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MGEScan / mgescan

A Galaxy based system for identifying retrotransposons in genome
http://mgescan.github.io/mgescan/
GNU General Public License v3.0
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Memory issue in MGEscan #25

Open andreaswallberg opened 3 years ago

andreaswallberg commented 3 years ago

Dear @lee212 ,

I am running mgescan from the command line like this:

MGESCAN_DEBUG=1 ./mgescan/mgescan/nonltr/run_MGEScan.pl -genome=data3 -data=output -hmmerv=2

However, I keep having an error that seems to occur as when my input sequence in the directory data3 becomes too long. A length of 101940 bp is ok but 107940 bp or larger is not. It appears to be the case the compiled MGEScan is unable to free memory correctly for long input files.

I assume that this software should run across chromosome-scale FASTA files. Is this not the case? Should it be run on a library of much shorter potential repeat sequences instead?

Grateful for feedback!

Error message:

*** Error in `/home/andreas/devel/mgescan/mgescan3/mgescan/mgescan/nonltr/hmm/MGEScan': free(): invalid next size (normal): 0x0000000000de4ff0 ***
======= Backtrace: =========
/lib64/libc.so.6(+0x81329)[0x2b9a690c0329]
/lib64/libc.so.6(fclose+0x177)[0x2b9a690ad247]
/home/andreas/devel/mgescan/mgescan3/mgescan/mgescan/nonltr/hmm/MGEScan[0x40258b]
/home/andreas/devel/mgescan/mgescan3/mgescan/mgescan/nonltr/hmm/MGEScan[0x402b23]
/home/andreas/devel/mgescan/mgescan3/mgescan/mgescan/nonltr/hmm/MGEScan[0x403734]
/home/andreas/devel/mgescan/mgescan3/mgescan/mgescan/nonltr/hmm/MGEScan[0x400efa]
/lib64/libc.so.6(__libc_start_main+0xf5)[0x2b9a69061555]
/home/andreas/devel/mgescan/mgescan3/mgescan/mgescan/nonltr/hmm/MGEScan[0x400f82]
======= Memory map: ========
00400000-00406000 r-xp 00000000 9cf:e7a10 1675344533304398600            /home/andreas/devel/mgescan/mgescan3/mgescan/mgescan/nonltr/hmm/MGEScan
00605000-00606000 r--p 00005000 9cf:e7a10 1675344533304398600            /home/andreas/devel/mgescan/mgescan3/mgescan/mgescan/nonltr/hmm/MGEScan
00606000-00607000 rw-p 00006000 9cf:e7a10 1675344533304398600            /home/andreas/devel/mgescan/mgescan3/mgescan/mgescan/nonltr/hmm/MGEScan
00dd8000-00df9000 rw-p 00000000 00:00 0                                  [heap]
2b9a68b19000-2b9a68b3b000 r-xp 00000000 fd:00 524018                     /usr/lib64/ld-2.17.so
2b9a68b3b000-2b9a68b3d000 rw-p 00000000 00:00 0 
2b9a68b60000-2b9a68b63000 rw-p 00000000 00:00 0 
2b9a68d3a000-2b9a68d3b000 r--p 00021000 fd:00 524018                     /usr/lib64/ld-2.17.so
2b9a68d3b000-2b9a68d3c000 rw-p 00022000 fd:00 524018                     /usr/lib64/ld-2.17.so
2b9a68d3c000-2b9a68d3d000 rw-p 00000000 00:00 0 
2b9a68d3d000-2b9a68e3e000 r-xp 00000000 fd:00 540465                     /usr/lib64/libm-2.17.so
2b9a68e3e000-2b9a6903d000 ---p 00101000 fd:00 540465                     /usr/lib64/libm-2.17.so
2b9a6903d000-2b9a6903e000 r--p 00100000 fd:00 540465                     /usr/lib64/libm-2.17.so
2b9a6903e000-2b9a6903f000 rw-p 00101000 fd:00 540465                     /usr/lib64/libm-2.17.so
2b9a6903f000-2b9a69203000 r-xp 00000000 fd:00 539996                     /usr/lib64/libc-2.17.so
2b9a69203000-2b9a69402000 ---p 001c4000 fd:00 539996                     /usr/lib64/libc-2.17.so
2b9a69402000-2b9a69406000 r--p 001c3000 fd:00 539996                     /usr/lib64/libc-2.17.so
2b9a69406000-2b9a69408000 rw-p 001c7000 fd:00 539996                     /usr/lib64/libc-2.17.so
2b9a69408000-2b9a6abdd000 rw-p 00000000 00:00 0 
2b9a6abdd000-2b9a6abf2000 r-xp 00000000 fd:00 524390                     /usr/lib64/libgcc_s-4.8.5-20150702.so.1
2b9a6abf2000-2b9a6adf1000 ---p 00015000 fd:00 524390                     /usr/lib64/libgcc_s-4.8.5-20150702.so.1
2b9a6adf1000-2b9a6adf2000 r--p 00014000 fd:00 524390                     /usr/lib64/libgcc_s-4.8.5-20150702.so.1
2b9a6adf2000-2b9a6adf3000 rw-p 00015000 fd:00 524390                     /usr/lib64/libgcc_s-4.8.5-20150702.so.1
2b9a6c000000-2b9a6c021000 rw-p 00000000 00:00 0 
2b9a6c021000-2b9a70000000 ---p 00000000 00:00 0 
7fff12892000-7fff128b6000 rw-p 00000000 00:00 0                          [stack]
7fff128f9000-7fff128fb000 r-xp 00000000 00:00 0                          [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0                  [vsyscall]
/home/andreas/devel/mgescan/mgescan3/mgescan/mgescan/nonltr/post_process.pl --dna=data3_b/ --out=output/b/ --rev=1
continue? (Y/n): Y
/home/andreas/devel/mgescan/mgescan3/mgescan/mgescan/nonltr/post_process2.pl --data_dir=output/ --hmmerv=2
continue? (Y/n): Y