Could not initialize gtc2vcf.so, neither run or init found

[oneilep]

Hello, I am trying to use the "Convert Illumina GTC files to VCF" example shown in the README, but I am getting this error:

Writing to .
Could not initialize gtc2vcf.so, neither run or init found
[E::bcf_hdr_read] Input is not detected as bcf or vcf format
Failed to open -: unknown file type
Failed to open -: unknown file type

Looking in the file, there is a run function defined, but no init function, and bcftools vcfplugin.c appears to be checking for both.

I am using bcftools version 1.9. Any idea what could be causing this?

[freeseek]

You don't need both init() and run() for a working bcftools plugin. Can you try to see whether the run() function is indeed in the shared object file?

objdump -T gtc2vcf.so | grep run

Also, try to run bcftools plugin with the -v verbose option. It might give you further insights into your issue.

[oneilep]

I don't see a run function in the output

$ objdump -T plugins/gtc2vcf.so

plugins/gtc2vcf.so: file format elf64-x86-64

DYNAMIC SYMBOL TABLE:
0000000000000560 l d .init 0000000000000000 .init
0000000000000000 w D UND 0000000000000000 gmon_start
0000000000000000 DF UND 0000000000000000 GLIBC_2.2.5 exit
0000000000000864 g DF .fini 0000000000000000 Base _fini
00000000000007f0 g DF .text 0000000000000030 Base hts_bcf_wmode
0000000000000000 w D UND 0000000000000000 _ITM_deregisterTMCloneTable
0000000000000000 DF UND 0000000000000000 GLIBC_2.2.5 vfprintf
0000000000000000 w D UND 0000000000000000 _ITM_registerTMCloneTable
0000000000000000 w DF UND 0000000000000000 GLIBC_2.2.5 __cxa_finalize
0000000000000720 g DF .text 0000000000000018 Base version
0000000000000740 g DF .text 00000000000000a3 Base error
0000000000200b30 g D ABS 0000000000000000 Base __bss_start
0000000000200b40 g D ABS 0000000000000000 Base _end
0000000000000000 DO UND 0000000000000000 GLIBC_2.2.5 stderr
0000000000200b30 g D ABS 0000000000000000 Base _edata
0000000000000000 D UND 0000000000000000 hts_version
0000000000000560 g DF .init 0000000000000000 Base _init

And -v didn't give any additional information.

[oneilep]

I was able to fix this. For some reason I had a completely empty gtc2vcf.c file and a gtc2vcf.c.1 file with the actual code (I guess the initial download failed?). After deleting the empty file and renaming the .1 copy it compiled correctly with the run function and everything.