"Illegal instruction: 4" error while running calib_cons

[kartikchandran]

Hi there,

I'm working on.an Apple M1 Pro Mac running OS X Monterey 12.2.1. I was able to run calib on my fastq files to generate the cluster file but calib_cons gives me an "Illegal instruction: 4" error.

I was able to run Calib fine on my previous Intel Mac so I thought this might be due to the change in chip architecture. I tried running in Rosetta mode by prefixing with "arch -x86_64" but that gave me the same error.

Look forward to your input on how to fix this.

Thanks!
Kartik

[kartikchandran]

I ran calib_cons in lldb and got the following output:

run -c /Users/kartik/ncbi/capseq/run2/calib/1WT-S_calib_cluster -q /Users/kartik/ncbi/capseq/run2/reoriented_reads/1WT-S_reoriented_R1.fastq /Users/kartik/ncbi/capseq/run2/reoriented_reads/1WT-S_reoriented_trimmed_R2.fastq -o 1WT-S_calib_R1 1WT-S_calib_R2
Process 41055 launched: '/usr/local/bin/calib_cons' (x86_64)
Reading cluster file: /Users/kartik/ncbi/capseq/run2/calib/1WT-S_calib_cluster
Reading fastq file: /Users/kartik/ncbi/capseq/run2/reoriented_reads/1WT-S_reoriented_R1.fastq
Writing output files: 1WT-S_calib_R1
Process 41055 stopped

• thread Find consensus of a cluster of reads #2, stop reason = EXC_BAD_INSTRUCTION (code=EXC_I386_INVOP, subcode=0x0)
  frame #0: 0x00000001000123ce calib_consspoa::createSimdAlignmentEngine(spoa::AlignmentType, signed char, signed char, signed char) + 94 calib_consspoa::createSimdAlignmentEngine:
  -> 0x1000123ce <+94>: vxorps %xmm0, %xmm0, %xmm0
  0x1000123d2 <+98>: vmovups %ymm0, (%rax)
  0x1000123d6 <+102>: movl $0x0, 0x20(%rax)
  0x1000123dd <+109>: vmovups %ymm0, 0x28(%rax)
  thread Add barcode length & error tolerance command-line flags #3, stop reason = EXC_BAD_INSTRUCTION (code=EXC_I386_INVOP, subcode=0x0)
  frame #0: 0x00000001000123ce calib_consspoa::createSimdAlignmentEngine(spoa::AlignmentType, signed char, signed char, signed char) + 94 calib_consspoa::createSimdAlignmentEngine:
  -> 0x1000123ce <+94>: vxorps %xmm0, %xmm0, %xmm0
  0x1000123d2 <+98>: vmovups %ymm0, (%rax)
  0x1000123d6 <+102>: movl $0x0, 0x20(%rax)
  0x1000123dd <+109>: vmovups %ymm0, 0x28(%rax)
  thread Change from lsh dictionary to lsh arraylist #4, stop reason = EXC_BAD_INSTRUCTION (code=EXC_I386_INVOP, subcode=0x0)
  frame #0: 0x00000001000123ce calib_consspoa::createSimdAlignmentEngine(spoa::AlignmentType, signed char, signed char, signed char) + 94 calib_consspoa::createSimdAlignmentEngine:
  -> 0x1000123ce <+94>: vxorps %xmm0, %xmm0, %xmm0
  0x1000123d2 <+98>: vmovups %ymm0, (%rax)
  0x1000123d6 <+102>: movl $0x0, 0x20(%rax)
  0x1000123dd <+109>: vmovups %ymm0, 0x28(%rax)
  thread Use igraph lib instead of using own implementation  #5, stop reason = EXC_BAD_INSTRUCTION (code=EXC_I386_INVOP, subcode=0x0)
  frame #0: 0x00000001000123ce calib_consspoa::createSimdAlignmentEngine(spoa::AlignmentType, signed char, signed char, signed char) + 94 calib_consspoa::createSimdAlignmentEngine:
  -> 0x1000123ce <+94>: vxorps %xmm0, %xmm0, %xmm0
  0x1000123d2 <+98>: vmovups %ymm0, (%rax)
  0x1000123d6 <+102>: movl $0x0, 0x20(%rax)
  0x1000123dd <+109>: vmovups %ymm0, 0x28(%rax)
  Target 0: (calib_cons) stopped.

[baraaorabi]

Hello @kartikchandran

Can share the commands used to install Calib and Calib cons module? I haven't done any testing on MACOS and I suspect this is a MACOS issue...