error while recode

[Jonathan Brassac]

Dear Meng Huang and BLINK users,

I am having an issue while I'm trying to generate the hmp file.

I have already used this function with an other dataset that worked (and still does).

The program seems to recognize the number of individual with the first command (compress) but not in the second command (recode)

Below is the terminal output.

Any idea is welcome!

Cheers

Nath

~/programs/BLINK-master/blink_linux --file test --compress --vcf

**************************
*   BLINK v0.01 start   *
**************************
****************************************************************
*   BLINK is written by Meng Huang and designed by Zhiwu Zhang  *
*  Please visit zzlab.net to get more information about BLINK  *
****************************************************************


Input arguments:   --file test --compress 1
one cycle include 1000 SNPs inside!
number of individuals is 185
number of markers is 53894
==The compressed binary files have been created successfully!==

~/programs/BLINK-master/blink_linux --file test --recode --out test --hapmap

**************************
*   BLINK v0.01 start   *
**************************
****************************************************************
*   BLINK is written by Meng Huang and designed by Zhiwu Zhang  *
*  Please visit zzlab.net to get more information about BLINK  *
****************************************************************


Input arguments:   --file test --out test
one cycle include 1000 SNPs inside!

The number of traits = 56

The number of marker = 53894
number of markers is 53894
number of individuals is 0
*** Error in `/home/dumortier/programs/BLINK-master/blink_linux': free(): invalid pointer: 0x0000000001ff2d90 ***
======= Backtrace: =========
/usr/lib64/libc.so.6(+0x81609)[0x7fd89ac57609]
/home/dumortier/programs/BLINK-master/blink_linux[0x410ac5]
/home/dumortier/programs/BLINK-master/blink_linux[0x415efc]
/usr/lib64/libc.so.6(__libc_start_main+0xf5)[0x7fd89abf8495]
/home/dumortier/programs/BLINK-master/blink_linux[0x400c39]
======= Memory map: ========
00400000-00419000 r-xp 00000000 fd:02 810878801                          /home/dumortier/programs/BLINK-master/blink_linux
00618000-00619000 r--p 00018000 fd:02 810878801                          /home/dumortier/programs/BLINK-master/blink_linux
00619000-0061a000 rw-p 00019000 fd:02 810878801                          /home/dumortier/programs/BLINK-master/blink_linux
01ff2000-02013000 rw-p 00000000 00:00 0                                  [heap]
7fd894000000-7fd894021000 rw-p 00000000 00:00 0
7fd894021000-7fd898000000 ---p 00000000 00:00 0
7fd89a9c0000-7fd89a9d5000 r-xp 00000000 fd:00 33615066                   /usr/lib64/libgcc_s-4.8.5-20150702.so.1
7fd89a9d5000-7fd89abd4000 ---p 00015000 fd:00 33615066                   /usr/lib64/libgcc_s-4.8.5-20150702.so.1
7fd89abd4000-7fd89abd5000 r--p 00014000 fd:00 33615066                   /usr/lib64/libgcc_s-4.8.5-20150702.so.1
7fd89abd5000-7fd89abd6000 rw-p 00015000 fd:00 33615066                   /usr/lib64/libgcc_s-4.8.5-20150702.so.1
7fd89abd6000-7fd89ad98000 r-xp 00000000 fd:00 33555994                   /usr/lib64/libc-2.17.so
7fd89ad98000-7fd89af98000 ---p 001c2000 fd:00 33555994                   /usr/lib64/libc-2.17.so
7fd89af98000-7fd89af9c000 r--p 001c2000 fd:00 33555994                   /usr/lib64/libc-2.17.so
7fd89af9c000-7fd89af9e000 rw-p 001c6000 fd:00 33555994                   /usr/lib64/libc-2.17.so
7fd89af9e000-7fd89afa3000 rw-p 00000000 00:00 0
7fd89afa3000-7fd89b0a4000 r-xp 00000000 fd:00 33576984                   /usr/lib64/libm-2.17.so
7fd89b0a4000-7fd89b2a3000 ---p 00101000 fd:00 33576984                   /usr/lib64/libm-2.17.so
7fd89b2a3000-7fd89b2a4000 r--p 00100000 fd:00 33576984                   /usr/lib64/libm-2.17.so
7fd89b2a4000-7fd89b2a5000 rw-p 00101000 fd:00 33576984                   /usr/lib64/libm-2.17.so
7fd89b2a5000-7fd89b2c7000 r-xp 00000000 fd:00 33555990                   /usr/lib64/ld-2.17.so
7fd89b4a0000-7fd89b4a3000 rw-p 00000000 00:00 0
7fd89b4c1000-7fd89b4c6000 rw-p 00000000 00:00 0
7fd89b4c6000-7fd89b4c7000 r--p 00021000 fd:00 33555990                   /usr/lib64/ld-2.17.so
7fd89b4c7000-7fd89b4c8000 rw-p 00022000 fd:00 33555990                   /usr/lib64/ld-2.17.so
7fd89b4c8000-7fd89b4c9000 rw-p 00000000 00:00 0
7fff73c56000-7fff73c78000 rw-p 00000000 00:00 0                          [stack]
7fff73db9000-7fff73dbb000 r-xp 00000000 00:00 0                          [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0                  [vsyscall]
Aborted (core dumped)

[Jonathan Brassac]

Sorry for this stupid error, I just realized that my phenotype fie was not fitting exactly to my genotype file, after adjusting this, it worked like a charm!

Cheers,

Nath

[Tom Matiyos]

ar Nath

I also get such problem and solved by checking each clumn. Check if any column contains # specialy in assambly column or any symbols before any worlds in the 1st row. Delete it the # or other symbols. Good luck
Temesgen