CALRK-S fails

[Jens]

Hi,

I've followed the instrucitons to setup a CLARK-S database:

Which worked fine:

> ll T*

T295:

total 21G

-rw-r--r--  1 jroatkul jan100jhmi 1.6G Jan 23 11:03 db_central_k31_t5772_s1610612741_m0_w22.tsk.sz

-rw-r--r--  1 jroatkul jan100jhmi 9.8G Jan 23 11:03 db_central_k31_t5772_s1610612741_m0_w22.tsk.lb

-rw-r--r--  1 jroatkul jan100jhmi 9.8G Jan 23 11:03 db_central_k31_t5772_s1610612741_m0_w22.tsk.ky

drwxr-xr-x  2 jroatkul jan100jhmi  33K Jan 23 11:03 ./

drwxr-xr-x 14 jroatkul jan100jhmi  41K Jan 23 14:41 ../

T58570:

total 21G

-rw-r--r--  1 jroatkul jan100jhmi 1.6G Jan 23 13:01 db_central_k31_t5772_s1610612741_m0_w22.tsk.sz

-rw-r--r--  1 jroatkul jan100jhmi 9.8G Jan 23 13:01 db_central_k31_t5772_s1610612741_m0_w22.tsk.lb

-rw-r--r--  1 jroatkul jan100jhmi 9.8G Jan 23 13:01 db_central_k31_t5772_s1610612741_m0_w22.tsk.ky

drwxr-xr-x  2 jroatkul jan100jhmi  33K Jan 23 13:01 ./

drwxr-xr-x 14 jroatkul jan100jhmi  41K Jan 23 14:41 ../

T38570:

total 21G

-rw-r--r--  1 jroatkul jan100jhmi 1.6G Jan 23 14:41 db_central_k31_t5772_s1610612741_m0_w22.tsk.sz

-rw-r--r--  1 jroatkul jan100jhmi 9.9G Jan 23 14:41 db_central_k31_t5772_s1610612741_m0_w22.tsk.lb

-rw-r--r--  1 jroatkul jan100jhmi 9.9G Jan 23 14:41 db_central_k31_t5772_s1610612741_m0_w22.tsk.ky

drwxr-xr-x 14 jroatkul jan100jhmi  41K Jan 23 14:41 ../

drwxr-xr-x  2 jroatkul jan100jhmi  33K Jan 23 14:41 ./

When I run the following command CLARK-S fails:

CLARK-S -m 0 -k 31 -t 0 -o 0 -n 20 -O IN.fq -R IN.spaced.results -T targets.txt -D path/to/clarkdb

CLARK version 1.2.3 (UCR CS&E. Copyright 2013-2016 Rachid Ounit, roun...@cs.ucr.edu)

*** glibc detected *** /projects/ps-janssen3/jhmi/jroatkul/bin/CLARKSCV1.2.3/exe/CLARK-S: double free or corruption (!prev): 0x000000000218ce70 ***

======= Backtrace: =========

/lib64/libc.so.6[0x369ca75f4e]

/lib64/libc.so.6[0x369ca78cf0]

/projects/ps-janssen3/jhmi/jroatkul/bin/CLARKSCV1.2.3/exe/CLARK-S[0x43a4d9]

/projects/ps-janssen3/jhmi/jroatkul/bin/CLARKSCV1.2.3/exe/CLARK-S[0x458384]

/projects/ps-janssen3/jhmi/jroatkul/bin/CLARKSCV1.2.3/exe/CLARK-S[0x4038db]

/lib64/libc.so.6(__libc_start_main+0xfd)[0x369ca1ed5d]

/projects/ps-janssen3/jhmi/jroatkul/bin/CLARKSCV1.2.3/exe/CLARK-S[0x404261]

======= Memory map: ========

00400000-00477000 r-xp 00000000 00:23 41553918                           /projects/ps-janssen3/jhmi/jroatkul/bin/CLARKSCV1.2.3/exe/CLARK-S

00677000-00678000 rw-p 00077000 00:23 41553918                           /projects/ps-janssen3/jhmi/jroatkul/bin/CLARKSCV1.2.3/exe/CLARK-S

01b7e000-021af000 rw-p 00000000 00:00 0                                  [heap]

369c600000-369c620000 r-xp 00000000 08:01 4718636                        /lib64/ld-2.12.so

369c81f000-369c820000 r--p 0001f000 08:01 4718636                        /lib64/ld-2.12.so

369c820000-369c821000 rw-p 00020000 08:01 4718636                        /lib64/ld-2.12.so

369c821000-369c822000 rw-p 00000000 00:00 0

369ca00000-369cb8a000 r-xp 00000000 08:01 4718640                        /lib64/libc-2.12.so

369cb8a000-369cd8a000 ---p 0018a000 08:01 4718640                        /lib64/libc-2.12.so

369cd8a000-369cd8e000 r--p 0018a000 08:01 4718640                        /lib64/libc-2.12.so

369cd8e000-369cd8f000 rw-p 0018e000 08:01 4718640                        /lib64/libc-2.12.so

369cd8f000-369cd94000 rw-p 00000000 00:00 0

369ce00000-369ce83000 r-xp 00000000 08:01 4718695                        /lib64/libm-2.12.so

369ce83000-369d082000 ---p 00083000 08:01 4718695                        /lib64/libm-2.12.so

369d082000-369d083000 r--p 00082000 08:01 4718695                        /lib64/libm-2.12.so

369d083000-369d084000 rw-p 00083000 08:01 4718695                        /lib64/libm-2.12.so

369d200000-369d217000 r-xp 00000000 08:01 4718654                        /lib64/libpthread-2.12.so

369d217000-369d417000 ---p 00017000 08:01 4718654                        /lib64/libpthread-2.12.so

369d417000-369d418000 r--p 00017000 08:01 4718654                        /lib64/libpthread-2.12.so

369d418000-369d419000 rw-p 00018000 08:01 4718654                        /lib64/libpthread-2.12.so

369d419000-369d41d000 rw-p 00000000 00:00 0

369da00000-369da07000 r-xp 00000000 08:01 4718655                        /lib64/librt-2.12.so

369da07000-369dc06000 ---p 00007000 08:01 4718655                        /lib64/librt-2.12.so

369dc06000-369dc07000 r--p 00006000 08:01 4718655                        /lib64/librt-2.12.so

369dc07000-369dc08000 rw-p 00007000 08:01 4718655                        /lib64/librt-2.12.so

2b04e4adc000-2b04e4ade000 rw-p 00000000 00:00 0

2b04e4ade000-2b04e4bd1000 r-xp 00000000 08:01 922724                     /opt/gnu/gcc/lib64/libstdc++.so.6.0.20

2b04e4bd1000-2b04e4dd0000 ---p 000f3000 08:01 922724                     /opt/gnu/gcc/lib64/libstdc++.so.6.0.20

2b04e4dd0000-2b04e4dd9000 r--p 000f2000 08:01 922724                     /opt/gnu/gcc/lib64/libstdc++.so.6.0.20

2b04e4dd9000-2b04e4ddb000 rw-p 000fb000 08:01 922724                     /opt/gnu/gcc/lib64/libstdc++.so.6.0.20

2b04e4ddb000-2b04e4df0000 rw-p 00000000 00:00 0

2b04e4e09000-2b04e4e1f000 r-xp 00000000 08:01 922689                     /opt/gnu/gcc/lib64/libgomp.so.1.0.0

2b04e4e1f000-2b04e501e000 ---p 00016000 08:01 922689                     /opt/gnu/gcc/lib64/libgomp.so.1.0.0

2b04e501e000-2b04e501f000 rw-p 00015000 08:01 922689                     /opt/gnu/gcc/lib64/libgomp.so.1.0.0

2b04e501f000-2b04e5020000 rw-p 00000000 00:00 0

2b04e5020000-2b04e5036000 r-xp 00000000 08:01 922663                     /opt/gnu/gcc/lib64/libgcc_s.so.1

2b04e5036000-2b04e5235000 ---p 00016000 08:01 922663                     /opt/gnu/gcc/lib64/libgcc_s.so.1

2b04e5235000-2b04e5236000 rw-p 00015000 08:01 922663                     /opt/gnu/gcc/lib64/libgcc_s.so.1

2b04e5236000-2b04e523c000 rw-p 00000000 00:00 0

2b04e569d000-2b04e571e000 rw-p 00000000 00:00 0

2b04e8000000-2b04e8021000 rw-p 00000000 00:00 0

2b04e8021000-2b04ec000000 ---p 00000000 00:00 0

7ffef1401000-7ffef141a000 rw-p 00000000 00:00 0                          [stack]

7ffef14ef000-7ffef14f0000 r-xp 00000000 00:00 0                          [vdso]

ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0                  [vsyscall]

[Rachid]

Hello Jens Kultima, 

Thank you for your interest. Let's take a look at this issue:

0) What is the information of your system (RAM, Core, etc.)? Please see the guidelines for reporting issues here. 

1) Is this error persistent with other sample files ? Have you tried to run CLARK-S with any of the public datasets we used in our peer-reviewed papers (http://doi.org/10.1186/s12864-015-1419-2, and https://doi.org/10.1093/bioinformatics/btw542)?

If not, could you please run CLARK-S and let us know the outcome.

2) If this error appears only for your data (i.e., IN.fq) then let us know and maybe send it to us, so we track the error and fix it.

3) Can you try to rerun CLARK this time without using the option "-o 0"  nor "-t 0" ?

PS: For your next bug/error report, could you please describe as specifically as possible the bug/error - I am afraid that a general and very short statement like "CLARK-S fails" is not likely to help easily future/other users looking for solutions to any issues similar to yours.

Thanks,

Rachid