bwa error in proovread install: make: *** [utils.o] Error 1
0
0
Entering edit mode
8.3 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 • 3.4k views
ADD COMMENT
1
Entering edit mode

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

ADD REPLY
0
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.

ADD REPLY

Login before adding your answer.

Traffic: 1313 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6