p 00000000 00:00 0 
7fd11efeb000-7fd11effa000 r--p 00000000 00:2b 10940355597678270174       /home/baorx/miniconda3/envs/cancerit/lib/libhts.so.1.21
7fd11effa000-7fd11f0cc000 r-xp 0000f000 00:2b 10940355597678270174       /home/baorx/miniconda3/envs/cancerit/lib/libhts.so.1.21
7fd11f0cc000-7fd11f0ef000 r--p 000e1000 00:2b 10940355597678270174       /home/baorx/miniconda3/envs/cancerit/lib/libhts.so.1.21
7fd11f0ef000-7fd11f0f1000 r--p 00103000 00:2b 10940355597678270174       /home/baorx/miniconda3/envs/cancerit/lib/libhts.so.1.21
7fd11f0f1000-7fd11f0f6000 rw-p 00105000 00:2b 10940355597678270174       /home/baorx/miniconda3/envs/cancerit/lib/libhts.so.1.21
7fd11f0f6000-7fd11f0f8000 rw-p 00000000 00:00 0 
7fd11f0f8000-7fd11f0f9000 r--p 00021000 fd:00 11016345                   /usr/lib64/ld-2.17.so
7fd11f0f9000-7fd11f0fa000 rw-p 00022000 fd:00 11016345                   /usr/lib64/ld-2.17.so
7fd11f0fa000-7fd11f0fb000 rw-p 00000000 00:00 0 
7ffc51151000-7ffc51172000 rw-p 00000000 00:00 0                          [stack]
7ffc511d1000-7ffc511d3000 r-xp 00000000 00:00 0                          [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0                  [vsyscall]
[E::sam_itr_next] Null iterator
[ERROR] (src/bam_access.c: bam_access_get_multi_position_base_counts:379 errno: None) Error detected (-2) when trying to iterate through region.
[ERROR] (./src/alleleCounter.c: main:432 errno: None) Error scanning through bam file for loci list with dense snps.
======= Backtrace: =========
/lib64/libc.so.6(+0x7f5e4)[0x7f40f78355e4]
/home/baorx/miniconda3/envs/cancerit/bin/alleleCounter(main+0x144)[0x561566826454]
/lib64/libc.so.6(__libc_start_main+0xf5)[0x7f40f77d8445]
/home/baorx/miniconda3/envs/cancerit/bin/alleleCounter(+0x2aa1)[0x561566826aa1]
======= Memory map: ========
561566824000-561566826000 r--p 00000000 00:2b 6384932095811731369        /home/baorx/miniconda3/envs/cancerit/bin/alleleCounter
561566826000-56156682a000 r-xp 00002000 00:2b 6384932095811731369        /home/baorx/miniconda3/envs/cancerit/bin/alleleCounter
56156682a000-56156682c000 r--p 00006000 00:2b 6384932095811731369        /home/baorx/miniconda3/envs/cancerit/bin/alleleCounter
56156682c000-56156682d000 r--p 00008000 00:2b 6384932095811731369        /home/baorx/miniconda3/envs/cancerit/bin/alleleCounter
56156682d000-56156682e000 rw-p 00009000 00:2b 6384932095811731369        /home/baorx/miniconda3/envs/cancerit/bin/alleleCounter
561566f6d000-561612e2d000 rw-p 00000000 00:00 0                          [heap]
7f40f75ae000-7f40f75b5000 r-xp 00000000 fd:00 11016382                   /usr/lib64/librt-2.17.so
7f40f75b5000-7f40f77b4000 ---p 00007000 fd:00 11016382                   /usr/lib64/librt-2.17.so
7f40f77b4000-7f40f77b5000 r--p 00006000 fd:00 11016382                   /usr/lib64/librt-2.17.so
7f40f77b5000-7f40f77b6000 rw-p 00007000 fd:00 11016382                   /usr/lib64/librt-2.17.so
7f40f77b6000-7f40f7979000 r-xp 00000000 fd:00 11016352                   /usr/lib64/libc-2.17.so
7f40f7979000-7f40f7b78000 ---p 001c3000 fd:00 11016352                   /usr/lib64/libc-2.17.so
7f40f7b78000-7f40f7b7c000 r--p 001c2000 fd:00 11016352                   /usr/lib64/libc-2.17.so
7f40f7b7c000-7f40f7b7e000 rw-p 001c6000 fd:00 11016352                   /usr/lib64/libc-2.17.so
7f40f7b7e000-7f40f7b83000 rw-p 00000000 00:00 0 
7f40f7b83000-7f40f7b85000 r-xp 00000000 fd:00 11016358                   /usr/lib64/libdl-2.17.so
7f40f7b85000-7f40f7d85000 ---p 00002000 fd:00 11016358                   /usr/lib64/libdl-2.17.so
7f40f7d85000-7f40f7d86000 r--p 00002000 fd:00 11016358                   /usr/lib64/libdl-2.17.so
7f40f7d86000-7f40f7d87000 rw-p 00003000 fd:00 11016358                   /usr/lib64/libdl-2.17.so
7f40f7d87000-7f40f7e88000 r-xp 00000000 fd:00 11016360                   /usr/lib64/libm-2.17.so
7f40f7e88000-7f40f8087000 ---p 00101000 fd:00 11016360                   /usr/lib64/libm-2.17.so
7f40f8087000-7f40f8088000 r--p 00100000 fd:00 11016360                   /usr/lib64/libm-2.17.so
7f40f8088000-7f40f8089000 rw-p 00101000 fd:00 11016360                   /usr/lib64/libm-2.17.so
7f40f8089000-7f40f80a0000 r-xp 00000000 fd:00 11016378                   /usr/lib64/libpthread-2.17.so
7f40f80a0000-7f40f829f000 ---p 00017000 fd:00 11016378                   /usr/lib64/libpthread-2.17.so
7f40f829f000-7f40f82a0000 r--p 00016000 fd:00 11016378                   /usr/lib64/libpthread-2.17.so
7f40f82a0000-7f40f82a1000 rw-p 00017000 fd:00 11016378                   /usr/lib64/libpthread-2.17.so
7f40f82a1000-7f40f82a5000 rw-p 00000000 00:00 0 
7f40f82a5000-7f40f82c7000 r-xp 00000000 fd:00 11016345                   /usr/lib64/ld-2.17.so
7f40f830d000-7f40f8311000 r--p 00000000 00:2b 12547459619057434142       /home/baorx/miniconda3/envs/cancerit/lib/libgcc_s.so.1
7f40f8311000-7f40f8326000 r-xp 00004000 00:2b 12547459619057434142       /home/baorx/miniconda3/envs/cancerit/lib/libgcc_s.so.1
7f40f8326000-7f40f832a000 r--p 00019000 00:2b 12547459619057434142       /home/baorx/miniconda3/envs/cancerit/lib/libgcc_s.so.1
7f40f832a000-7f40f832b000 r--p 0001c000 00:2b 12547459619057434142       /home/baorx/miniconda3/envs/cancerit/lib/libgcc_s.so.1
7f40f832b000-7f40f832c000 rw-p 0001d000 00:2b 12547459619057434142       /home/baorx/miniconda3/envs/cancerit/lib/libgcc_s.so.1
7f40f832c000-7f40f8330000 rw-p 00000000 00:00 0 
7f40f8330000-7f40f8331000 r--p 00000000 00:2b 4384565586930135332        /home/baorx/miniconda3/envs/cancerit/lib/libdeflate.so.0
7f40f8331000-7f40f8340000 r-xp 00001000 00:2b 4384565586930135332        /home/baorx/miniconda3/envs/cancerit/lib/libdeflate.so.0
7f40f8340000-7f40f8345000 r--p 00010000 00:2b 4384565586930135332        /home/baorx/miniconda3/envs/cancerit/lib/libdeflate.so.0
7f40f8345000-7f40f8346000 r--p 00014000 00:2b 4384565586930135332        /home/baorx/miniconda3/envs/cancerit/lib/libdeflate.so.0
7f40f8346000-7f40f8347000 rw-p 00015000 00:2b 4384565586930135332        /home/baorx/miniconda3/envs/cancerit/lib/libdeflate.so.0
7f40f8347000-7f40f8348000 rw-p 00000000 00:00 0 
7f40f8348000-7f40f834c000 r--p 00000000 00:2b 14885991866705956940       /home/baorx/miniconda3/envs/cancerit/lib/liblzma.so.5.2.6
7f40f834c000-7f40f8363000 r-xp 00004000 00:2b 14885991866705956940       /home/baorx/miniconda3/envs/cancerit/lib/liblzma.so.5.2.6
7f40f8363000-7f40f836e000 r--p 0001b000 00:2b 14885991866705956940       /home/baorx/miniconda3/envs/cancerit/lib/liblzma.so.5.2.6
7f40f836e000-7f40f836f000 ---p 00026000 00:2b 14885991866705956940       /home/baorx/miniconda3/envs/cancerit/lib/liblzma.so.5.2.6
7f40f836f000-7f40f8370000 r--p 00026000 00:2b 14885991866705956940       /home/baorx/miniconda3/envs/cancerit/lib/liblzma.so.5.2.6
7f40f8370000-7f40f8371000 rw-p 00027000 00:2b 14885991866705956940       /home/baorx/miniconda3/envs/cancerit/lib/liblzma.so.5.2.6
7f40f8371000-7f40f8372000 rw-p 00000000 00:00 0 
7f40f8372000-7f40f8374000 r--p 00000000 00:2b 2988501068377944316        /home/baorx/miniconda3/envs/cancerit/lib/libbz2.so.1.0.8
7f40f8374000-7f40f8382000 r-xp 00002000 00:2b 2988501068377944316        /home/baorx/miniconda3/envs/cancerit/lib/libbz2.so.1.0.8
7f40f8382000-7f40f8384000 r--p 00010000 00:2b 2988501068377944316        /home/baorx/miniconda3/envs/cancerit/lib/libbz2.so.1.0.8
7f40f8384000-7f40f8385000 r--p 00011000 00:2b 2988501068377944316        /home/baorx/miniconda3/envs/cancerit/lib/libbz2.so.1.0.8
7f40f8385000-7f40f8386000 rw-p 00012000 00:2b 2988501068377944316        /home/baorx/miniconda3/envs/cancerit/lib/libbz2.so.1.0.8
7f40f8386000-7f40f8389000 r--p 00000000 00:2b 11235798539474949561       /home/baorx/miniconda3/envs/cancerit/lib/libz.so.1.3.1
7f40f8389000-7f40f8398000 r-xp 00003000 00:2b 11235798539474949561       /home/baorx/miniconda3/envs/cancerit/lib/libz.so.1.3.1
7f40f8398000-7f40f839f000 r--p 00012000 00:2b 11235798539474949561       /home/baorx/miniconda3/envs/cancerit/lib/libz.so.1.3.1
7f40f839f000-7f40f83a0000 r--p 00018000 00:2b 11235798539474949561       /home/baorx/miniconda3/envs/cancerit/lib/libz.so.1.3.1
7f40f83a0000-7f40f83a1000 rw-p 00019000 00:2b 11235798539474949561       /home/baorx/miniconda3/envs/cancerit/lib/libz.so.1.3.1
7f40f83a1000-7f40f83a2000 rw-p 00000000 00:00 0 
7f40f83b8000-7f40f83b9000 rw-p 00000000 00:00 0 
7f40f83b9000-7f40f83c8000 r--p 00000000 00:2b 10940355597678270174       /home/baorx/miniconda3/envs/cancerit/lib/libhts.so.1.21
7f40f83c8000-7f40f849a000 r-xp 0000f000 00:2b 10940355597678270174       /home/baorx/miniconda3/envs/cancerit/lib/libhts.so.1.21
7f40f849a000-7f40f84bd000 r--p 000e1000 00:2b 10940355597678270174       /home/baorx/miniconda3/envs/cancerit/lib/libhts.so.1.21
7f40f84bd000-7f40f84bf000 r--p 00103000 00:2b 10940355597678270174       /home/baorx/miniconda3/envs/cancerit/lib/libhts.so.1.21
7f40f84bf000-7f40f84c4000 rw-p 00105000 00:2b 10940355597678270174       /home/baorx/miniconda3/envs/cancerit/lib/libhts.so.1.21
7f40f84c4000-7f40f84c6000 rw-p 00000000 00:00 0 
7f40f84c6000-7f40f84c7000 r--p 00021000 fd:00 11016345                   /usr/lib64/ld-2.17.so
7f40f84c7000-7f40f84c8000 rw-p 00022000 fd:00 11016345                   /usr/lib64/ld-2.17.so
7f40f84c8000-7f40f84c9000 rw-p 00000000 00:00 0 
7ffe29a61000-7ffe29a82000 rw-p 00000000 00:00 0                          [stack]
7ffe29a9c000-7ffe29a9e000 r-xp 00000000 00:00 0                          [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0                  [vsyscall]
======= Backtrace: =========
/lib64/libc.so.6(+0x7f5e4)[0x7f9f805c85e4]
/home/baorx/miniconda3/envs/cancerit/bin/alleleCounter(main+0x144)[0x55b972137454]
/lib64/libc.so.6(__libc_start_main+0xf5)[0x7f9f8056b445]
/home/baorx/miniconda3/envs/cancerit/bin/alleleCounter(+0x2aa1)[0x55b972137aa1]
======= Memory map: ========
55b972135000-55b972137000 r--p 00000000 00:2b 6384932095811731369        /home/baorx/miniconda3/envs/cancerit/bin/alleleCounter
55b972137000-55b97213b000 r-xp 00002000 00:2b 6384932095811731369        /home/baorx/miniconda3/envs/cancerit/bin/alleleCounter
55b97213b000-55b97213d000 r--p 00006000 00:2b 6384932095811731369        /home/baorx/miniconda3/envs/cancerit/bin/alleleCounter
55b97213d000-55b97213e000 r--p 00008000 00:2b 6384932095811731369        /home/baorx/miniconda3/envs/cancerit/bin/alleleCounter
55b97213e000-55b97213f000 rw-p 00009000 00:2b 6384932095811731369        /home/baorx/miniconda3/envs/cancerit/bin/alleleCounter
55b973b80000-55b9d4c94000 rw-p 00000000 00:00 0                          [heap]
7f9f80341000-7f9f80348000 r-xp 00000000 fd:00 11016382                   /usr/lib64/librt-2.17.so
7f9f80348000-7f9f80547000 ---p 00007000 fd:00 11016382                   /usr/lib64/librt-2.17.so
7f9f80547000-7f9f80548000 r--p 00006000 fd:00 11016382                   /usr/lib64/librt-2.17.so
7f9f80548000-7f9f80549000 rw-p 00007000 fd:00 11016382                   /usr/lib64/librt-2.17.so
7f9f80549000-7f9f8070c000 r-xp 00000000 fd:00 11016352                   /usr/lib64/libc-2.17.so
7f9f8070c000-7f9f8090b000 ---p 001c3000 fd:00 11016352                   /usr/lib64/libc-2.17.so
7f9f8090b000-7f9f8090f000 r--p 001c2000 fd:00 11016352                   /usr/lib64/libc-2.17.so
7f9f8090f000-7f9f80911000 rw-p 001c6000 fd:00 11016352                   /usr/lib64/libc-2.17.so
7f9f80911000-7f9f80916000 rw-p 00000000 00:00 0 
7f9f80916000-7f9f80918000 r-xp 00000000 fd:00 11016358                   /usr/lib64/libdl-2.17.so
7f9f80918000-7f9f80b18000 ---p 00002000 fd:00 11016358                   /usr/lib64/libdl-2.17.so
7f9f80b18000-7f9f80b19000 r--p 00002000 fd:00 11016358                   /usr/lib64/libdl-2.17.so
7f9f80b19000-7f9f80b1a000 rw-p 00003000 fd:00 11016358                   /usr/lib64/libdl-2.17.so
7f9f80b1a000-7f9f80c1b000 r-xp 00000000 fd:00 11016360                   /usr/lib64/libm-2.17.so
7f9f80c1b000-7f9f80e1a000 ---p 00101000 fd:00 11016360                   /usr/lib64/libm-2.17.so
7f9f80e1a000-7f9f80e1b000 r--p 00100000 fd:00 11016360                   /usr/lib64/libm-2.17.so
7f9f80e1b000-7f9f80e1c000 rw-p 00101000 fd:00 11016360                   /usr/lib64/libm-2.17.so
7f9f80e1c000-7f9f80e33000 r-xp 00000000 fd:00 11016378                   /usr/lib64/libpthread-2.17.so
7f9f80e33000-7f9f81032000 ---p 00017000 fd:00 11016378                   /usr/lib64/libpthread-2.17.so
7f9f81032000-7f9f81033000 r--p 00016000 fd:00 11016378                   /usr/lib64/libpthread-2.17.so
7f9f81033000-7f9f81034000 rw-p 00017000 fd:00 11016378                   /usr/lib64/libpthread-2.17.so
7f9f81034000-7f9f81038000 rw-p 00000000 00:00 0 
7f9f81038000-7f9f8105a000 r-xp 00000000 fd:00 11016345                   /usr/lib64/ld-2.17.so
7f9f810a0000-7f9f810a4000 r--p 00000000 00:2b 12547459619057434142       /home/baorx/miniconda3/envs/cancerit/lib/libgcc_s.so.1
7f9f810a4000-7f9f810b9000 r-xp 00004000 00:2b 12547459619057434142       /home/baorx/miniconda3/envs/cancerit/lib/libgcc_s.so.1
7f9f810b9000-7f9f810bd000 r--p 00019000 00:2b 12547459619057434142       /home/baorx/miniconda3/envs/cancerit/lib/libgcc_s.so.1
7f9f810bd000-7f9f810be000 r--p 0001c000 00:2b 12547459619057434142       /home/baorx/miniconda3/envs/cancerit/lib/libgcc_s.so.1
7f9f810be000-7f9f810bf000 rw-p 0001d000 00:2b 12547459619057434142       /home/baorx/miniconda3/envs/cancerit/lib/libgcc_s.so.1
7f9f810bf000-7f9f810c3000 rw-p 00000000 00:00 0 
7f9f810c3000-7f9f810c4000 r--p 00000000 00:2b 4384565586930135332        /home/baorx/miniconda3/envs/cancerit/lib/libdeflate.so.0
7f9f810c4000-7f9f810d3000 r-xp 00001000 00:2b 4384565586930135332        /home/baorx/miniconda3/envs/cancerit/lib/libdeflate.so.0
7f9f810d3000-7f9f810d8000 r--p 00010000 00:2b 4384565586930135332        /home/baorx/miniconda3/envs/cancerit/lib/libdeflate.so.0
7f9f810d8000-7f9f810d9000 r--p 00014000 00:2b 4384565586930135332        /home/baorx/miniconda3/envs/cancerit/lib/libdeflate.so.0
7f9f810d9000-7f9f810da000 rw-p 00015000 00:2b 4384565586930135332        /home/baorx/miniconda3/envs/cancerit/lib/libdeflate.so.0
7f9f810da000-7f9f810db000 rw-p 00000000 00:00 0 
7f9f810db000-7f9f810df000 r--p 00000000 00:2b 14885991866705956940       /home/baorx/miniconda3/envs/cancerit/lib/liblzma.so.5.2.6
7f9f810df000-7f9f810f6000 r-xp 00004000 00:2b 14885991866705956940       /home/baorx/miniconda3/envs/cancerit/lib/liblzma.so.5.2.6
7f9f810f6000-7f9f81101000 r--p 0001b000 00:2b 14885991866705956940       /home/baorx/miniconda3/envs/cancerit/lib/liblzma.so.5.2.6
7f9f81101000-7f9f81102000 ---p 00026000 00:2b 14885991866705956940       /home/baorx/miniconda3/envs/cancerit/lib/liblzma.so.5.2.6
7f9f81102000-7f9f81103000 r--p 00026000 00:2b 14885991866705956940       /home/baorx/miniconda3/envs/cancerit/lib/liblzma.so.5.2.6
7f9f81103000-7f9f81104000 rw-p 00027000 00:2b 14885991866705956940       /home/baorx/miniconda3/envs/cancerit/lib/liblzma.so.5.2.6
7f9f81104000-7f9f81105000 rw-p 00000000 00:00 0 
7f9f81105000-7f9f81107000 r--p 00000000 00:2b 2988501068377944316        /home/baorx/miniconda3/envs/cancerit/lib/libbz2.so.1.0.8
7f9f81107000-7f9f81115000 r-xp 00002000 00:2b 2988501068377944316        /home/baorx/miniconda3/envs/cancerit/lib/libbz2.so.1.0.8
7f9f81115000-7f9f81117000 r--p 00010000 00:2b 2988501068377944316        /home/baorx/miniconda3/envs/cancerit/lib/libbz2.so.1.0.8
7f9f81117000-7f9f81118000 r--p 00011000 00:2b 2988501068377944316        /home/baorx/miniconda3/envs/cancerit/lib/libbz2.so.1.0.8
7f9f81118000-7f9f81119000 rw-p 00012000 00:2b 2988501068377944316        /home/baorx/miniconda3/envs/cancerit/lib/libbz2.so.1.0.8
7f9f81119000-7f9f8111c000 r--p 00000000 00:2b 11235798539474949561       /home/baorx/miniconda3/envs/cancerit/lib/libz.so.1.3.1
7f9f8111c000-7f9f8112b000 r-xp 00003000 00:2b 11235798539474949561       /home/baorx/miniconda3/envs/cancerit/lib/libz.so.1.3.1
7f9f8112b000-7f9f81132000 r--p 00012000 00:2b 11235798539474949561       /home/baorx/miniconda3/envs/cancerit/lib/libz.so.1.3.1
7f9f81132000-7f9f81133000 r--p 00018000 00:2b 11235798539474949561       /home/baorx/miniconda3/envs/cancerit/lib/libz.so.1.3.1
7f9f81133000-7f9f81134000 rw-p 00019000 00:2b 11235798539474949561       /home/baorx/miniconda3/envs/cancerit/lib/libz.so.1.3.1
7f9f81134000-7f9f81135000 rw-p 00000000 00:00 0 
7f9f8114b000-7f9f8114c000 rw-p 00000000 00:00 0 
7f9f8114c000-7f9f8115b000 r--p 00000000 00:2b 10940355597678270174       /home/baorx/miniconda3/envs/cancerit/lib/libhts.so.1.21
7f9f8115b000-7f9f8122d000 r-xp 0000f000 00:2b 10940355597678270174       /home/baorx/miniconda3/envs/cancerit/lib/libhts.so.1.21
7f9f8122d000-7f9f81250000 r--p 000e1000 00:2b 10940355597678270174       /home/baorx/miniconda3/envs/cancerit/lib/libhts.so.1.21
7f9f81250000-7f9f81252000 r--p 00103000 00:2b 10940355597678270174       /home/baorx/miniconda3/envs/cancerit/lib/libhts.so.1.21
7f9f81252000-7f9f81257000 rw-p 00105000 00:2b 10940355597678270174       /home/baorx/miniconda3/envs/cancerit/lib/libhts.so.1.21
7f9f81257000-7f9f81259000 rw-p 00000000 00:00 0 
7f9f81259000-7f9f8125a000 r--p 00021000 fd:00 11016345                   /usr/lib64/ld-2.17.so
7f9f8125a000-7f9f8125b000 rw-p 00022000 fd:00 11016345                   /usr/lib64/ld-2.17.so
7f9f8125b000-7f9f8125c000 rw-p 00000000 00:00 0 
7ffd56484000-7ffd564a5000 rw-p 00000000 00:00 0                          [stack]
7ffd565d0000-7ffd565d2000 r-xp 00000000 00:00 0                          [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0                  [vsyscall]
*** Error in `/home/baorx/miniconda3/envs/cancerit/bin/alleleCounter': munmap_chunk(): invalid pointer: 0x00007fffad126455 ***
Done reading locis
Multi pos start:
[E::sam_itr_next] Null iterator
[ERROR] (src/bam_access.c: bam_access_get_multi_position_base_counts:379 errno: None) Error detected (-2) when trying to iterate through region.
[ERROR] (./src/alleleCounter.c: main:432 errno: None) Error scanning through bam file for loci list with dense snps.
======= Backtrace: =========
/lib64/libc.so.6(+0x7f5e4)[0x7f8e4c16c5e4]
/home/baorx/miniconda3/envs/cancerit/bin/alleleCounter(main+0x144)[0x556507992454]
/lib64/libc.so.6(__libc_start_main+0xf5)[0x7f8e4c10f445]
/home/baorx/miniconda3/envs/cancerit/bin/alleleCounter(+0x2aa1)[0x556507992aa1]
======= Memory map: ========
556507990000-556507992000 r--p 00000000 00:2b 6384932095811731369        /home/baorx/miniconda3/envs/cancerit/bin/alleleCounter
556507992000-556507996000 r-xp 00002000 00:2b 6384932095811731369        /home/baorx/miniconda3/envs/cancerit/bin/alleleCounter
556507996000-556507998000 r--p 00006000 00:2b 6384932095811731369        /home/baorx/miniconda3/envs/cancerit/bin/alleleCounter
556507998000-556507999000 r--p 00008000 00:2b 6384932095811731369        /home/baorx/miniconda3/envs/cancerit/bin/alleleCounter
556507999000-55650799a000 rw-p 00009000 00:2b 6384932095811731369        /home/baorx/miniconda3/envs/cancerit/bin/alleleCounter
556509373000-5565af9b7000 rw-p 00000000 00:00 0                          [heap]
7f8e4bee5000-7f8e4beec000 r-xp 00000000 fd:00 11016382                   /usr/lib64/librt-2.17.so
7f8e4beec000-7f8e4c0eb000 ---p 00007000 fd:00 11016382                   /usr/lib64/librt-2.17.so
7f8e4c0eb000-7f8e4c0ec000 r--p 00006000 fd:00 11016382                   /usr/lib64/librt-2.17.so
7f8e4c0ec000-7f8e4c0ed000 rw-p 00007000 fd:00 11016382                   /usr/lib64/librt-2.17.so
7f8e4c0ed000-7f8e4c2b0000 r-xp 00000000 fd:00 11016352                   /usr/lib64/libc-2.17.so
7f8e4c2b0000-7f8e4c4af000 ---p 001c3000 fd:00 11016352                   /usr/lib64/libc-2.17.so
7f8e4c4af000-7f8e4c4b3000 r--p 001c2000 fd:00 11016352                   /usr/lib64/libc-2.17.so
7f8e4c4b3000-7f8e4c4b5000 rw-p 001c6000 fd:00 11016352                   /usr/lib64/libc-2.17.so
7f8e4c4b5000-7f8e4c4ba000 rw-p 00000000 00:00 0 
7f8e4c4ba000-7f8e4c4bc000 r-xp 00000000 fd:00 11016358                   /usr/lib64/libdl-2.17.so
7f8e4c4bc000-7f8e4c6bc000 ---p 00002000 fd:00 11016358                   /usr/lib64/libdl-2.17.so
7f8e4c6bc000-7f8e4c6bd000 r--p 00002000 fd:00 11016358                   /usr/lib64/libdl-2.17.so
7f8e4c6bd000-7f8e4c6be000 rw-p 00003000 fd:00 11016358                   /usr/lib64/libdl-2.17.so
7f8e4c6be000-7f8e4c7bf000 r-xp 00000000 fd:00 11016360                   /usr/lib64/libm-2.17.so
7f8e4c7bf000-7f8e4c9be000 ---p 00101000 fd:00 11016360                   /usr/lib64/libm-2.17.so
7f8e4c9be000-7f8e4c9bf000 r--p 00100000 fd:00 11016360                   /usr/lib64/libm-2.17.so
7f8e4c9bf000-7f8e4c9c0000 rw-p 00101000 fd:00 11016360                   /usr/lib64/libm-2.17.so
7f8e4c9c0000-7f8e4c9d7000 r-xp 00000000 fd:00 11016378                   /usr/lib64/libpthread-2.17.so
7f8e4c9d7000-7f8e4cbd6000 ---p 00017000 fd:00 11016378                   /usr/lib64/libpthread-2.17.so
7f8e4cbd6000-7f8e4cbd7000 r--p 00016000 fd:00 11016378                   /usr/lib64/libpthread-2.17.so
7f8e4cbd7000-7f8e4cbd8000 rw-p 00017000 fd:00 11016378                   /usr/lib64/libpthread-2.17.so
7f8e4cbd8000-7f8e4cbdc000 rw-p 00000000 00:00 0 
7f8e4cbdc000-7f8e4cbfe000 r-xp 00000000 fd:00 11016345                   /usr/lib64/ld-2.17.so
7f8e4cc44000-7f8e4cc48000 r--p 00000000 00:2b 12547459619057434142       /home/baorx/miniconda3/envs/cancerit/lib/libgcc_s.so.1
7f8e4cc48000-7f8e4cc5d000 r-xp 00004000 00:2b 12547459619057434142       /home/baorx/miniconda3/envs/cancerit/lib/libgcc_s.so.1
7f8e4cc5d000-7f8e4cc61000 r--p 00019000 00:2b 12547459619057434142       /home/baorx/miniconda3/envs/cancerit/lib/libgcc_s.so.1
7f8e4cc61000-7f8e4cc62000 r--p 0001c000 00:2b 12547459619057434142       /home/baorx/miniconda3/envs/cancerit/lib/libgcc_s.so.1
7f8e4cc62000-7f8e4cc63000 rw-p 0001d000 00:2b 12547459619057434142       /home/baorx/miniconda3/envs/cancerit/lib/libgcc_s.so.1
7f8e4cc63000-7f8e4cc67000 rw-p 00000000 00:00 0 
7f8e4cc67000-7f8e4cc68000 r--p 00000000 00:2b 4384565586930135332        /home/baorx/miniconda3/envs/cancerit/lib/libdeflate.so.0
7f8e4cc68000-7f8e4cc77000 r-xp 00001000 00:2b 4384565586930135332        /home/baorx/miniconda3/envs/cancerit/lib/libdeflate.so.0
7f8e4cc77000-7f8e4cc7c000 r--p 00010000 00:2b 4384565586930135332        /home/baorx/miniconda3/envs/cancerit/lib/libdeflate.so.0
7f8e4cc7c000-7f8e4cc7d000 r--p 00014000 00:2b 4384565586930135332        /home/baorx/miniconda3/envs/cancerit/lib/libdeflate.so.0
7f8e4cc7d000-7f8e4cc7e000 rw-p 00015000 00:2b 4384565586930135332        /home/baorx/miniconda3/envs/cancerit/lib/libdeflate.so.0
7f8e4cc7e000-7f8e4cc7f000 rw-p 00000000 00:00 0 
7f8e4cc7f000-7f8e4cc83000 r--p 00000000 00:2b 14885991866705956940       /home/baorx/miniconda3/envs/cancerit/lib/liblzma.so.5.2.6
7f8e4cc83000-7f8e4cc9a000 r-xp 00004000 00:2b 14885991866705956940       /home/baorx/miniconda3/envs/cancerit/lib/liblzma.so.5.2.6
7f8e4cc9a000-7f8e4cca5000 r--p 0001b000 00:2b 14885991866705956940       /home/baorx/miniconda3/envs/cancerit/lib/liblzma.so.5.2.6
7f8e4cca5000-7f8e4cca6000 ---p 00026000 00:2b 14885991866705956940       /home/baorx/miniconda3/envs/cancerit/lib/liblzma.so.5.2.6
7f8e4cca6000-7f8e4cca7000 r--p 00026000 00:2b 14885991866705956940       /home/baorx/miniconda3/envs/cancerit/lib/liblzma.so.5.2.6
7f8e4cca7000-7f8e4cca8000 rw-p 00027000 00:2b 14885991866705956940       /home/baorx/miniconda3/envs/cancerit/lib/liblzma.so.5.2.6
7f8e4cca8000-7f8e4cca9000 rw-p 00000000 00:00 0 
7f8e4cca9000-7f8e4ccab000 r--p 00000000 00:2b 2988501068377944316        /home/baorx/miniconda3/envs/cancerit/lib/libbz2.so.1.0.8
7f8e4ccab000-7f8e4ccb9000 r-xp 00002000 00:2b 2988501068377944316        /home/baorx/miniconda3/envs/cancerit/lib/libbz2.so.1.0.8
7f8e4ccb9000-7f8e4ccbb000 r--p 00010000 00:2b 2988501068377944316        /home/baorx/miniconda3/envs/cancerit/lib/libbz2.so.1.0.8
7f8e4ccbb000-7f8e4ccbc000 r--p 00011000 00:2b 2988501068377944316        /home/baorx/miniconda3/envs/cancerit/lib/libbz2.so.1.0.8
7f8e4ccbc000-7f8e4ccbd000 rw-p 00012000 00:2b 2988501068377944316        /home/baorx/miniconda3/envs/cancerit/lib/libbz2.so.1.0.8
7f8e4ccbd000-7f8e4ccc0000 r--p 00000000 00:2b 11235798539474949561       /home/baorx/miniconda3/envs/cancerit/lib/libz.so.1.3.1
7f8e4ccc0000-7f8e4cccf000 r-xp 00003000 00:2b 11235798539474949561       /home/baorx/miniconda3/envs/cancerit/lib/libz.so.1.3.1
7f8e4cccf000-7f8e4ccd6000 r--p 00012000 00:2b 11235798539474949561       /home/baorx/miniconda3/envs/cancerit/lib/libz.so.1.3.1
7f8e4ccd6000-7f8e4ccd7000 r--p 00018000 00:2b 11235798539474949561       /home/baorx/miniconda3/envs/cancerit/lib/libz.so.1.3.1
7f8e4ccd7000-7f8e4ccd8000 rw-p 00019000 00:2b 11235798539474949561       /home/baorx/miniconda3/envs/cancerit/lib/libz.so.1.3.1
7f8e4ccd8000-7f8e4ccd9000 rw-p 00000000 00:00 0 
7f8e4ccef000-7f8e4ccf0000 rw-p 00000000 00:00 0 
7f8e4ccf0000-7f8e4ccff000 r--p 00000000 00:2b 10940355597678270174       /home/baorx/miniconda3/envs/cancerit/lib/libhts.so.1.21
7f8e4ccff000-7f8e4cdd1000 r-xp 0000f000 00:2b 10940355597678270174       /home/baorx/miniconda3/envs/cancerit/lib/libhts.so.1.21
7f8e4cdd1000-7f8e4cdf4000 r--p 000e1000 00:2b 10940355597678270174       /home/baorx/miniconda3/envs/cancerit/lib/libhts.so.1.21
7f8e4cdf4000-7f8e4cdf6000 r--p 00103000 00:2b 10940355597678270174       /home/baorx/miniconda3/envs/cancerit/lib/libhts.so.1.21
7f8e4cdf6000-7f8e4cdfb000 rw-p 00105000 00:2b 10940355597678270174       /home/baorx/miniconda3/envs/cancerit/lib/libhts.so.1.21
7f8e4cdfb000-7f8e4cdfd000 rw-p 00000000 00:00 0 
7f8e4cdfd000-7f8e4cdfe000 r--p 00021000 fd:00 11016345                   /usr/lib64/ld-2.17.so
7f8e4cdfe000-7f8e4cdff000 rw-p 00022000 fd:00 11016345                   /usr/lib64/ld-2.17.so
7f8e4cdff000-7f8e4ce00000 rw-p 00000000 00:00 0 
7fffad106000-7fffad127000 rw-p 00000000 00:00 0                          [stack]
7fffad1bd000-7fffad1bf000 r-xp 00000000 00:00 0                          [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0                  [vsyscall]
*** Error in `/home/baorx/miniconda3/envs/cancerit/bin/alleleCounter': munmap_chunk(): invalid pointer: 0x00007fffc3c8b457 ***
*** Error in `/home/baorx/miniconda3/envs/cancerit/bin/alleleCounter': munmap_chunk(): invalid pointer: 0x00007ffe1cec7457 ***
Done reading locis
Multi pos start:
[E::sam_itr_next] Null iterator
[ERROR] (src/bam_access.c: bam_access_get_multi_position_base_counts:379 errno: None) Error detected (-2) when trying to iterate through region.
[ERROR] (./src/alleleCounter.c: main:432 errno: None) Error scanning through bam file for loci list with dense snps.
======= Backtrace: =========
/lib64/libc.so.6(+0x7f5e4)[0x7f8b2aaaf5e4]
/home/baorx/miniconda3/envs/cancerit/bin/alleleCounter(main+0x144)[0x560ced259454]
/lib64/libc.so.6(__libc_start_main+0xf5)[0x7f8b2aa52445]
/home/baorx/miniconda3/envs/cancerit/bin/alleleCounter(+0x2aa1)[0x560ced259aa1]
======= Memory map: ========
560ced257000-560ced259000 r--p 00000000 00:2b 6384932095811731369        /home/baorx/miniconda3/envs/cancerit/bin/alleleCounter
560ced259000-560ced25d000 r-xp 00002000 00:2b 6384932095811731369        /home/baorx/miniconda3/envs/cancerit/bin/alleleCounter
560ced25d000-560ced25f000 r--p 00006000 00:2b 6384932095811731369        /home/baorx/miniconda3/envs/cancerit/bin/alleleCounter
560ced25f000-560ced260000 r--p 00008000 00:2b 6384932095811731369        /home/baorx/miniconda3/envs/cancerit/bin/alleleCounter
560ced260000-560ced261000 rw-p 00009000 00:2b 6384932095811731369        /home/baorx/miniconda3/envs/cancerit/bin/alleleCounter
560ceedf2000-560db26a6000 rw-p 00000000 00:00 0                          [heap]
7f8b2a828000-7f8b2a82f000 r-xp 00000000 fd:00 11016382                   /usr/lib64/librt-2.17.so
7f8b2a82f000-7f8b2aa2e000 ---p 00007000 fd:00 11016382                   /usr/lib64/librt-2.17.so
7f8b2aa2e000-7f8b2aa2f000 r--p 00006000 fd:00 11016382                   /usr/lib64/librt-2.17.so
7f8b2aa2f000-7f8b2aa30000 rw-p 00007000 fd:00 11016382                   /usr/lib64/librt-2.17.so
7f8b2aa30000-7f8b2abf3000 r-xp 00000000 fd:00 11016352                   /usr/lib64/libc-2.17.so
7f8b2abf3000-7f8b2adf2000 ---p 001c3000 fd:00 11016352                   /usr/lib64/libc-2.17.so
7f8b2adf2000-7f8b2adf6000 r--p 001c2000 fd:00 11016352                   /usr/lib64/libc-2.17.so
7f8b2adf6000-7f8b2adf8000 rw-p 001c6000 fd:00 11016352                   /usr/lib64/libc-2.17.so
7f8b2adf8000-7f8b2adfd000 rw-p 00000000 00:00 0 
7f8b2adfd000-7f8b2adff000 r-xp 00000000 fd:00 11016358                   /usr/lib64/libdl-2.17.so
7f8b2adff000-7f8b2afff000 ---p 00002000 fd:00 11016358                   /usr/lib64/libdl-2.17.so
7f8b2afff000-7f8b2b000000 r--p 00002000 fd:00 11016358                   /usr/lib64/libdl-2.17.so
7f8b2b000000-7f8b2b001000 rw-p 00003000 fd:00 11016358                   /usr/lib64/libdl-2.17.so
7f8b2b001000-7f8b2b102000 r-xp 00000000 fd:00 11016360                   /usr/lib64/libm-2.17.so
7f8b2b102000-7f8b2b301000 ---p 00101000 fd:00 11016360                   /usr/lib64/libm-2.17.so
7f8b2b301000-7f8b2b302000 r--p 00100000 fd:00 11016360                   /usr/lib64/libm-2.17.so
7f8b2b302000-7f8b2b303000 rw-p 00101000 fd:00 11016360                   /usr/lib64/libm-2.17.so
7f8b2b303000-7f8b2b31a000 r-xp 00000000 fd:00 11016378                   /usr/lib64/libpthread-2.17.so
7f8b2b31a000-7f8b2b519000 ---p 00017000 fd:00 11016378                   /usr/lib64/libpthread-2.17.so
7f8b2b519000-7f8b2b51a000 r--p 00016000 fd:00 11016378                   /usr/lib64/libpthread-2.17.so
7f8b2b51a000-7f8b2b51b000 rw-p 00017000 fd:00 11016378                   /usr/lib64/libpthread-2.17.so
7f8b2b51b000-7f8b2b51f000 rw-p 00000000 00:00 0 
7f8b2b51f000-7f8b2b541000 r-xp 00000000 fd:00 11016345                   /usr/lib64/ld-2.17.so
7f8b2b587000-7f8b2b58b000 r--p 00000000 00:2b 12547459619057434142       /home/baorx/miniconda3/envs/cancerit/lib/libgcc_s.so.1
7f8b2b58b000-7f8b2b5a0000 r-xp 00004000 00:2b 12547459619057434142       /home/baorx/miniconda3/envs/cancerit/lib/libgcc_s.so.1
7f8b2b5a0000-7f8b2b5a4000 r--p 00019000 00:2b 12547459619057434142       /home/baorx/miniconda3/envs/cancerit/lib/libgcc_s.so.1
7f8b2b5a4000-7f8b2b5a5000 r--p 0001c000 00:2b 12547459619057434142       /home/baorx/miniconda3/envs/cancerit/lib/libgcc_s.so.1
7f8b2b5a5000-7f8b2b5a6000 rw-p 0001d000 00:2b 12547459619057434142       /home/baorx/miniconda3/envs/cancerit/lib/libgcc_s.so.1
7f8b2b5a6000-7f8b2b5aa000 rw-p 00000000 00:00 0 
7f8b2b5aa000-7f8b2b5ab000 r--p 00000000 00:2b 4384565586930135332        /home/baorx/miniconda3/envs/cancerit/lib/libdeflate.so.0
7f8b2b5ab000-7f8b2b5ba000 r-xp 00001000 00:2b 4384565586930135332        /home/baorx/miniconda3/envs/cancerit/lib/libdeflate.so.0
7f8b2b5ba000-7f8b2b5bf000 r--p 00010000 00:2b 4384565586930135332        /home/baorx/miniconda3/envs/cancerit/lib/libdeflate.so.0
7f8b2b5bf000-7f8b2b5c0000 r--p 00014000 00:2b 4384565586930135332        /home/baorx/miniconda3/envs/cancerit/lib/libdeflate.so.0
7f8b2b5c0000-7f8b2b5c1000 rw-p 00015000 00:2b 4384565586930135332        /home/baorx/miniconda3/envs/cancerit/lib/libdeflate.so.0
7f8b2b5c1000-7f8b2b5c2000 rw-p 00000000 00:00 0 
7f8b2b5c2000-7f8b2b5c6000 r--p 00000000 00:2b 14885991866705956940       /home/baorx/miniconda3/envs/cancerit/lib/liblzma.so.5.2.6
7f8b2b5c6000-7f8b2b5dd000 r-xp 00004000 00:2b 14885991866705956940       /home/baorx/miniconda3/envs/cancerit/lib/liblzma.so.5.2.6
7f8b2b5dd000-7f8b2b5e8000 r--p 0001b000 00:2b 14885991866705956940       /home/baorx/miniconda3/envs/cancerit/lib/liblzma.so.5.2.6
7f8b2b5e8000-7f8b2b5e9000 ---p 00026000 00:2b 14885991866705956940       /home/baorx/miniconda3/envs/cancerit/lib/liblzma.so.5.2.6
7f8b2b5e9000-7f8b2b5ea000 r--p 00026000 00:2b 14885991866705956940       /home/baorx/miniconda3/envs/cancerit/lib/liblzma.so.5.2.6
7f8b2b5ea000-7f8b2b5eb000 rw-p 00027000 00:2b 14885991866705956940       /home/baorx/miniconda3/envs/cancerit/lib/liblzma.so.5.2.6
7f8b2b5eb000-7f8b2b5ec000 rw-p 00000000 00:00 0 
7f8b2b5ec000-7f8b2b5ee000 r--p 00000000 00:2b 2988501068377944316        /home/baorx/miniconda3/envs/cancerit/lib/libbz2.so.1.0.8
7f8b2b5ee000-7f8b2b5fc000 r-xp 00002000 00:2b 2988501068377944316        /home/baorx/miniconda3/envs/cancerit/lib/libbz2.so.1.0.8
7f8b2b5fc000-7f8b2b5fe000 r--p 00010000 00:2b 2988501068377944316        /home/baorx/miniconda3/envs/cancerit/lib/libbz2.so.1.0.8
7f8b2b5fe000-7f8b2b5ff000 r--p 00011000 00:2b 2988501068377944316        /home/baorx/miniconda3/envs/cancerit/lib/libbz2.so.1.0.8
7f8b2b5ff000-7f8b2b600000 rw-p 00012000 00:2b 2988501068377944316        /home/baorx/miniconda3/envs/cancerit/lib/libbz2.so.1.0.8
7f8b2b600000-7f8b2b603000 r--p 00000000 00:2b 11235798539474949561       /home/baorx/miniconda3/envs/cancerit/lib/libz.so.1.3.1
7f8b2b603000-7f8b2b612000 r-xp 00003000 00:2b 11235798539474949561       /home/baorx/miniconda3/envs/cancerit/lib/libz.so.1.3.1
7f8b2b612000-7f8b2b619000 r--p 00012000 00:2b 11235798539474949561       /home/baorx/miniconda3/envs/cancerit/lib/libz.so.1.3.1
7f8b2b619000-7f8b2b61a000 r--p 00018000 00:2b 11235798539474949561       /home/baorx/miniconda3/envs/cancerit/lib/libz.so.1.3.1
7f8b2b61a000-7f8b2b61b000 rw-p 00019000 00:2b 11235798539474949561       /home/baorx/miniconda3/envs/cancerit/lib/libz.so.1.3.1
7f8b2b61b000-7f8b2b61c000 rw-p 00000000 00:00 0 
7f8b2b632000-7f8b2b633000 rw-p 00000000 00:00 0 
7f8b2b633000-7f8b2b642000 r--p 00000000 00:2b 10940355597678270174       /home/baorx/miniconda3/envs/cancerit/lib/libhts.so.1.21
7f8b2b642000-7f8b2b714000 r-xp 0000f000 00:2b 10940355597678270174       /home/baorx/miniconda3/envs/cancerit/lib/libhts.so.1.21
7f8b2b714000-7f8b2b737000 r--p 000e1000 00:2b 10940355597678270174       /home/baorx/miniconda3/envs/cancerit/lib/libhts.so.1.21
7f8b2b737000-7f8b2b739000 r--p 00103000 00:2b 10940355597678270174       /home/baorx/miniconda3/envs/cancerit/lib/libhts.so.1.21
7f8b2b739000-7f8b2b73e000 rw-p 00105000 00:2b 10940355597678270174       /home/baorx/miniconda3/envs/cancerit/lib/libhts.so.1.21
7f8b2b73e000-7f8b2b740000 rw-p 00000000 00:00 0 
7f8b2b740000-7f8b2b741000 r--p 00021000 fd:00 11016345                   /usr/lib64/ld-2.17.so
7f8b2b741000-7f8b2b742000 rw-p 00022000 fd:00 11016345                   /usr/lib64/ld-2.17.so
7f8b2b742000-7f8b2b743000 rw-p 00000000 00:00 0 
7fffc3c6b000-7fffc3c8c000 rw-p 00000000 00:00 0                          [stack]
7fffc3d4d000-7fffc3d4f000 r-xp 00000000 00:00 0                          [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0                  [vsyscall]
Done reading locis
Multi pos start:
======= Backtrace: =========
/lib64/libc.so.6(+0x7f5e4)[0x7f927d1335e4]
/home/baorx/miniconda3/envs/cancerit/bin/alleleCounter(main+0x144)[0x55cb99e6d454]
/lib64/libc.so.6(__libc_start_main+0xf5)[0x7f927d0d6445]
/home/baorx/miniconda3/envs/cancerit/bin/alleleCounter(+0x2aa1)[0x55cb99e6daa1]
======= Memory map: ========
55cb99e6b000-55cb99e6d000 r--p 00000000 00:2b 6384932095811731369        /home/baorx/miniconda3/envs/cancerit/bin/alleleCounter
55cb99e6d000-55cb99e71000 r-xp 00002000 00:2b 6384932095811731369        /home/baorx/miniconda3/envs/cancerit/bin/alleleCounter
55cb99e71000-55cb99e73000 r--p 00006000 00:2b 6384932095811731369        /home/baorx/miniconda3/envs/cancerit/bin/alleleCounter
55cb99e73000-55cb99e74000 r--p 00008000 00:2b 6384932095811731369        /home/baorx/miniconda3/envs/cancerit/bin/alleleCounter
55cb99e74000-55cb99e75000 rw-p 00009000 00:2b 6384932095811731369        /home/baorx/miniconda3/envs/cancerit/bin/alleleCounter
55cb9b306000-55cc788eb000 rw-p 00000000 00:00 0                          [heap]
7f927ceac000-7f927ceb3000 r-xp 00000000 fd:00 11016382                   /usr/lib64/librt-2.17.so
7f927ceb3000-7f927d0b2000 ---p 00007000 fd:00 11016382                   /usr/lib64/librt-2.17.so
7f927d0b2000-7f927d0b3000 r--p 00006000 fd:00 11016382                   /usr/lib64/librt-2.17.so
7f927d0b3000-7f927d0b4000 rw-p 00007000 fd:00 11016382                   /usr/lib64/librt-2.17.so
7f927d0b4000-7f927d277000 r-xp 00000000 fd:00 11016352                   /usr/lib64/libc-2.17.so
7f927d277000-7f927d476000 ---p 001c3000 fd:00 11016352                   /usr/lib64/libc-2.17.so
7f927d476000-7f927d47a000 r--p 001c2000 fd:00 11016352                   /usr/lib64/libc-2.17.so
7f927d47a000-7f927d47c000 rw-p 001c6000 fd:00 11016352                   /usr/lib64/libc-2.17.so
7f927d47c000-7f927d481000 rw-p 00000000 00:00 0 
7f927d481000-7f927d483000 r-xp 00000000 fd:00 11016358                   /usr/lib64/libdl-2.17.so
7f927d483000-7f927d683000 ---p 00002000 fd:00 11016358                   /usr/lib64/libdl-2.17.so
7f927d683000-7f927d684000 r--p 00002000 fd:00 11016358                   /usr/lib64/libdl-2.17.so
7f927d684000-7f927d685000 rw-p 00003000 fd:00 11016358                   /usr/lib64/libdl-2.17.so
7f927d685000-7f927d786000 r-xp 00000000 fd:00 11016360                   /usr/lib64/libm-2.17.so
7f927d786000-7f927d985000 ---p 00101000 fd:00 11016360                   /usr/lib64/libm-2.17.so
7f927d985000-7f927d986000 r--p 00100000 fd:00 11016360                   /usr/lib64/libm-2.17.so
7f927d986000-7f927d987000 rw-p 00101000 fd:00 11016360                   /usr/lib64/libm-2.17.so
7f927d987000-7f927d99e000 r-xp 00000000 fd:00 11016378                   /usr/lib64/libpthread-2.17.so
7f927d99e000-7f927db9d000 ---p 00017000 fd:00 11016378                   /usr/lib64/libpthread-2.17.so
7f927db9d000-7f927db9e000 r--p 00016000 fd:00 11016378                   /usr/lib64/libpthread-2.17.so
7f927db9e000-7f927db9f000 rw-p 00017000 fd:00 11016378                   /usr/lib64/libpthread-2.17.so
7f927db9f000-7f927dba3000 rw-p 00000000 00:00 0 
7f927dba3000-7f927dbc5000 r-xp 00000000 fd:00 11016345                   /usr/lib64/ld-2.17.so
7f927dc0b000-7f927dc0f000 r--p 00000000 00:2b 12547459619057434142       /home/baorx/miniconda3/envs/cancerit/lib/libgcc_s.so.1
7f927dc0f000-7f927dc24000 r-xp 00004000 00:2b 12547459619057434142       /home/baorx/miniconda3/envs/cancerit/lib/libgcc_s.so.1
7f927dc24000-7f927dc28000 r--p 00019000 00:2b 12547459619057434142       /home/baorx/miniconda3/envs/cancerit/lib/libgcc_s.so.1
7f927dc28000-7f927dc29000 r--p 0001c000 00:2b 12547459619057434142       /home/baorx/miniconda3/envs/cancerit/lib/libgcc_s.so.1
7f927dc29000-7f927dc2a000 rw-p 0001d000 00:2b 12547459619057434142       /home/baorx/miniconda3/envs/cancerit/lib/libgcc_s.so.1
7f927dc2a000-7f927dc2e000 rw-p 00000000 00:00 0 
7f927dc2e000-7f927dc2f000 r--p 00000000 00:2b 4384565586930135332        /home/baorx/miniconda3/envs/cancerit/lib/libdeflate.so.0
7f927dc2f000-7f927dc3e000 r-xp 00001000 00:2b 4384565586930135332        /home/baorx/miniconda3/envs/cancerit/lib/libdeflate.so.0
7f927dc3e000-7f927dc43000 r--p 00010000 00:2b 4384565586930135332        /home/baorx/miniconda3/envs/cancerit/lib/libdeflate.so.0
7f927dc43000-7f927dc44000 r--p 00014000 00:2b 4384565586930135332        /home/baorx/miniconda3/envs/cancerit/lib/libdeflate.so.0
7f927dc44000-7f927dc45000 rw-p 00015000 00:2b 4384565586930135332        /home/baorx/miniconda3/envs/cancerit/lib/libdeflate.so.0
7f927dc45000-7f927dc46000 rw-p 00000000 00:00 0 
7f927dc46000-7f927dc4a000 r--p 00000000 00:2b 14885991866705956940       /home/baorx/miniconda3/envs/cancerit/lib/liblzma.so.5.2.6
7f927dc4a000-7f927dc61000 r-xp 00004000 00:2b 14885991866705956940       /home/baorx/miniconda3/envs/cancerit/lib/liblzma.so.5.2.6
7f927dc61000-7f927dc6c000 r--p 0001b000 00:2b 14885991866705956940       /home/baorx/miniconda3/envs/cancerit/lib/liblzma.so.5.2.6
7f927dc6c000-7f927dc6d000 ---p 00026000 00:2b 14885991866705956940       /home/baorx/miniconda3/envs/cancerit/lib/liblzma.so.5.2.6
7f927dc6d000-7f927dc6e000 r--p 00026000 00:2b 14885991866705956940       /home/baorx/miniconda3/envs/cancerit/lib/liblzma.so.5.2.6
7f927dc6e000-7f927dc6f000 rw-p 00027000 00:2b 14885991866705956940       /home/baorx/miniconda3/envs/cancerit/lib/liblzma.so.5.2.6
7f927dc6f000-7f927dc70000 rw-p 00000000 00:00 0 
7f927dc70000-7f927dc72000 r--p 00000000 00:2b 2988501068377944316        /home/baorx/miniconda3/envs/cancerit/lib/libbz2.so.1.0.8
7f927dc72000-7f927dc80000 r-xp 00002000 00:2b 2988501068377944316        /home/baorx/miniconda3/envs/cancerit/lib/libbz2.so.1.0.8
7f927dc80000-7f927dc82000 r--p 00010000 00:2b 2988501068377944316        /home/baorx/miniconda3/envs/cancerit/lib/libbz2.so.1.0.8
7f927dc82000-7f927dc83000 r--p 00011000 00:2b 2988501068377944316        /home/baorx/miniconda3/envs/cancerit/lib/libbz2.so.1.0.8
7f927dc83000-7f927dc84000 rw-p 00012000 00:2b 2988501068377944316        /home/baorx/miniconda3/envs/cancerit/lib/libbz2.so.1.0.8
7f927dc84000-7f927dc87000 r--p 00000000 00:2b 11235798539474949561       /home/baorx/miniconda3/envs/cancerit/lib/libz.so.1.3.1
7f927dc87000-7f927dc96000 r-xp 00003000 00:2b 11235798539474949561       /home/baorx/miniconda3/envs/cancerit/lib/libz.so.1.3.1
7f927dc96000-7f927dc9d000 r--p 00012000 00:2b 11235798539474949561       /home/baorx/miniconda3/envs/cancerit/lib/libz.so.1.3.1
7f927dc9d000-7f927dc9e000 r--p 00018000 00:2b 11235798539474949561       /home/baorx/miniconda3/envs/cancerit/lib/libz.so.1.3.1
7f927dc9e000-7f927dc9f000 rw-p 00019000 00:2b 11235798539474949561       /home/baorx/miniconda3/envs/cancerit/lib/libz.so.1.3.1
7f927dc9f000-7f927dca0000 rw-p 00000000 00:00 0 
7f927dcb6000-7f927dcb7000 rw-p 00000000 00:00 0 
7f927dcb7000-7f927dcc6000 r--p 00000000 00:2b 10940355597678270174       /home/baorx/miniconda3/envs/cancerit/lib/libhts.so.1.21
7f927dcc6000-7f927dd98000 r-xp 0000f000 00:2b 10940355597678270174       /home/baorx/miniconda3/envs/cancerit/lib/libhts.so.1.21
7f927dd98000-7f927ddbb000 r--p 000e1000 00:2b 10940355597678270174       /home/baorx/miniconda3/envs/cancerit/lib/libhts.so.1.21
7f927ddbb000-7f927ddbd000 r--p 00103000 00:2b 10940355597678270174       /home/baorx/miniconda3/envs/cancerit/lib/libhts.so.1.21
7f927ddbd000-7f927ddc2000 rw-p 00105000 00:2b 10940355597678270174       /home/baorx/miniconda3/envs/cancerit/lib/libhts.so.1.21
7f927ddc2000-7f927ddc4000 rw-p 00000000 00:00 0 
7f927ddc4000-7f927ddc5000 r--p 00021000 fd:00 11016345                   /usr/lib64/ld-2.17.so
7f927ddc5000-7f927ddc6000 rw-p 00022000 fd:00 11016345                   /usr/lib64/ld-2.17.so
7f927ddc6000-7f927ddc7000 rw-p 00000000 00:00 0 
7ffe1cea7000-7ffe1cec8000 rw-p 00000000 00:00 0                          [stack]
7ffe1cf91000-7ffe1cf93000 r-xp 00000000 00:00 0                          [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0                  [vsyscall]
[E::sam_itr_next] Null iterator
[ERROR] (src/bam_access.c: bam_access_get_multi_position_base_counts:379 errno: None) Error detected (-2) when trying to iterate through region.
[ERROR] (./src/alleleCounter.c: main:432 errno: None) Error scanning through bam file for loci list with dense snps.
*** Error in `/home/baorx/miniconda3/envs/cancerit/bin/alleleCounter': munmap_chunk(): invalid pointer: 0x00007ffcfbb80457 ***
Done reading locis
Multi pos start:
======= Backtrace: =========
/lib64/libc.so.6(+0x7f5e4)[0x7fba756355e4]
/home/baorx/miniconda3/envs/cancerit/bin/alleleCounter(main+0x144)[0x564c2297f454]
/lib64/libc.so.6(__libc_start_main+0xf5)[0x7fba755d8445]
/home/baorx/miniconda3/envs/cancerit/bin/alleleCounter(+0x2aa1)[0x564c2297faa1]
======= Memory map: ========
564c2297d000-564c2297f000 r--p 00000000 00:2b 6384932095811731369        /home/baorx/miniconda3/envs/cancerit/bin/alleleCounter
564c2297f000-564c22983000 r-xp 00002000 00:2b 6384932095811731369        /home/baorx/miniconda3/envs/cancerit/bin/alleleCounter
564c22983000-564c22985000 r--p 00006000 00:2b 6384932095811731369        /home/baorx/miniconda3/envs/cancerit/bin/alleleCounter
564c22985000-564c22986000 r--p 00008000 00:2b 6384932095811731369        /home/baorx/miniconda3/envs/cancerit/bin/alleleCounter
564c22986000-564c22987000 rw-p 00009000 00:2b 6384932095811731369        /home/baorx/miniconda3/envs/cancerit/bin/alleleCounter
564c23835000-564d3302f000 rw-p 00000000 00:00 0                          [heap]
7fba753ae000-7fba753b5000 r-xp 00000000 fd:00 11016382                   /usr/lib64/librt-2.17.so
7fba753b5000-7fba755b4000 ---p 00007000 fd:00 11016382                   /usr/lib64/librt-2.17.so
7fba755b4000-7fba755b5000 r--p 00006000 fd:00 11016382                   /usr/lib64/librt-2.17.so
7fba755b5000-7fba755b6000 rw-p 00007000 fd:00 11016382                   /usr/lib64/librt-2.17.so
7fba755b6000-7fba75779000 r-xp 00000000 fd:00 11016352                   /usr/lib64/libc-2.17.so
7fba75779000-7fba75978000 ---p 001c3000 fd:00 11016352                   /usr/lib64/libc-2.17.so
7fba75978000-7fba7597c000 r--p 001c2000 fd:00 11016352                   /usr/lib64/libc-2.17.so
7fba7597c000-7fba7597e000 rw-p 001c6000 fd:00 11016352                   /usr/lib64/libc-2.17.so
7fba7597e000-7fba75983000 rw-p 00000000 00:00 0 
7fba75983000-7fba75985000 r-xp 00000000 fd:00 11016358                   /usr/lib64/libdl-2.17.so
7fba75985000-7fba75b85000 ---p 00002000 fd:00 11016358                   /usr/lib64/libdl-2.17.so
7fba75b85000-7fba75b86000 r--p 00002000 fd:00 11016358                   /usr/lib64/libdl-2.17.so
7fba75b86000-7fba75b87000 rw-p 00003000 fd:00 11016358                   /usr/lib64/libdl-2.17.so
7fba75b87000-7fba75c88000 r-xp 00000000 fd:00 11016360                   /usr/lib64/libm-2.17.so
7fba75c88000-7fba75e87000 ---p 00101000 fd:00 11016360                   /usr/lib64/libm-2.17.so
7fba75e87000-7fba75e88000 r--p 00100000 fd:00 11016360                   /usr/lib64/libm-2.17.so
7fba75e88000-7fba75e89000 rw-p 00101000 fd:00 11016360                   /usr/lib64/libm-2.17.so
7fba75e89000-7fba75ea0000 r-xp 00000000 fd:00 11016378                   /usr/lib64/libpthread-2.17.so
7fba75ea0000-7fba7609f000 ---p 00017000 fd:00 11016378                   /usr/lib64/libpthread-2.17.so
7fba7609f000-7fba760a0000 r--p 00016000 fd:00 11016378                   /usr/lib64/libpthread-2.17.so
7fba760a0000-7fba760a1000 rw-p 00017000 fd:00 11016378                   /usr/lib64/libpthread-2.17.so
7fba760a1000-7fba760a5000 rw-p 00000000 00:00 0 
7fba760a5000-7fba760c7000 r-xp 00000000 fd:00 11016345                   /usr/lib64/ld-2.17.so
7fba7610d000-7fba76111000 r--p 00000000 00:2b 12547459619057434142       /home/baorx/miniconda3/envs/cancerit/lib/libgcc_s.so.1
7fba76111000-7fba76126000 r-xp 00004000 00:2b 12547459619057434142       /home/baorx/miniconda3/envs/cancerit/lib/libgcc_s.so.1
7fba76126000-7fba7612a000 r--p 00019000 00:2b 12547459619057434142       /home/baorx/miniconda3/envs/cancerit/lib/libgcc_s.so.1
7fba7612a000-7fba7612b000 r--p 0001c000 00:2b 12547459619057434142       /home/baorx/miniconda3/envs/cancerit/lib/libgcc_s.so.1
7fba7612b000-7fba7612c000 rw-p 0001d000 00:2b 12547459619057434142       /home/baorx/miniconda3/envs/cancerit/lib/libgcc_s.so.1
7fba7612c000-7fba76130000 rw-p 00000000 00:00 0 
7fba76130000-7fba76131000 r--p 00000000 00:2b 4384565586930135332        /home/baorx/miniconda3/envs/cancerit/lib/libdeflate.so.0
7fba76131000-7fba76140000 r-xp 00001000 00:2b 4384565586930135332        /home/baorx/miniconda3/envs/cancerit/lib/libdeflate.so.0
7fba76140000-7fba76145000 r--p 00010000 00:2b 4384565586930135332        /home/baorx/miniconda3/envs/cancerit/lib/libdeflate.so.0
7fba76145000-7fba76146000 r--p 00014000 00:2b 4384565586930135332        /home/baorx/miniconda3/envs/cancerit/lib/libdeflate.so.0
7fba76146000-7fba76147000 rw-p 00015000 00:2b 4384565586930135332        /home/baorx/miniconda3/envs/cancerit/lib/libdeflate.so.0
7fba76147000-7fba76148000 rw-p 00000000 00:00 0 
7fba76148000-7fba7614c000 r--p 00000000 00:2b 14885991866705956940       /home/baorx/miniconda3/envs/cancerit/lib/liblzma.so.5.2.6
7fba7614c000-7fba76163000 r-xp 00004000 00:2b 14885991866705956940       /home/baorx/miniconda3/envs/cancerit/lib/liblzma.so.5.2.6
7fba76163000-7fba7616e000 r--p 0001b000 00:2b 14885991866705956940       /home/baorx/miniconda3/envs/cancerit/lib/liblzma.so.5.2.6
7fba7616e000-7fba7616f000 ---p 00026000 00:2b 14885991866705956940       /home/baorx/miniconda3/envs/cancerit/lib/liblzma.so.5.2.6
7fba7616f000-7fba76170000 r--p 00026000 00:2b 14885991866705956940       /home/baorx/miniconda3/envs/cancerit/lib/liblzma.so.5.2.6
7fba76170000-7fba76171000 rw-p 00027000 00:2b 14885991866705956940       /home/baorx/miniconda3/envs/cancerit/lib/liblzma.so.5.2.6
7fba76171000-7fba76172000 rw-p 00000000 00:00 0 
7fba76172000-7fba76174000 r--p 00000000 00:2b 2988501068377944316        /home/baorx/miniconda3/envs/cancerit/lib/libbz2.so.1.0.8
7fba76174000-7fba76182000 r-xp 00002000 00:2b 2988501068377944316        /home/baorx/miniconda3/envs/cancerit/lib/libbz2.so.1.0.8
7fba76182000-7fba76184000 r--p 00010000 00:2b 2988501068377944316        /home/baorx/miniconda3/envs/cancerit/lib/libbz2.so.1.0.8
7fba76184000-7fba76185000 r--p 00011000 00:2b 2988501068377944316        /home/baorx/miniconda3/envs/cancerit/lib/libbz2.so.1.0.8
7fba76185000-7fba76186000 rw-p 00012000 00:2b 2988501068377944316        /home/baorx/miniconda3/envs/cancerit/lib/libbz2.so.1.0.8
7fba76186000-7fba76189000 r--p 00000000 00:2b 11235798539474949561       /home/baorx/miniconda3/envs/cancerit/lib/libz.so.1.3.1
7fba76189000-7fba76198000 r-xp 00003000 00:2b 11235798539474949561       /home/baorx/miniconda3/envs/cancerit/lib/libz.so.1.3.1
7fba76198000-7fba7619f000 r--p 00012000 00:2b 11235798539474949561       /home/baorx/miniconda3/envs/cancerit/lib/libz.so.1.3.1
7fba7619f000-7fba761a0000 r--p 00018000 00:2b 11235798539474949561       /home/baorx/miniconda3/envs/cancerit/lib/libz.so.1.3.1
7fba761a0000-7fba761a1000 rw-p 00019000 00:2b 11235798539474949561       /home/baorx/miniconda3/envs/cancerit/lib/libz.so.1.3.1
7fba761a1000-7fba761a2000 rw-p 00000000 00:00 0 
7fba761b8000-7fba761b9000 rw-p 00000000 00:00 0 
7fba761b9000-7fba761c8000 r--p 00000000 00:2b 10940355597678270174       /home/baorx/miniconda3/envs/cancerit/lib/libhts.so.1.21
7fba761c8000-7fba7629a000 r-xp 0000f000 00:2b 10940355597678270174       /home/baorx/miniconda3/envs/cancerit/lib/libhts.so.1.21
7fba7629a000-7fba762bd000 r--p 000e1000 00:2b 10940355597678270174       /home/baorx/miniconda3/envs/cancerit/lib/libhts.so.1.21
7fba762bd000-7fba762bf000 r--p 00103000 00:2b 10940355597678270174       /home/baorx/miniconda3/envs/cancerit/lib/libhts.so.1.21
7fba762bf000-7fba762c4000 rw-p 00105000 00:2b 10940355597678270174       /home/baorx/miniconda3/envs/cancerit/lib/libhts.so.1.21
7fba762c4000-7fba762c6000 rw-p 00000000 00:00 0 
7fba762c6000-7fba762c7000 r--p 00021000 fd:00 11016345                   /usr/lib64/ld-2.17.so
7fba762c7000-7fba762c8000 rw-p 00022000 fd:00 11016345                   /usr/lib64/ld-2.17.so
7fba762c8000-7fba762c9000 rw-p 00000000 00:00 0 
7ffcfbb60000-7ffcfbb81000 rw-p 00000000 00:00 0                          [stack]
7ffcfbb90000-7ffcfbb92000 r-xp 00000000 00:00 0                          [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0                  [vsyscall]
[E::sam_itr_next] Null iterator
[ERROR] (src/bam_access.c: bam_access_get_multi_position_base_counts:379 errno: None) Error detected (-2) when trying to iterate through region.
[ERROR] (./src/alleleCounter.c: main:432 errno: None) Error scanning through bam file for loci list with dense snps.
*** Error in `/home/baorx/miniconda3/envs/cancerit/bin/alleleCounter': munmap_chunk(): invalid pointer: 0x00007ffc00c5b457 ***
*** Error in `/home/baorx/miniconda3/envs/cancerit/bin/alleleCounter': munmap_chunk(): invalid pointer: 0x00007ffda2071457 ***
======= Backtrace: =========
/lib64/libc.so.6(+0x7f5e4)[0x7f69278055e4]
/home/baorx/miniconda3/envs/cancerit/bin/alleleCounter(main+0x144)[0x55cf412c1454]
/lib64/libc.so.6(__libc_start_main+0xf5)[0x7f69277a8445]
/home/baorx/miniconda3/envs/cancerit/bin/alleleCounter(+0x2aa1)[0x55cf412c1aa1]
======= Memory map: ========
55cf412bf000-55cf412c1000 r--p 00000000 00:2b 6384932095811731369        /home/baorx/miniconda3/envs/cancerit/bin/alleleCounter
55cf412c1000-55cf412c5000 r-xp 00002000 00:2b 6384932095811731369        /home/baorx/miniconda3/envs/cancerit/bin/alleleCounter
55cf412c5000-55cf412c7000 r--p 00006000 00:2b 6384932095811731369        /home/baorx/miniconda3/envs/cancerit/bin/alleleCounter
55cf412c7000-55cf412c8000 r--p 00008000 00:2b 6384932095811731369        /home/baorx/miniconda3/envs/cancerit/bin/alleleCounter
55cf412c8000-55cf412c9000 rw-p 00009000 00:2b 6384932095811731369        /home/baorx/miniconda3/envs/cancerit/bin/alleleCounter
55cf414af000-55d024614000 rw-p 00000000 00:00 0                          [heap]
7f692757e000-7f6927585000 r-xp 00000000 fd:00 11016382                   /usr/lib64/librt-2.17.so
7f6927585000-7f6927784000 ---p 00007000 fd:00 11016382                   /usr/lib64/librt-2.17.so
7f6927784000-7f6927785000 r--p 00006000 fd:00 11016382                   /usr/lib64/librt-2.17.so
7f6927785000-7f6927786000 rw-p 00007000 fd:00 11016382                   /usr/lib64/librt-2.17.so
7f6927786000-7f6927949000 r-xp 00000000 fd:00 11016352                   /usr/lib64/libc-2.17.so
7f6927949000-7f6927b48000 ---p 001c3000 fd:00 11016352                   /usr/lib64/libc-2.17.so
7f6927b48000-7f6927b4c000 r--p 001c2000 fd:00 11016352                   /usr/lib64/libc-2.17.so
7f6927b4c000-7f6927b4e000 rw-p 001c6000 fd:00 11016352                   /usr/lib64/libc-2.17.so
7f6927b4e000-7f6927b53000 rw-p 00000000 00:00 0 
7f6927b53000-7f6927b55000 r-xp 00000000 fd:00 11016358                   /usr/lib64/libdl-2.17.so
7f6927b55000-7f6927d55000 ---p 00002000 fd:00 11016358                   /usr/lib64/libdl-2.17.so
7f6927d55000-7f6927d56000 r--p 00002000 fd:00 11016358                   /usr/lib64/libdl-2.17.so
7f6927d56000-7f6927d57000 rw-p 00003000 fd:00 11016358                   /usr/lib64/libdl-2.17.so
7f6927d57000-7f6927e58000 r-xp 00000000 fd:00 11016360                   /usr/lib64/libm-2.17.so
7f6927e58000-7f6928057000 ---p 00101000 fd:00 11016360                   /usr/lib64/libm-2.17.so
7f6928057000-7f6928058000 r--p 00100000 fd:00 11016360                   /usr/lib64/libm-2.17.so
7f6928058000-7f6928059000 rw-p 00101000 fd:00 11016360                   /usr/lib64/libm-2.17.so
7f6928059000-7f6928070000 r-xp 00000000 fd:00 11016378                   /usr/lib64/libpthread-2.17.so
7f6928070000-7f692826f000 ---p 00017000 fd:00 11016378                   /usr/lib64/libpthread-2.17.so
7f692826f000-7f6928270000 r--p 00016000 fd:00 11016378                   /usr/lib64/libpthread-2.17.so
7f6928270000-7f6928271000 rw-p 00017000 fd:00 11016378                   /usr/lib64/libpthread-2.17.so
7f6928271000-7f6928275000 rw-p 00000000 00:00 0 
7f6928275000-7f6928297000 r-xp 00000000 fd:00 11016345                   /usr/lib64/ld-2.17.so
7f69282dd000-7f69282e1000 r--p 00000000 00:2b 12547459619057434142       /home/baorx/miniconda3/envs/cancerit/lib/libgcc_s.so.1
7f69282e1000-7f69282f6000 r-xp 00004000 00:2b 12547459619057434142       /home/baorx/miniconda3/envs/cancerit/lib/libgcc_s.so.1
7f69282f6000-7f69282fa000 r--p 00019000 00:2b 12547459619057434142       /home/baorx/miniconda3/envs/cancerit/lib/libgcc_s.so.1
7f69282fa000-7f69282fb000 r--p 0001c000 00:2b 12547459619057434142       /home/baorx/miniconda3/envs/cancerit/lib/libgcc_s.so.1
7f69282fb000-7f69282fc000 rw-p 0001d000 00:2b 12547459619057434142       /home/baorx/miniconda3/envs/cancerit/lib/libgcc_s.so.1
7f69282fc000-7f6928300000 rw-p 00000000 00:00 0 
7f6928300000-7f6928301000 r--p 00000000 00:2b 4384565586930135332        /home/baorx/miniconda3/envs/cancerit/lib/libdeflate.so.0
7f6928301000-7f6928310000 r-xp 00001000 00:2b 4384565586930135332        /home/baorx/miniconda3/envs/cancerit/lib/libdeflate.so.0
7f6928310000-7f6928315000 r--p 00010000 00:2b 4384565586930135332        /home/baorx/miniconda3/envs/cancerit/lib/libdeflate.so.0
7f6928315000-7f6928316000 r--p 00014000 00:2b 4384565586930135332        /home/baorx/miniconda3/envs/cancerit/lib/libdeflate.so.0
7f6928316000-7f6928317000 rw-p 00015000 00:2b 4384565586930135332        /home/baorx/miniconda3/envs/cancerit/lib/libdeflate.so.0
7f6928317000-7f6928318000 rw-p 00000000 00:00 0 
7f6928318000-7f692831c000 r--p 00000000 00:2b 14885991866705956940       /home/baorx/miniconda3/envs/cancerit/lib/liblzma.so.5.2.6
7f692831c000-7f6928333000 r-xp 00004000 00:2b 14885991866705956940       /home/baorx/miniconda3/envs/cancerit/lib/liblzma.so.5.2.6
7f6928333000-7f692833e000 r--p 0001b000 00:2b 14885991866705956940       /home/baorx/miniconda3/envs/cancerit/lib/liblzma.so.5.2.6
7f692833e000-7f692833f000 ---p 00026000 00:2b 14885991866705956940       /home/baorx/miniconda3/envs/cancerit/lib/liblzma.so.5.2.6
7f692833f000-7f6928340000 r--p 00026000 00:2b 14885991866705956940       /home/baorx/miniconda3/envs/cancerit/lib/liblzma.so.5.2.6
7f6928340000-7f6928341000 rw-p 00027000 00:2b 14885991866705956940       /home/baorx/miniconda3/envs/cancerit/lib/liblzma.so.5.2.6
7f6928341000-7f6928342000 rw-p 00000000 00:00 0 
7f6928342000-7f6928344000 r--p 00000000 00:2b 2988501068377944316        /home/baorx/miniconda3/envs/cancerit/lib/libbz2.so.1.0.8
7f6928344000-7f6928352000 r-xp 00002000 00:2b 2988501068377944316        /home/baorx/miniconda3/envs/cancerit/lib/libbz2.so.1.0.8
7f6928352000-7f6928354000 r--p 00010000 00:2b 2988501068377944316        /home/baorx/miniconda3/envs/cancerit/lib/libbz2.so.1.0.8
7f6928354000-7f6928355000 r--p 00011000 00:2b 2988501068377944316        /home/baorx/miniconda3/envs/cancerit/lib/libbz2.so.1.0.8
7f6928355000-7f6928356000 rw-p 00012000 00:2b 2988501068377944316        /home/baorx/miniconda3/envs/cancerit/lib/libbz2.so.1.0.8
7f6928356000-7f6928359000 r--p 00000000 00:2b 11235798539474949561       /home/baorx/miniconda3/envs/cancerit/lib/libz.so.1.3.1
7f6928359000-7f6928368000 r-xp 00003000 00:2b 11235798539474949561       /home/baorx/miniconda3/envs/cancerit/lib/libz.so.1.3.1
7f6928368000-7f692836f000 r--p 00012000 00:2b 11235798539474949561       /home/baorx/miniconda3/envs/cancerit/lib/libz.so.1.3.1
7f692836f000-7f6928370000 r--p 00018000 00:2b 11235798539474949561       /home/baorx/miniconda3/envs/cancerit/lib/libz.so.1.3.1
7f6928370000-7f6928371000 rw-p 00019000 00:2b 11235798539474949561       /home/baorx/miniconda3/envs/cancerit/lib/libz.so.1.3.1
7f6928371000-7f6928372000 rw-p 00000000 00:00 0 
7f6928388000-7f6928389000 rw-p 00000000 00:00 0 
7f6928389000-7f6928398000 r--p 00000000 00:2b 10940355597678270174       /home/baorx/miniconda3/envs/cancerit/lib/libhts.so.1.21
7f6928398000-7f692846a000 r-xp 0000f000 00:2b 10940355597678270174       /home/baorx/miniconda3/envs/cancerit/lib/libhts.so.1.21
7f692846a000-7f692848d000 r--p 000e1000 00:2b 10940355597678270174       /home/baorx/miniconda3/envs/cancerit/lib/libhts.so.1.21
7f692848d000-7f692848f000 r--p 00103000 00:2b 10940355597678270174       /home/baorx/miniconda3/envs/cancerit/lib/libhts.so.1.21
7f692848f000-7f6928494000 rw-p 00105000 00:2b 10940355597678270174       /home/baorx/miniconda3/envs/cancerit/lib/libhts.so.1.21
7f6928494000-7f6928496000 rw-p 00000000 00:00 0 
7f6928496000-7f6928497000 r--p 00021000 fd:00 11016345                   /usr/lib64/ld-2.17.so
7f6928497000-7f6928498000 rw-p 00022000 fd:00 11016345                   /usr/lib64/ld-2.17.so
7f6928498000-7f6928499000 rw-p 00000000 00:00 0 
7ffc00c3b000-7ffc00c5c000 rw-p 00000000 00:00 0                          [stack]
7ffc00c90000-7ffc00c92000 r-xp 00000000 00:00 0                          [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0                  [vsyscall]
======= Backtrace: =========
/lib64/libc.so.6(+0x7f5e4)[0x7f551e09e5e4]
/home/baorx/miniconda3/envs/cancerit/bin/alleleCounter(main+0x144)[0x557f8c9ae454]
/lib64/libc.so.6(__libc_start_main+0xf5)[0x7f551e041445]
/home/baorx/miniconda3/envs/cancerit/bin/alleleCounter(+0x2aa1)[0x557f8c9aeaa1]
======= Memory map: ========
557f8c9ac000-557f8c9ae000 r--p 00000000 00:2b 6384932095811731369        /home/baorx/miniconda3/envs/cancerit/bin/alleleCounter
557f8c9ae000-557f8c9b2000 r-xp 00002000 00:2b 6384932095811731369        /home/baorx/miniconda3/envs/cancerit/bin/alleleCounter
557f8c9b2000-557f8c9b4000 r--p 00006000 00:2b 6384932095811731369        /home/baorx/miniconda3/envs/cancerit/bin/alleleCounter
557f8c9b4000-557f8c9b5000 r--p 00008000 00:2b 6384932095811731369        /home/baorx/miniconda3/envs/cancerit/bin/alleleCounter
557f8c9b5000-557f8c9b6000 rw-p 00009000 00:2b 6384932095811731369        /home/baorx/miniconda3/envs/cancerit/bin/alleleCounter
557f8e09f000-5580b4aad000 rw-p 00000000 00:00 0                          [heap]
7f551de17000-7f551de1e000 r-xp 00000000 fd:00 11016382                   /usr/lib64/librt-2.17.so
7f551de1e000-7f551e01d000 ---p 00007000 fd:00 11016382                   /usr/lib64/librt-2.17.so
7f551e01d000-7f551e01e000 r--p 00006000 fd:00 11016382                   /usr/lib64/librt-2.17.so
7f551e01e000-7f551e01f000 rw-p 00007000 fd:00 11016382                   /usr/lib64/librt-2.17.so
7f551e01f000-7f551e1e2000 r-xp 00000000 fd:00 11016352                   /usr/lib64/libc-2.17.so
7f551e1e2000-7f551e3e1000 ---p 001c3000 fd:00 11016352                   /usr/lib64/libc-2.17.so
7f551e3e1000-7f551e3e5000 r--p 001c2000 fd:00 11016352                   /usr/lib64/libc-2.17.so
7f551e3e5000-7f551e3e7000 rw-p 001c6000 fd:00 11016352                   /usr/lib64/libc-2.17.so
7f551e3e7000-7f551e3ec000 rw-p 00000000 00:00 0 
7f551e3ec000-7f551e3ee000 r-xp 00000000 fd:00 11016358                   /usr/lib64/libdl-2.17.so
7f551e3ee000-7f551e5ee000 ---p 00002000 fd:00 11016358                   /usr/lib64/libdl-2.17.so
7f551e5ee000-7f551e5ef000 r--p 00002000 fd:00 11016358                   /usr/lib64/libdl-2.17.so
7f551e5ef000-7f551e5f0000 rw-p 00003000 fd:00 11016358                   /usr/lib64/libdl-2.17.so
7f551e5f0000-7f551e6f1000 r-xp 00000000 fd:00 11016360                   /usr/lib64/libm-2.17.so
7f551e6f1000-7f551e8f0000 ---p 00101000 fd:00 11016360                   /usr/lib64/libm-2.17.so
7f551e8f0000-7f551e8f1000 r--p 00100000 fd:00 11016360                   /usr/lib64/libm-2.17.so
7f551e8f1000-7f551e8f2000 rw-p 00101000 fd:00 11016360                   /usr/lib64/libm-2.17.so
7f551e8f2000-7f551e909000 r-xp 00000000 fd:00 11016378                   /usr/lib64/libpthread-2.17.so
7f551e909000-7f551eb08000 ---p 00017000 fd:00 11016378                   /usr/lib64/libpthread-2.17.so
7f551eb08000-7f551eb09000 r--p 00016000 fd:00 11016378                   /usr/lib64/libpthread-2.17.so
7f551eb09000-7f551eb0a000 rw-p 00017000 fd:00 11016378                   /usr/lib64/libpthread-2.17.so
7f551eb0a000-7f551eb0e000 rw-p 00000000 00:00 0 
7f551eb0e000-7f551eb30000 r-xp 00000000 fd:00 11016345                   /usr/lib64/ld-2.17.so
7f551eb76000-7f551eb7a000 r--p 00000000 00:2b 12547459619057434142       /home/baorx/miniconda3/envs/cancerit/lib/libgcc_s.so.1
7f551eb7a000-7f551eb8f000 r-xp 00004000 00:2b 12547459619057434142       /home/baorx/miniconda3/envs/cancerit/lib/libgcc_s.so.1
7f551eb8f000-7f551eb93000 r--p 00019000 00:2b 12547459619057434142       /home/baorx/miniconda3/envs/cancerit/lib/libgcc_s.so.1
7f551eb93000-7f551eb94000 r--p 0001c000 00:2b 12547459619057434142       /home/baorx/miniconda3/envs/cancerit/lib/libgcc_s.so.1
7f551eb94000-7f551eb95000 rw-p 0001d000 00:2b 12547459619057434142       /home/baorx/miniconda3/envs/cancerit/lib/libgcc_s.so.1
7f551eb95000-7f551eb99000 rw-p 00000000 00:00 0 
7f551eb99000-7f551eb9a000 r--p 00000000 00:2b 4384565586930135332        /home/baorx/miniconda3/envs/cancerit/lib/libdeflate.so.0
7f551eb9a000-7f551eba9000 r-xp 00001000 00:2b 4384565586930135332        /home/baorx/miniconda3/envs/cancerit/lib/libdeflate.so.0
7f551eba9000-7f551ebae000 r--p 00010000 00:2b 4384565586930135332        /home/baorx/miniconda3/envs/cancerit/lib/libdeflate.so.0
7f551ebae000-7f551ebaf000 r--p 00014000 00:2b 4384565586930135332        /home/baorx/miniconda3/envs/cancerit/lib/libdeflate.so.0
7f551ebaf000-7f551ebb0000 rw-p 00015000 00:2b 4384565586930135332        /home/baorx/miniconda3/envs/cancerit/lib/libdeflate.so.0
7f551ebb0000-7f551ebb1000 rw-p 00000000 00:00 0 
7f551ebb1000-7f551ebb5000 r--p 00000000 00:2b 14885991866705956940       /home/baorx/miniconda3/envs/cancerit/lib/liblzma.so.5.2.6
7f551ebb5000-7f551ebcc000 r-xp 00004000 00:2b 14885991866705956940       /home/baorx/miniconda3/envs/cancerit/lib/liblzma.so.5.2.6
7f551ebcc000-7f551ebd7000 r--p 0001b000 00:2b 14885991866705956940       /home/baorx/miniconda3/envs/cancerit/lib/liblzma.so.5.2.6
7f551ebd7000-7f551ebd8000 ---p 00026000 00:2b 14885991866705956940       /home/baorx/miniconda3/envs/cancerit/lib/liblzma.so.5.2.6
7f551ebd8000-7f551ebd9000 r--p 00026000 00:2b 14885991866705956940       /home/baorx/miniconda3/envs/cancerit/lib/liblzma.so.5.2.6
7f551ebd9000-7f551ebda000 rw-p 00027000 00:2b 14885991866705956940       /home/baorx/miniconda3/envs/cancerit/lib/liblzma.so.5.2.6
7f551ebda000-7f551ebdb000 rw-p 00000000 00:00 0 
7f551ebdb000-7f551ebdd000 r--p 00000000 00:2b 2988501068377944316        /home/baorx/miniconda3/envs/cancerit/lib/libbz2.so.1.0.8
7f551ebdd000-7f551ebeb000 r-xp 00002000 00:2b 2988501068377944316        /home/baorx/miniconda3/envs/cancerit/lib/libbz2.so.1.0.8
7f551ebeb000-7f551ebed000 r--p 00010000 00:2b 2988501068377944316        /home/baorx/miniconda3/envs/cancerit/lib/libbz2.so.1.0.8
7f551ebed000-7f551ebee000 r--p 00011000 00:2b 2988501068377944316        /home/baorx/miniconda3/envs/cancerit/lib/libbz2.so.1.0.8
7f551ebee000-7f551ebef000 rw-p 00012000 00:2b 2988501068377944316        /home/baorx/miniconda3/envs/cancerit/lib/libbz2.so.1.0.8
7f551ebef000-7f551ebf2000 r--p 00000000 00:2b 11235798539474949561       /home/baorx/miniconda3/envs/cancerit/lib/libz.so.1.3.1
7f551ebf2000-7f551ec01000 r-xp 00003000 00:2b 11235798539474949561       /home/baorx/miniconda3/envs/cancerit/lib/libz.so.1.3.1
7f551ec01000-7f551ec08000 r--p 00012000 00:2b 11235798539474949561       /home/baorx/miniconda3/envs/cancerit/lib/libz.so.1.3.1
7f551ec08000-7f551ec09000 r--p 00018000 00:2b 11235798539474949561       /home/baorx/miniconda3/envs/cancerit/lib/libz.so.1.3.1
7f551ec09000-7f551ec0a000 rw-p 00019000 00:2b 11235798539474949561       /home/baorx/miniconda3/envs/cancerit/lib/libz.so.1.3.1
7f551ec0a000-7f551ec0b000 rw-p 00000000 00:00 0 
7f551ec21000-7f551ec22000 rw-p 00000000 00:00 0 
7f551ec22000-7f551ec31000 r--p 00000000 00:2b 10940355597678270174       /home/baorx/miniconda3/envs/cancerit/lib/libhts.so.1.21
7f551ec31000-7f551ed03000 r-xp 0000f000 00:2b 10940355597678270174       /home/baorx/miniconda3/envs/cancerit/lib/libhts.so.1.21
7f551ed03000-7f551ed26000 r--p 000e1000 00:2b 10940355597678270174       /home/baorx/miniconda3/envs/cancerit/lib/libhts.so.1.21
7f551ed26000-7f551ed28000 r--p 00103000 00:2b 10940355597678270174       /home/baorx/miniconda3/envs/cancerit/lib/libhts.so.1.21
7f551ed28000-7f551ed2d000 rw-p 00105000 00:2b 10940355597678270174       /home/baorx/miniconda3/envs/cancerit/lib/libhts.so.1.21
7f551ed2d000-7f551ed2f000 rw-p 00000000 00:00 0 
7f551ed2f000-7f551ed30000 r--p 00021000 fd:00 11016345                   /usr/lib64/ld-2.17.so
7f551ed30000-7f551ed31000 rw-p 00022000 fd:00 11016345                   /usr/lib64/ld-2.17.so
7f551ed31000-7f551ed32000 rw-p 00000000 00:00 0 
7ffda2051000-7ffda2072000 rw-p 00000000 00:00 0                          [stack]
7ffda2189000-7ffda218b000 r-xp 00000000 00:00 0                          [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0                  [vsyscall]
<gcap> 2024-09-18 09:27:34 fatal [value[[3L]]]: job M7 failed in ASCAT due to following error
<gcap> 2024-09-18 09:27:34 info [value[[3L]]]: task 1 failed - "EXIT_CODE == 0 is not TRUE"
<gcap> 2024-09-18 09:27:34 info [value[[3L]]]: =====
<gcap> 2024-09-18 09:27:34 info [value[[3L]]]: Please check your input bam files (if missing bam index? if its alignment quality is lower?)
<gcap> 2024-09-18 09:27:34 info [value[[3L]]]: =====
<gcap> 2024-09-18 09:27:34 info [gcap.runASCAT]: ASCAT analysis done, check /home/baorx/test1/gcap/gcap for results
<gcap> 2024-09-18 09:27:34 info [gcap.workflow]: checking ASCAT result files
<gcap> 2024-09-18 09:27:34 warn [FUN]: result file /home/baorx/test1/gcap/gcap/M7.ASCAT.rds does not exist, the corresponding ASCAT calling has error occurred 
<gcap> 2024-09-18 09:27:34 warn [FUN]: /home/baorx/test1/gcap/gcap/M7.ASCAT.rds contains a failed ASCAT job, will discard it before next step
<gcap> 2024-09-18 09:27:34 fatal [gcap.workflow]: no sucessful ASCAT result file to proceed!
<gcap> 2024-09-18 09:27:34 fatal [gcap.workflow]: check your ASCAT setting before make sure this case could not be used!
Error in gcap.workflow(tumourseqfile = "/home/baorx/test1/gcap/bam/M9-T_bwa.bam",  : 

how can i solve it, please