Error line 6565: error on call: probluid

[Louis-MG]

Hello, I managed to install braker and want to run it with --UTR=on. I provided a bam, a masked genome (soft) and a fasta for the proteins. I had the warning about the "|" in the headers so i took care of that in case it might be the cause of the problem. I still get the following error: The most common problem is an expired or not present file ~/.gm_key! I dig into the GeneMark-ES.stdout and it shows the following:

create directories
commit input data
soft_mask is in the 'auto' mode. soft_mask was set to: 100
data report
error on call: /home/lmgueguen/gmes_linux_64/probuild  --seq data/dna.fna  --allow_x  --stat_fasta info/dna.multi_fasta

There is only one empty file in /data/training/ , the program stops after a minute or so. Th other error file GeneMark-ES.stderr shows: (in cleanup) (in cleanup) at /usr/local/share/perl/5.30.0/Object/InsideOut.pm line 1953 during global destruction. Any hint on the problem ?

[tomasbruna]

Hello,

this could be the same problem as you encountered in https://github.com/Gaius-Augustus/BRAKER/issues/96.

Do you get a segmentation fault when running the following command?

/home/lmgueguen/gmes_linux_64/probuild  --seq data/dna.fna  --allow_x  --stat_fasta info/dna.multi_fasta

If not, what is the error message?

The (in cleanup) (in cleanup) error is only related to memory management of one of the Perl modules used, it is not really a problem.

Best, Tomas

[Louis-MG]

Well I set up the braker pipeline on another machine with sudo access as I am in a hurry.

I thought about it indeed, but the gmhmme3 did not yield a segmentation fault when I tried the same command as the last time. The command you give produces nothing particular.

[Louis-MG]

Update @tomasbruna : Because the command did not show any error I decided to give my script another try, and this time I got the following (did not change anything):

build initial ES model
running step ES_A
running gm.hmm on local system
6550 contigs in training
error on open file: /home/lmgueguen/braker_wd/GeneMark-ES/run/ES_A_1/hmmout/dna.fa_740.out
error on open file: /home/lmgueguen/braker_wd/GeneMark-ES/run/ES_A_1/hmmout/dna.fa_741.out
error on open file: /home/lmgueguen/braker_wd/GeneMark-ES/run/ES_A_1/hmmout/dna.fa_742.out
error on open file: /home/lmgueguen/braker_wd/GeneMark-ES/run/ES_A_1/hmmout/dna.fa_750.out
error on open file: /home/lmgueguen/braker_wd/GeneMark-ES/run/ES_A_1/hmmout/dna.fa_760.out
error on open file: /home/lmgueguen/braker_wd/GeneMark-ES/run/ES_A_1/hmmout/dna.fa_761.out
error on open file: /home/lmgueguen/braker_wd/GeneMark-ES/run/ES_A_1/hmmout/dna.fa_763.out
error on open file: /home/lmgueguen/braker_wd/GeneMark-ES/run/ES_A_1/hmmout/dna.fa_776.out
error on open file: /home/lmgueguen/braker_wd/GeneMark-ES/run/ES_A_1/hmmout/dna.fa_783.out
error on open file: /home/lmgueguen/braker_wd/GeneMark-ES/run/ES_A_1/hmmout/dna.fa_787.out
error on open file: /home/lmgueguen/braker_wd/GeneMark-ES/run/ES_A_1/hmmout/dna.fa_791.out
error on open file: /home/lmgueguen/braker_wd/GeneMark-ES/run/ES_A_1/hmmout/dna.fa_793.out
error on open file: /home/lmgueguen/braker_wd/GeneMark-ES/run/ES_A_1/hmmout/dna.fa_794.out
error on open file: /home/lmgueguen/braker_wd/GeneMark-ES/run/ES_A_1/hmmout/dna.fa_796.out
error on open file: /home/lmgueguen/braker_wd/GeneMark-ES/run/ES_A_1/hmmout/dna.fa_802.out
error on open file: /home/lmgueguen/braker_wd/GeneMark-ES/run/ES_A_1/hmmout/dna.fa_804.out
error on open file: /home/lmgueguen/braker_wd/GeneMark-ES/run/ES_A_1/hmmout/dna.fa_809.out
error on open file: /home/lmgueguen/braker_wd/GeneMark-ES/run/ES_A_1/hmmout/dna.fa_822.out
error on open file: /home/lmgueguen/braker_wd/GeneMark-ES/run/ES_A_1/hmmout/dna.fa_825.out
error on open file: /home/lmgueguen/braker_wd/GeneMark-ES/run/ES_A_1/hmmout/dna.fa_826.out
error on open file: /home/lmgueguen/braker_wd/GeneMark-ES/run/ES_A_1/hmmout/dna.fa_827.out
error on open file: /home/lmgueguen/braker_wd/GeneMark-ES/run/ES_A_1/hmmout/dna.fa_828.out
error on open file: /home/lmgueguen/braker_wd/GeneMark-ES/run/ES_A_1/hmmout/dna.fa_831.out
error on open file: /home/lmgueguen/braker_wd/GeneMark-ES/run/ES_A_1/hmmout/dna.fa_833.out
error on open file: /home/lmgueguen/braker_wd/GeneMark-ES/run/ES_A_1/hmmout/dna.fa_835.out
error on open file: /home/lmgueguen/braker_wd/GeneMark-ES/run/ES_A_1/hmmout/dna.fa_837.out
error on open file: /home/lmgueguen/braker_wd/GeneMark-ES/run/ES_A_1/hmmout/dna.fa_838.out
error on open file: /home/lmgueguen/braker_wd/GeneMark-ES/run/ES_A_1/hmmout/dna.fa_840.out
error on open file: /home/lmgueguen/braker_wd/GeneMark-ES/run/ES_A_1/hmmout/dna.fa_844.out
error on open file: /home/lmgueguen/braker_wd/GeneMark-ES/run/ES_A_1/hmmout/dna.fa_845.out
error on open file: /home/lmgueguen/braker_wd/GeneMark-ES/run/ES_A_1/hmmout/dna.fa_848.out
error on open file: /home/lmgueguen/braker_wd/GeneMark-ES/run/ES_A_1/hmmout/dna.fa_851.out
error on open file: /home/lmgueguen/braker_wd/GeneMark-ES/run/ES_A_1/hmmout/dna.fa_852.out
error on open file: /home/lmgueguen/braker_wd/GeneMark-ES/run/ES_A_1/hmmout/dna.fa_857.out
error on open file: /home/lmgueguen/braker_wd/GeneMark-ES/run/ES_A_1/hmmout/dna.fa_858.out
error on open file: /home/lmgueguen/braker_wd/GeneMark-ES/run/ES_A_1/hmmout/dna.fa_860.out
error on open file: /home/lmgueguen/braker_wd/GeneMark-ES/run/ES_A_1/hmmout/dna.fa_862.out
error on open file: /home/lmgueguen/braker_wd/GeneMark-ES/run/ES_A_1/hmmout/dna.fa_863.out
error on open file: /home/lmgueguen/braker_wd/GeneMark-ES/run/ES_A_1/hmmout/dna.fa_865.out
error on open file: /home/lmgueguen/braker_wd/GeneMark-ES/run/ES_A_1/hmmout/dna.fa_866.out
error on open file: /home/lmgueguen/braker_wd/GeneMark-ES/run/ES_A_1/hmmout/dna.fa_867.out
error on open file: /home/lmgueguen/braker_wd/GeneMarkconcatenate predictions: /home/lmgueguen/braker_wd/GeneMark-ES/run/ES_A_1
training level ES_A: /home/lmgueguen/braker_wd/GeneMark-ES/run/ES_A_1
Initial	20232
Internal	32278
Terminal	20024
Single	2470
Intron:	53847	140793207
Intergenic:	12039	103631168
error, no valid sequences were found
error on call: /home/lmgueguen/gmes_linux_64/make_nt_freq_mat.pl --cfg /home/lmgueguen/braker_wd/GeneMark-ES/run.cfg --section start_ATG   --format INI

I will run it again later to see if that is consistant.

Update: still running, no error so far. Lacking storage maybe ?

[tomasbruna]

Update: still running, no error so far. Lacking storage maybe?

That could well be, I have never experienced an instability like this -- GeneMark either always fails, or always runs.

Fingers crossed for this run

[mengguoqingup]

hello ， i have a same problem when i run genemark -es along. how did you solved this problem? thank you! Initial 0 Internal 1 Terminal 1 Single 1 Intron: 2 12346 Intergenic: 1 25645 error, no valid sequences were found error on call: /opt/biosoft/gmes_linux_64/make_nt_freq_mat.pl --cfg /home/annotation/mengguoqing/Rosa/rosa_rugosa_chinesis/megahit_asme/GM/run.cfg --section stop_TGA --format TERM_TGA

Initial 0 Internal 1 Terminal 1 Single 1 Intron: 2 12346 Intergenic: 1 25645 error, no valid sequences were found error on call: /opt/biosoft/gmes_linux_64/make_nt_freq_mat.pl --cfg /home/annotation/mengguoqing/Rosa/rosa_rugosa_chinesis/megahit_asme/GM/run.cfg --section stop_TGA --format TERM_TGA

[tomasbruna]

Hello @mengguoqingup,

in your case, GeneMark-ES fails because it only predicts 3 exons in the iteration. How large is your input sequence and how long are the contigs? I wonder if this problem is caused by the input being too small.

Best, Tomas

[mengguoqingup]

@tomasbruna @ Thank you so much! I am sorry to bother again， but now I have a new problem in genemark. may help?thank you warning on: /opt/biosoft/gmes_linux_64/gmhmme3 -m /home/annotation/mengguoqing/Rosa/yingcaoqiangwei/megahit_asme/GM/output/gmhmm.mod -f lst -n -o output/gmhmm/dna.fa_152074.out /home/annotation/mengguoqing/Rosa/yingcaoqiangwei/megahit_asme/GM/output/data/dna.fa_152074 warning on: /opt/biosoft/gmes_linux_64/gmhmme3 -m /home/annotation/mengguoqing/Rosa/yingcaoqiangwei/megahit_asme/GM/output/gmhmm.mod -f lst -n -o output/gmhmm/dna.fa_152169.out /home/annotation/mengguoqing/Rosa/yingcaoqiangwei/megahit_asme/GM/output/data/dna.fa_152169 *** glibc detected *** /opt/biosoft/gmes_linux_64/gmhmme3: double free or corruption (!prev): 0x00000000015c13d0 *** ======= Backtrace: ========= [0x49df1a] [0x4a0cec] [0x401792] [0x47ec7e] [0x4003e9] ======= Memory map: ======== 00400000-00560000 r-xp 00000000 fd:03 807547933 /opt/biosoft/gmes_linux_64/gmhmme3 0075f000-00762000 rw-p 0015f000 fd:03 807547933 /opt/biosoft/gmes_linux_64/gmhmme3 00762000-00779000 rw-p 00000000 00:00 0 0142a000-015f0000 rw-p 00000000 00:00 0 [heap] 7f71c8000000-7f71c8027000 rw-p 00000000 00:00 0 7f71c8027000-7f71cc000000 ---p 00000000 00:00 0 7f71cd7ac000-7f71cda57000 rw-p 00000000 00:00 0 7fffe3cc5000-7fffe3ce7000 rw-p 00000000 00:00 0 [stack] 7fffe3cf0000-7fffe3cf2000 r-xp 00000000 00:00 0 [vdso] ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall] warning on: /opt/biosoft/gmes_linux_64/gmhmme3 -m /home/annotation/mengguoqing/Rosa/yingcaoqiangwei/megahit_asme/GM/output/gmhmm.mod -f lst -n -o output/gmhmm/dna.fa_159532.out /home/annotation/mengguoqing/Rosa/yingcaoqiangwei/megahit_asme/GM/output/data/dna.fa_159532

[tomasbruna]

Hi @mengguoqingup,

what was the solution for the original problem? Was the input sequence just too short?

This new error is something I have not seen before, it might be caused by something unexpected in your input. Can you share the intermediate input files, these ones?

• /home/annotation/mengguoqing/Rosa/yingcaoqiangwei/megahit_asme/GM/output/gmhmm.mod
• /home/annotation/mengguoqing/Rosa/yingcaoqiangwei/megahit_asme/GM/output/data/dna.fa_152169

I will try to run gmhmme3 and see if I can reproduce this error.

By the way, what version of gmhmme3 do you have? This can be determined by running gmhmme3 without arguments, like this:

 /opt/biosoft/gmes_linux_64/gmhmme3

Tomas