bam2hints problem

[dep]

Hello All!

I am trying to use BRAKER1 pipeline for a fungus genome annotation, but I experience problems with bam2hints program that is part of the Augustus package. When the pipeline comes to using bam2hints it returns the following error and I have no idea what to do with it. Any ideas on whether I can do something with it on my computer, or it is something wrong with the program itself?

Thank you.

NEXT STEP: make hints from BAM file /home/xxx/xxx.bam
Wait a moment, calculating maximum block size that needs to be allocated... .. done
*** Error in `/home/dmitrii/biotools/augustus-3.1/config//../bin/bam2hints': free(): invalid next size (normal): 0x00000000008a29f0 ***
======= Backtrace: =========
/lib64/libc.so.6(+0x7d1fd)[0x7fadd0bd81fd]
/home/dmitrii/biotools/augustus-3.1/config//../bin/bam2hints[0x419f61]
/home/dmitrii/biotools/augustus-3.1/config//../bin/bam2hints[0x41a11e]
/home/dmitrii/biotools/augustus-3.1/config//../bin/bam2hints[0x41a2d9]
/home/dmitrii/biotools/augustus-3.1/config//../bin/bam2hints[0x409888]
/lib64/libc.so.6(__libc_start_main+0xf5)[0x7fadd0b7caf5]
/home/dmitrii/biotools/augustus-3.1/config//../bin/bam2hints[0x406c09]
======= Memory map: ========
00400000-00464000 r-xp 00000000 fd:02 2221854534 /home/dmitrii/biotools/augustus-3.1/bin/bam2hints
00663000-00664000 r--p 00063000 fd:02 2221854534 /home/dmitrii/biotools/augustus-3.1/bin/bam2hints
00664000-00665000 rw-p 00064000 fd:02 2221854534 /home/dmitrii/biotools/augustus-3.1/bin/bam2hints
00665000-00666000 rw-p 00000000 00:00 0
006e8000-00923000 rw-p 00000000 00:00 0 [heap]
7fadd0b5b000-7fadd0d11000 r-xp 00000000 fd:01 201327590 /usr/lib64/libc-2.17.so
7fadd0d11000-7fadd0f11000 ---p 001b6000 fd:01 201327590 /usr/lib64/libc-2.17.so
7fadd0f11000-7fadd0f15000 r--p 001b6000 fd:01 201327590 /usr/lib64/libc-2.17.so
7fadd0f15000-7fadd0f17000 rw-p 001ba000 fd:01 201327590 /usr/lib64/libc-2.17.so
7fadd0f17000-7fadd0f1c000 rw-p 00000000 00:00 0
7fadd0f1c000-7fadd0f31000 r-xp 00000000 fd:01 205263047 /usr/lib64/libgcc_s-4.8.3-20140911.so.1
7fadd0f31000-7fadd1130000 ---p 00015000 fd:01 205263047 /usr/lib64/libgcc_s-4.8.3-20140911.so.1
7fadd1130000-7fadd1131000 r--p 00014000 fd:01 205263047 /usr/lib64/libgcc_s-4.8.3-20140911.so.1
7fadd1131000-7fadd1132000 rw-p 00015000 fd:01 205263047 /usr/lib64/libgcc_s-4.8.3-20140911.so.1
7fadd1132000-7fadd1233000 r-xp 00000000 fd:01 201327598 /usr/lib64/libm-2.17.so
7fadd1233000-7fadd1432000 ---p 00101000 fd:01 201327598 /usr/lib64/libm-2.17.so
7fadd1432000-7fadd1433000 r--p 00100000 fd:01 201327598 /usr/lib64/libm-2.17.so
7fadd1433000-7fadd1434000 rw-p 00101000 fd:01 201327598 /usr/lib64/libm-2.17.so
7fadd1434000-7fadd151d000 r-xp 00000000 fd:01 201332502 /usr/lib64/libstdc++.so.6.0.19
7fadd151d000-7fadd171c000 ---p 000e9000 fd:01 201332502 /usr/lib64/libstdc++.so.6.0.19
7fadd171c000-7fadd1724000 r--p 000e8000 fd:01 201332502 /usr/lib64/libstdc++.so.6.0.19
7fadd1724000-7fadd1726000 rw-p 000f0000 fd:01 201332502 /usr/lib64/libstdc++.so.6.0.19
7fadd1726000-7fadd173b000 rw-p 00000000 00:00 0
7fadd173b000-7fadd1750000 r-xp 00000000 fd:01 201332494 /usr/lib64/libz.so.1.2.7
7fadd1750000-7fadd194f000 ---p 00015000 fd:01 201332494 /usr/lib64/libz.so.1.2.7
7fadd194f000-7fadd1950000 r--p 00014000 fd:01 201332494 /usr/lib64/libz.so.1.2.7
7fadd1950000-7fadd1951000 rw-p 00015000 fd:01 201332494 /usr/lib64/libz.so.1.2.7
7fadd1951000-7fadd1972000 r-xp 00000000 fd:01 203145045 /usr/lib64/ld-2.17.so
7fadd1b56000-7fadd1b5b000 rw-p 00000000 00:00 0
7fadd1b6e000-7fadd1b72000 rw-p 00000000 00:00 0
7fadd1b72000-7fadd1b73000 r--p 00021000 fd:01 203145045 /usr/lib64/ld-2.17.so
7fadd1b73000-7fadd1b74000 rw-p 00022000 fd:01 203145045 /usr/lib64/ld-2.17.so
7fadd1b74000-7fadd1b75000 rw-p 00000000 00:00 0
7fff0ef6d000-7fff0ef8e000 rw-p 00000000 00:00 0 [stack]
7fff0effe000-7fff0f000000 r-xp 00000000 00:00 0 [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]
sh: line 1: 21387 Aborted (core dumped) /home/dmitrii/biotools/augustus-3.1/config//../bin/bam2hints --intronsonly --in=/home/xxx/xxx.bam --out=/home/xxx/bam2hints.temp.gff 2> /home/xxx/errors/bam2hints.0.stderr
failed to execute: Inappropriate ioctl for device

[Macspider]

Any ideas on whether I can do something with it on my computer, or it is something wrong with the program itself?

I know it's been a while, but I've been recently through the same error and I solved it trying the solutions suggested here.

https://gist.github.com/macmanes/bc5598e0d079ff6d71f2

Have you by chance encountered any other problem using BRAKER1, later on?
I stumbled on a new problem, which is related to gene mark ET. It keeps saying:

failed to execute: perl /software/genemark/GeneMark_ES_ET_4.32/gmes_petap.pl --sequence=/../genome.fa --ET=/../hintsfile.gff --cores=20 1>/../GeneMark-ET.stdout 2>/../GeneMark-ET.stderr

(I shortened the paths for an improved readability)

When I read the stdout and stderr files, and when I run the pipeline with debug mode, it always says:

error, no valid sequences were found
error on call: /software/genemark/GeneMark_ES_ET_4.32/make_nt_freq_mat.pl --cfg /../run.cfg --section start_ATG  --format INI

Any clue? (I'm also opening a new thread about this)