Comments (6)
hmm. I'm not sure how to debug this.
can you try building with the -x
flag to hts_nim_static_builder? that turns on debug build so we might bet a bit more information.
I'll see if I can find some old nodes to test on as well.
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Nice, didn't notice that flag:
Traceback (most recent call last)
/local/src/covtobed2.nim(254) covtobed2
/local/src/covtobed2.nim(229) main
/root/.nimble/pkgs/hts-0.3.11/hts/bam.nim(373) open
SIGILL: Illegal operation.
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is the file local? can you show the code in cov2bed2?
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you may also be able to run your binary under gdb to get a better backtrace.
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I'm sorry, gdb seems too complicated for me.
cov2bed2
is basically an empty script to read a BAM file, as I never tried htslib in the past (I was used to libbamtools).
I compiled the hts_nim_tools from your repository using again the static builder.
I compiled (as I did in the first example) from an Ubuntu VM and the path was /local/giovanni/...
, that pops out in the traceback:
./hts_nim_static_builder -x -n hts_nim_tools.nimble -s src/hts_nim_tools.nim
The command hts_nim_tools bam-filter is_proper_pair ./test_output/mini.mapping.bam
works fine from any intel node, and again fails in the Opteron ones. This is not necessarily a terrible thing, but if it's easy to update the builder this would give a broader use to the compiled tools...
~/tmp/hts_nim_tools bam-filter is_proper_pair ./test_output/mini.mapping.bam
Traceback (most recent call last)
/local/giovanni/hts-nim-tools/src/hts_nim_tools.nim(50) hts_nim_tools
/local/giovanni/hts-nim-tools/src/hts_nim_tools.nim(47) main
/local/giovanni/hts-nim-tools/src/bam_filter.nim(53) bam_filter
/root/.nimble/pkgs/hts-0.3.4/hts/bam.nim(337) open
SIGILL: Illegal operation.
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I'd like to fix this, but I'm not sure how. :(
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Related Issues (20)
- VCF: Clear all INFO field HOT 2
- Multiple iterators with items*(v:VCF) HOT 3
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- Failure to compile when using new Nim Gas (ORC and ARC) HOT 2
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- Trouble with newRecord "undeclared identifier" in bam HOT 7
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