bwa error in proovread install: make: *** [utils.o] Error 1
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Entering edit mode
5.4 years ago
xiachongjing ▴ 10

Hello everyone:

I am trying to run Proovread 2.13.13 to correct my PacBio data. I follow this https://github.com/BioInf-Wuerzburg/proovread. I got error when I was trying to install bwa. Here is the command I use:

$ cd proovread/util/bwa/

$ make

Then I got error like this:

gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS utils.c -o utils.o /tmp/cc2DC8ae.s: Assembler messages: /tmp/cc2DC8ae.s:47: Error: unknown .loc sub-directive discriminator' /tmp/cc2DC8ae.s:47: Error: junk at end of line, first unrecognized character is3' /tmp/cc2DC8ae.s:72: Error: unknown .loc sub-directive discriminator' /tmp/cc2DC8ae.s:72: Error: junk at end of line, first unrecognized character is2' /tmp/cc2DC8ae.s:82: Error: unknown .loc sub-directive discriminator' /tmp/cc2DC8ae.s:82: Error: junk at end of line, first unrecognized character is1' /tmp/cc2DC8ae.s:95: Error: unknown .loc sub-directive discriminator' /tmp/cc2DC8ae.s:95: Error: junk at end of line, first unrecognized character is2' /tmp/cc2DC8ae.s:111: Error: unknown .loc sub-directive discriminator' /tmp/cc2DC8ae.s:111: Error: junk at end of line, first unrecognized character is1' /tmp/cc2DC8ae.s:117: Error: unknown .loc sub-directive discriminator' /tmp/cc2DC8ae.s:117: Error: junk at end of line, first unrecognized character is2' /tmp/cc2DC8ae.s:127: Error: unknown .loc sub-directive discriminator' /tmp/cc2DC8ae.s:127: Error: junk at end of line, first unrecognized character is1' /tmp/cc2DC8ae.s:168: Error: unknown .loc sub-directive discriminator' /tmp/cc2DC8ae.s:168: Error: junk at end of line, first unrecognized character is1' /tmp/cc2DC8ae.s:204: Error: unknown .loc sub-directive discriminator' /tmp/cc2DC8ae.s:204: Error: junk at end of line, first unrecognized character is1' /tmp/cc2DC8ae.s:220: Error: unknown .loc sub-directive discriminator' /tmp/cc2DC8ae.s:220: Error: junk at end of line, first unrecognized character is2' /tmp/cc2DC8ae.s:234: Error: unknown .loc sub-directive discriminator' /tmp/cc2DC8ae.s:234: Error: junk at end of line, first unrecognized character is1' /tmp/cc2DC8ae.s:241: Error: unknown .loc sub-directive discriminator' /tmp/cc2DC8ae.s:241: Error: junk at end of line, first unrecognized character is2' /tmp/cc2DC8ae.s:247: Error: unknown .loc sub-directive discriminator' /tmp/cc2DC8ae.s:247: Error: junk at end of line, first unrecognized character is1' /tmp/cc2DC8ae.s:276: Error: unknown .loc sub-directive discriminator' /tmp/cc2DC8ae.s:276: Error: junk at end of line, first unrecognized character is2' /tmp/cc2DC8ae.s:292: Error: unknown .loc sub-directive discriminator' /tmp/cc2DC8ae.s:292: Error: junk at end of line, first unrecognized character is1' /tmp/cc2DC8ae.s:300: Error: unknown .loc sub-directive discriminator' /tmp/cc2DC8ae.s:300: Error: junk at end of line, first unrecognized character is2' /tmp/cc2DC8ae.s:330: Error: unknown .loc sub-directive discriminator' /tmp/cc2DC8ae.s:330: Error: junk at end of line, first unrecognized character is2' /tmp/cc2DC8ae.s:346: Error: unknown .loc sub-directive discriminator' /tmp/cc2DC8ae.s:346: Error: junk at end of line, first unrecognized character is3' /tmp/cc2DC8ae.s:376: Error: unknown .loc sub-directive discriminator' /tmp/cc2DC8ae.s:376: Error: junk at end of line, first unrecognized character is1' /tmp/cc2DC8ae.s:386: Error: unknown .loc sub-directive discriminator' /tmp/cc2DC8ae.s:386: Error: junk at end of line, first unrecognized character is2' /tmp/cc2DC8ae.s:403: Error: unknown .loc sub-directive discriminator' /tmp/cc2DC8ae.s:403: Error: junk at end of line, first unrecognized character is1' /tmp/cc2DC8ae.s:491: Error: unknown .loc sub-directive discriminator' /tmp/cc2DC8ae.s:491: Error: junk at end of line, first unrecognized character is1' /tmp/cc2DC8ae.s:503: Error: unknown .loc sub-directive discriminator' /tmp/cc2DC8ae.s:503: Error: junk at end of line, first unrecognized character is2' /tmp/cc2DC8ae.s:531: Error: unknown .loc sub-directive discriminator' /tmp/cc2DC8ae.s:531: Error: junk at end of line, first unrecognized character is2' /tmp/cc2DC8ae.s:547: Error: unknown .loc sub-directive discriminator' /tmp/cc2DC8ae.s:547: Error: junk at end of line, first unrecognized character is1' /tmp/cc2DC8ae.s:612: Error: unknown .loc sub-directive discriminator' /tmp/cc2DC8ae.s:612: Error: junk at end of line, first unrecognized character is2' /tmp/cc2DC8ae.s:668: Error: unknown .loc sub-directive discriminator' /tmp/cc2DC8ae.s:668: Error: junk at end of line, first unrecognized character is2' /tmp/cc2DC8ae.s:731: Error: unknown .loc sub-directive discriminator' /tmp/cc2DC8ae.s:731: Error: junk at end of line, first unrecognized character is1' /tmp/cc2DC8ae.s:752: Error: unknown .loc sub-directive discriminator' /tmp/cc2DC8ae.s:752: Error: junk at end of line, first unrecognized character is2' /tmp/cc2DC8ae.s:772: Error: unknown .loc sub-directive discriminator' /tmp/cc2DC8ae.s:772: Error: junk at end of line, first unrecognized character is1' /tmp/cc2DC8ae.s:783: Error: unknown .loc sub-directive discriminator' /tmp/cc2DC8ae.s:783: Error: junk at end of line, first unrecognized character is2' /tmp/cc2DC8ae.s:794: Error: unknown .loc sub-directive discriminator' /tmp/cc2DC8ae.s:794: Error: junk at end of line, first unrecognized character is1' /tmp/cc2DC8ae.s:811: Error: unknown .loc sub-directive discriminator' /tmp/cc2DC8ae.s:811: Error: junk at end of line, first unrecognized character is3' /tmp/cc2DC8ae.s:814: Error: unknown .loc sub-directive discriminator' /tmp/cc2DC8ae.s:814: Error: junk at end of line, first unrecognized character is1' /tmp/cc2DC8ae.s:899: Error: unknown .loc sub-directive discriminator' /tmp/cc2DC8ae.s:899: Error: junk at end of line, first unrecognized character is1' /tmp/cc2DC8ae.s:917: Error: unknown .loc sub-directive discriminator' /tmp/cc2DC8ae.s:917: Error: junk at end of line, first unrecognized character is1' /tmp/cc2DC8ae.s:963: Error: unknown .loc sub-directive discriminator' /tmp/cc2DC8ae.s:963: Error: junk at end of line, first unrecognized character is2' /tmp/cc2DC8ae.s:967: Error: unknown .loc sub-directive discriminator' /tmp/cc2DC8ae.s:967: Error: junk at end of line, first unrecognized character is1' /tmp/cc2DC8ae.s:974: Error: unknown .loc sub-directive discriminator' /tmp/cc2DC8ae.s:974: Error: junk at end of line, first unrecognized character is2' /tmp/cc2DC8ae.s:991: Error: unknown .loc sub-directive discriminator' /tmp/cc2DC8ae.s:991: Error: junk at end of line, first unrecognized character is3' /tmp/cc2DC8ae.s:1012: Error: unknown .loc sub-directive discriminator' /tmp/cc2DC8ae.s:1012: Error: junk at end of line, first unrecognized character is1' /tmp/cc2DC8ae.s:1021: Error: unknown .loc sub-directive discriminator' /tmp/cc2DC8ae.s:1021: Error: junk at end of line, first unrecognized character is2' ... ... /tmp/cc2DC8ae.s:4033: Error: unknown .loc sub-directive discriminator' /tmp/cc2DC8ae.s:4033: Error: junk at end of line, first unrecognized character is1' /tmp/cc2DC8ae.s:4049: Error: unknown .loc sub-directive discriminator' /tmp/cc2DC8ae.s:4049: Error: junk at end of line, first unrecognized character is1' /tmp/cc2DC8ae.s:4056: Error: unknown .loc sub-directive discriminator' /tmp/cc2DC8ae.s:4056: Error: junk at end of line, first unrecognized character is2' /tmp/cc2DC8ae.s:4064: Error: unknown .loc sub-directive discriminator' /tmp/cc2DC8ae.s:4064: Error: junk at end of line, first unrecognized character is1' /tmp/cc2DC8ae.s:4101: Error: unknown .loc sub-directive discriminator' /tmp/cc2DC8ae.s:4101: Error: junk at end of line, first unrecognized character is2' /tmp/cc2DC8ae.s:4127: Error: unknown .loc sub-directive discriminator' /tmp/cc2DC8ae.s:4127: Error: junk at end of line, first unrecognized character is1' /tmp/cc2DC8ae.s:4142: Error: unknown .loc sub-directive discriminator' /tmp/cc2DC8ae.s:4142: Error: junk at end of line, first unrecognized character is2' /tmp/cc2DC8ae.s:4147: Error: unknown .loc sub-directive discriminator' /tmp/cc2DC8ae.s:4147: Error: junk at end of line, first unrecognized character is1' /tmp/cc2DC8ae.s:4151: Error: unknown .loc sub-directive discriminator' /tmp/cc2DC8ae.s:4151: Error: junk at end of line, first unrecognized character is2' /tmp/cc2DC8ae.s:4161: Error: unknown .loc sub-directive discriminator' /tmp/cc2DC8ae.s:4161: Error: junk at end of line, first unrecognized character is1' /tmp/cc2DC8ae.s:4248: Error: unknown .loc sub-directive discriminator' /tmp/cc2DC8ae.s:4248: Error: junk at end of line, first unrecognized character is1' /tmp/cc2DC8ae.s:4280: Error: unknown .loc sub-directive discriminator' /tmp/cc2DC8ae.s:4280: Error: junk at end of line, first unrecognized character is2' /tmp/cc2DC8ae.s:4307: Error: unknown .loc sub-directive discriminator' /tmp/cc2DC8ae.s:4307: Error: junk at end of line, first unrecognized character is1' /tmp/cc2DC8ae.s:4321: Error: unknown .loc sub-directive discriminator' /tmp/cc2DC8ae.s:4321: Error: junk at end of line, first unrecognized character is2' /tmp/cc2DC8ae.s:4325: Error: unknown .loc sub-directive discriminator' /tmp/cc2DC8ae.s:4325: Error: junk at end of line, first unrecognized character is1' /tmp/cc2DC8ae.s:4352: Error: unknown .loc sub-directive discriminator' /tmp/cc2DC8ae.s:4352: Error: junk at end of line, first unrecognized character is1' /tmp/cc2DC8ae.s:4394: Error: unknown .loc sub-directive discriminator' /tmp/cc2DC8ae.s:4394: Error: junk at end of line, first unrecognized character is2' /tmp/cc2DC8ae.s:4414: Error: unknown .loc sub-directive discriminator' /tmp/cc2DC8ae.s:4414: Error: junk at end of line, first unrecognized character is2' /tmp/cc2DC8ae.s:4426: Error: unknown .loc sub-directive discriminator' /tmp/cc2DC8ae.s:4426: Error: junk at end of line, first unrecognized character is1' /tmp/cc2DC8ae.s:4453: Error: unknown .loc sub-directive discriminator' /tmp/cc2DC8ae.s:4453: Error: junk at end of line, first unrecognized character is1' /tmp/cc2DC8ae.s:4483: Error: unknown .loc sub-directive discriminator' /tmp/cc2DC8ae.s:4483: Error: junk at end of line, first unrecognized character is2' /tmp/cc2DC8ae.s:4514: Error: unknown .loc sub-directive discriminator' /tmp/cc2DC8ae.s:4514: Error: junk at end of line, first unrecognized character is1' /tmp/cc2DC8ae.s:4565: Error: unknown .loc sub-directive discriminator' /tmp/cc2DC8ae.s:4565: Error: junk at end of line, first unrecognized character is2' /tmp/cc2DC8ae.s:4571: Error: unknown .loc sub-directive discriminator' /tmp/cc2DC8ae.s:4571: Error: junk at end of line, first unrecognized character is1' /tmp/cc2DC8ae.s:4584: Error: unknown .loc sub-directive discriminator' /tmp/cc2DC8ae.s:4584: Error: junk at end of line, first unrecognized character is3' /tmp/cc2DC8ae.s:4631: Error: unknown .loc sub-directive discriminator' /tmp/cc2DC8ae.s:4631: Error: junk at end of line, first unrecognized character is1' /tmp/cc2DC8ae.s:4813: Error: unknown .loc sub-directive discriminator' /tmp/cc2DC8ae.s:4813: Error: junk at end of line, first unrecognized character is1' /tmp/cc2DC8ae.s:4893: Error: unknown .loc sub-directive discriminator' /tmp/cc2DC8ae.s:4893: Error: junk at end of line, first unrecognized character is1' /tmp/cc2DC8ae.s:5128: Error: unknown .loc sub-directive discriminator' /tmp/cc2DC8ae.s:5128: Error: junk at end of line, first unrecognized character is1' /tmp/cc2DC8ae.s:5171: Error: unknown .loc sub-directive discriminator' /tmp/cc2DC8ae.s:5171: Error: junk at end of line, first unrecognized character is1' /tmp/cc2DC8ae.s:5217: Error: unknown .loc sub-directive discriminator' /tmp/cc2DC8ae.s:5217: Error: junk at end of line, first unrecognized character is2' /tmp/cc2DC8ae.s:5222: Error: unknown .loc sub-directive discriminator' /tmp/cc2DC8ae.s:5222: Error: junk at end of line, first unrecognized character is3' /tmp/cc2DC8ae.s:5228: Error: unknown .loc sub-directive discriminator' /tmp/cc2DC8ae.s:5228: Error: junk at end of line, first unrecognized character is1' make: * [utils.o] Error 1

Any help will be highly appreciated. Thanks in advance.

software error • 2.7k views
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Entering edit mode

What OS is this? Web search seems to indicate that you likely have an old version of binutils.

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Entering edit mode

You are right. The problem is my binutils is too old. Now I reinstalled my binutils (v2.24), and issue was solved. And the bwa is also installed successfully. Thanks so much for your suggestion.

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