linux - (清理中)在全局销毁期间无法在未定义的值 Object/InsideOut.pm 行 1953 上调用方法 "FETCH"

Question

原始命令:

nohup time -v --output=time_braker2_RNAonly.log braker.pl --species=BUSCO_BUSCO_sunbird_trimPLK_881882613 --useexisting --cores=40 --genome=/home/cch/sunbird/sunbird_RepeatMasker_trim/sunbird_platanus_trim_kraken_scaff_gapclosed_1000.fa.masked --softmasking 1 --hints=/home/cch/sunbird/sunbird_HISAT2_trim/sunbird_trim_hints_AS_400K.gff,/home/cch/sunbird/sunbird_HISAT2_trim/sunbird_trim_hints_China_400K.gff --UTR=off &

当我运行 BRAKER2 时，我无法继续并在 GeneMark-ET.stderr 中不断收到此错误消息:

(in cleanup) Can't call method "FETCH" on an undefined value at /usr/local/share/perl/5.22.1/Object/InsideOut.pm line 1953 during global destruction

我尝试更新 Object::InsideOut 模块但没有任何帮助

这是 perl 文件中的第 1953 行:

head -n 1953 /usr/local/share/perl/5.22.1/Object/InsideOut.pm | tail -n 10
    return if (! $$self);

    # Grab any error coming into this routine
    my $err = $@;

    # Preserve other error variables
    local($!, $^E, $?);

    # Workaround for Perl's "in cleanup" bug
    if ($Config::Config{useithreads} &&

getAnnoFastaJoingenes..stderr 中的另一个错误消息

usage: getAnnoFastaFromJoingenes.py [-h] -g GENOME -f GTF -o OUT
                                    [-t TRANSLATION_TABLE] [-s FILTER]
getAnnoFastaFromJoingenes.py: error: argument -o/--out: expected one argument

这是我的 nohup 文件:

Use of uninitialized value $_ in substitution (s///) at /opt/BRAKER/scripts/braker.pl line 7970.
ERROR in file /opt/BRAKER/scripts/braker.pl at line 7986
Failed to execute: perl /opt/Augustus/scripts/join_aug_pred.pl < /home/cch/sunbird/sunbird_BRAKER2_RNAonly_trim/braker/BUSCO_BUSCO_sunbird_trimPLK_881882613/augustus.tmp.gff > /home/cch/sunbird/sunbird_BRAKER2_RNAonly_trim/braker/BUSCO_BUSCO_sunbird_trimPLK_881882613/augustus.hints.gff

这是我的日志文件结束的地方:

#Thu Dec 27 20:34:03 2018: Making a fasta file with protein sequences of /home/cch/sunbird/sunbird_BRAKER2_RNAonly_trim/braker/BUSCO_BUSCO_sunbird_trimPLK_881882613/augustus.hints.gtf
/usr/bin/python3 /opt/Augustus/scripts/getAnnoFastaFromJoingenes.py -g /home/cch/sunbird/sunbird_BRAKER2_RNAonly_trim/braker/BUSCO_BUSCO_sunbird_trimPLK_881882613/genome.fa -f /home/cch/sunbird/sunbird_BRAKER2_RNAonly_trim/braker/BUSCO_BUSCO_sunbird_trimPLK_881882613/augustus.hints.gtf -o 1> /home/cch/sunbird/sunbird_BRAKER2_RNAonly_trim/braker/BUSCO_BUSCO_sunbird_trimPLK_881882613/getAnnoFasta..stdout 2>/home/cch/sunbird/sunbird_BRAKER2_RNAonly_trim/braker/BUSCO_BUSCO_sunbird_trimPLK_881882613/errors/getAnnoFastaJoingenes..stderr

我检查了 braker.pl 7970 行:

head -n 7970 /opt/BRAKER/scripts/braker.pl | tail -n 10

sub get_anno_fasta {
    my $AUG_pred = shift;
    print LOG "\# "
        . (localtime)
        . ": Making a fasta file with protein sequences of $AUG_pred\n"
        if ($v > 2);
    my $name_base = $AUG_pred;
    $name_base = s/[^\.]+$//;

和 braker.pl 7986 行:

head -n 7986 /opt/BRAKER/scripts/braker.pl | tail -n 10

my $pythonCmdString = "";
if ($nice) {
    $pythonCmdString .= "nice ";
}
$pythonCmdString .= "$PYTHON3_PATH/python3 $string -g $genome -f $AUG_pred "
                 .  "-o $name_base 1> $outfile 2>$errorfile";

print LOG "$pythonCmdString\n\n" if ($v > 3);
system("$pythonCmdString") == 0
    or die("ERROR in file " . __FILE__ ." at line ". __LINE__

如果有人对此有任何想法，我将不胜感激，我试图查看是否有任何在线解决方案，但几乎没有任何来源，而且我对这些的理解有限......

Answer 1

除了 perl 警告外，我发现 2018 年 12 月 22 日从 BRAKER2 下载的 perl 脚本有一个错误，该错误已在最新版本中修复:

$name_base = s/[^.]+$//在 = 之后缺少一个 ~

$name_base =~ s/[^\.]+$//

检查最新版本的 BRAKER.pl 他们已经编辑并添加了很多行。