clone filter error message

[Tina Meyer]

Hi all,

I am analysing ddRAD data using paired end reads. I want to run clone_filter 2.54 and it worked for 39 out of 46 samples.

The command I used is:

clone_filter -1 /work/tina/1_demultiplex/Ba_2007-03.1.fq -2 /work/tina/1_demultiplex/Ba_2007-03.2.fq  -o /work/tina/clone_filter_out/ -D

The sample ID is more or less the same for all 46 samples. (e.g. sample-ID.1.fq and sample-ID.2.fq)

The error message I get is:
Processing paired-end data.
No oligo sequence specified, will use single and paired-end reads to determine clones.
Found 1 paired input file(s).
Processing file 1 of 1 [Ba_2007-03.1.fq]
Reading data from:
Ba_2007-03.1.fq and
Ba_2007-03.1.fq 
munmap_chunk(): invalid pointer
Aborted

I also tried to run the command on a local linux computer and I got this error message:

Processing paired-end data.
No oligo sequence specified, will use single and paired-end reads to determine clones.
Found 1 paired input file(s).
Processing file 1 of 1 [Ba_2007-03.1.fq]
Reading data from:
  .../User_files/Tina/1_demultiplex/Ba_2007-03.1.fq and
 .../User_files/Tina/1_demultiplex/Ba_2007-03.2.fq
*** Error in `clone_filter': corrupted size vs. prev_size: 0x00000000026329a0 ***
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(+0x777f5)[0x7fbf119747f5]
/lib/x86_64-linux-gnu/libc.so.6(+0x82b03)[0x7fbf1197fb03]
/lib/x86_64-linux-gnu/libc.so.6(__libc_malloc+0x54)[0x7fbf119811d4]
/usr/lib/x86_64-linux-gnu/libstdc++.so.6(_Znwm+0x18)[0x7fbf12490e78]
clone_filter[0x4140de]
clone_filter[0x412e8c]
clone_filter[0x4068b4]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0)[0x7fbf1191d840]
clone_filter[0x409539]
======= Memory map: ========
00400000-004bc000 r-xp 00000000 08:03 41428018                           /usr/local/bin/clone_filter
006bb000-006bc000 r--p 000bb000 08:03 41428018                           /usr/local/bin/clone_filter
006bc000-006be000 rw-p 000bc000 08:03 41428018                           /usr/local/bin/clone_filter
006be000-006bf000 rw-p 00000000 00:00 0
0261b000-0264d000 rw-p 00000000 00:00 0                                  [heap]
7fbf0c000000-7fbf0c021000 rw-p 00000000 00:00 0
7fbf0c021000-7fbf10000000 ---p 00000000 00:00 0
7fbf118fd000-7fbf11abd000 r-xp 00000000 08:03 74842331                   /lib/x86_64-linux-gnu/libc-2.23.so
7fbf11abd000-7fbf11cbd000 ---p 001c0000 08:03 74842331                   /lib/x86_64-linux-gnu/libc-2.23.so
7fbf11cbd000-7fbf11cc1000 r--p 001c0000 08:03 74842331                   /lib/x86_64-linux-gnu/libc-2.23.so
7fbf11cc1000-7fbf11cc3000 rw-p 001c4000 08:03 74842331                   /lib/x86_64-linux-gnu/libc-2.23.so
7fbf11cc3000-7fbf11cc7000 rw-p 00000000 00:00 0
7fbf11cc7000-7fbf11cdf000 r-xp 00000000 08:03 74842313                   /lib/x86_64-linux-gnu/libpthread-2.23.so
7fbf11cdf000-7fbf11ede000 ---p 00018000 08:03 74842313                   /lib/x86_64-linux-gnu/libpthread-2.23.so
7fbf11ede000-7fbf11edf000 r--p 00017000 08:03 74842313                   /lib/x86_64-linux-gnu/libpthread-2.23.so
7fbf11edf000-7fbf11ee0000 rw-p 00018000 08:03 74842313                   /lib/x86_64-linux-gnu/libpthread-2.23.so
7fbf11ee0000-7fbf11ee4000 rw-p 00000000 00:00 0
7fbf11ee4000-7fbf11efa000 r-xp 00000000 08:03 74846633                   /lib/x86_64-linux-gnu/libgcc_s.so.1
7fbf11efa000-7fbf120f9000 ---p 00016000 08:03 74846633                   /lib/x86_64-linux-gnu/libgcc_s.so.1
7fbf120f9000-7fbf120fa000 rw-p 00015000 08:03 74846633                   /lib/x86_64-linux-gnu/libgcc_s.so.1
7fbf120fa000-7fbf12202000 r-xp 00000000 08:03 74842326                   /lib/x86_64-linux-gnu/libm-2.23.so
7fbf12202000-7fbf12401000 ---p 00108000 08:03 74842326                   /lib/x86_64-linux-gnu/libm-2.23.so
7fbf12401000-7fbf12402000 r--p 00107000 08:03 74842326                   /lib/x86_64-linux-gnu/libm-2.23.so
7fbf12402000-7fbf12403000 rw-p 00108000 08:03 74842326                   /lib/x86_64-linux-gnu/libm-2.23.so
7fbf12403000-7fbf12575000 r-xp 00000000 08:03 40894614                   /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
7fbf12575000-7fbf12775000 ---p 00172000 08:03 40894614                   /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
7fbf12775000-7fbf1277f000 r--p 00172000 08:03 40894614                   /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
7fbf1277f000-7fbf12781000 rw-p 0017c000 08:03 40894614                   /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
7fbf12781000-7fbf12785000 rw-p 00000000 00:00 0
7fbf12785000-7fbf1279e000 r-xp 00000000 08:03 74842394                   /lib/x86_64-linux-gnu/libz.so.1.2.8
7fbf1279e000-7fbf1299d000 ---p 00019000 08:03 74842394                   /lib/x86_64-linux-gnu/libz.so.1.2.8
7fbf1299d000-7fbf1299e000 r--p 00018000 08:03 74842394                   /lib/x86_64-linux-gnu/libz.so.1.2.8
7fbf1299e000-7fbf1299f000 rw-p 00019000 08:03 74842394                   /lib/x86_64-linux-gnu/libz.so.1.2.8
7fbf1299f000-7fbf129c5000 r-xp 00000000 08:03 74842323                   /lib/x86_64-linux-gnu/ld-2.23.so
7fbf12b9e000-7fbf12ba5000 rw-p 00000000 00:00 0
7fbf12bc3000-7fbf12bc4000 rw-p 00000000 00:00 0
7fbf12bc4000-7fbf12bc5000 r--p 00025000 08:03 74842323                   /lib/x86_64-linux-gnu/ld-2.23.so
7fbf12bc5000-7fbf12bc6000 rw-p 00026000 08:03 74842323                   /lib/x86_64-linux-gnu/ld-2.23.so
7fbf12bc6000-7fbf12bc7000 rw-p 00000000 00:00 0
7fff98b93000-7fff98bb5000 rw-p 00000000 00:00 0                          [stack]
7fff98be2000-7fff98be5000 r--p 00000000 00:00 0                          [vvar]
7fff98be5000-7fff98be7000 r-xp 00000000 00:00 0                          [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0                  [vsyscall]
Aborted (core dumped)

Do you know how I could fix this problem?

Best,

Tina

[Catchen, Julian]

Hi Tina,

 

Do your ddRAD data have random oligos to identify the potential PCR clones? If not, then you do not want to run clone_filter on the data as clones cannot be determined from plain ddRAD data and it will just throw all of your data away. The clone_filter program should only be used on ddRAD data produced with protocols such as 3RAD. Other single-digest paired-end data can be processed for PCR duplicates directly in gstacks and they do not require clone_filter.

 

Best,

 

julian

[Tina Meyer]

Hi Julian,

I have no random oligos, then I do not have to run clone_filter.

Thank you for your help!

Best,

Tina