GenPro_create_db.pl potentially has issue

[akotlar]

for ((i=1;i<27;i++)); do GenPro_create_db.pl -g hg38 -c $i --genedir hg38/gene --geneset refGene -f hg38/chr -o hg38/idx & done

###...some time later
[1]   Done                    GenPro_create_db.pl -g hg38 -c $i --genedir hg38/gene --geneset refGene -f hg38/chr -o hg38/idx
[2]   Done                    GenPro_create_db.pl -g hg38 -c $i --genedir hg38/gene --geneset refGene -f hg38/chr -o hg38/idx
[3]   Done                    GenPro_create_db.pl -g hg38 -c $i --genedir hg38/gene --geneset refGene -f hg38/chr -o hg38/idx
[4]   Done                    GenPro_create_db.pl -g hg38 -c $i --genedir hg38/gene --geneset refGene -f hg38/chr -o hg38/idx
[5]   Done                    GenPro_create_db.pl -g hg38 -c $i --genedir hg38/gene --geneset refGene -f hg38/chr -o hg38/idx
[6]   Done                    GenPro_create_db.pl -g hg38 -c $i --genedir hg38/gene --geneset refGene -f hg38/chr -o hg38/idx
[7]   Done                    GenPro_create_db.pl -g hg38 -c $i --genedir hg38/gene --geneset refGene -f hg38/chr -o hg38/idx
[8]   Done                    GenPro_create_db.pl -g hg38 -c $i --genedir hg38/gene --geneset refGene -f hg38/chr -o hg38/idx
[9]   Done                    GenPro_create_db.pl -g hg38 -c $i --genedir hg38/gene --geneset refGene -f hg38/chr -o hg38/idx
[10]   Done                    GenPro_create_db.pl -g hg38 -c $i --genedir hg38/gene --geneset refGene -f hg38/chr -o hg38/idx
[11]   Done                    GenPro_create_db.pl -g hg38 -c $i --genedir hg38/gene --geneset refGene -f hg38/chr -o hg38/idx
[12]   Done                    GenPro_create_db.pl -g hg38 -c $i --genedir hg38/gene --geneset refGene -f hg38/chr -o hg38/idx
[13]   Done                    GenPro_create_db.pl -g hg38 -c $i --genedir hg38/gene --geneset refGene -f hg38/chr -o hg38/idx
[14]   Done                    GenPro_create_db.pl -g hg38 -c $i --genedir hg38/gene --geneset refGene -f hg38/chr -o hg38/idx
[15]   Done                    GenPro_create_db.pl -g hg38 -c $i --genedir hg38/gene --geneset refGene -f hg38/chr -o hg38/idx
[16]   Done                    GenPro_create_db.pl -g hg38 -c $i --genedir hg38/gene --geneset refGene -f hg38/chr -o hg38/idx
[17]   Done                    GenPro_create_db.pl -g hg38 -c $i --genedir hg38/gene --geneset refGene -f hg38/chr -o hg38/idx
[18]   Done                    GenPro_create_db.pl -g hg38 -c $i --genedir hg38/gene --geneset refGene -f hg38/chr -o hg38/idx
[19]   Done                    GenPro_create_db.pl -g hg38 -c $i --genedir hg38/gene --geneset refGene -f hg38/chr -o hg38/idx
[20]   Done                    GenPro_create_db.pl -g hg38 -c $i --genedir hg38/gene --geneset refGene -f hg38/chr -o hg38/idx
[21]   Done                    GenPro_create_db.pl -g hg38 -c $i --genedir hg38/gene --geneset refGene -f hg38/chr -o hg38/idx
[22]   Done                    GenPro_create_db.pl -g hg38 -c $i --genedir hg38/gene --geneset refGene -f hg38/chr -o hg38/idx
[23]   Done                    GenPro_create_db.pl -g hg38 -c $i --genedir hg38/gene --geneset refGene -f hg38/chr -o hg38/idx
[24]   Done                    GenPro_create_db.pl -g hg38 -c $i --genedir hg38/gene --geneset refGene -f hg38/chr -o hg38/idx
[25]-  Exit 1                  GenPro_create_db.pl -g hg38 -c $i --genedir hg38/gene --geneset refGene -f hg38/chr -o hg38/idx
[26]+  Done                    GenPro_create_db.pl -g hg38 -c $i --genedir hg38/gene --geneset refGene -f hg38/chr -o hg38/idx

Not sure yet why we are looking for 26 chromosomes instead of 25.

#25 seems to exit improperly

Exit code 1        General errors, Miscellaneous errors, such as "divide by zero" and other impermissible operations

[akotlar]

Ok, running the following, I see the problem

Error: unrecognized chromosome: 25

ec2-user@ip-172-31-8-9:~/GenPro$ for ((i=1;i<27;i++)); do
> GenPro_make_refprotdb.pl --chr $i -l hg38/idx/ -n hg38 -o /mnt/annotator/genpro/hg38/refProteins &
> done
[1] 78137
[2] 78138
[3] 78139
[4] 78140
[5] 78141
[6] 78142
[7] 78143
[8] 78144
[9] 78145
[10] 78146
[11] 78147
[12] 78148
[13] 78149
[14] 78150
[15] 78151
[16] 78152
[17] 78153
[18] 78154
[19] 78155
[20] 78156
[21] 78157
[22] 78158
[23] 78159
[24] 78160
[25] 78161
[26] 78162
ec2-user@ip-172-31-8-9:~/GenPro$ reading genome for 'chr2'...
reading genome for 'chr1'...
reading genome for 'chr5'...
reading genome for 'chr10'...
reading genome for 'chr4'...
reading genome for 'chr11'...
reading genome for 'chr3'...
reading genome for 'chr14'...
reading genome for 'chr16'...
reading genome for 'chr12'...
reading genome for 'chrX'...
reading genome for 'chr18'...
reading genome for 'chr6'...
reading genome for 'chr13'...
reading genome for 'chr8'...
reading genome for 'chr9'...
reading genome for 'chr7'...
reading genome for 'chr15'...
reading genome for 'chrY'...
reading genome for 'chr19'...
reading genome for 'chr17'...
reading genome for 'chrM'...
reading genome for 'chr21'...
reading genome for 'chr22'...
Error: unrecognized chromosome: 25
reading genome for 'chr20'...
done.
Writing protein data for 'chrM'...
done

In GenPro::CleanChr M is mapped to 26, not 25 as suspected. This should probably be changed to 25.

sub CleanChr {
  my $chr = shift;

  my @chrs = ( 1 .. 22, 'X', 'Y', 'M' );
  my %chrOk = map { $_ => 1 } (@chrs);
  my %chrNumToLetter = ( 23 => 'X', 24 => 'Y', 26 => 'M' );

  $chr = uc($chr);
  $chr =~ s/\ACHR//xm;
  if ( exists $chrOk{$chr} ) {
    return "chr" . $chr;
  }
  elsif ( exists $chrNumToLetter{$chr} ) {
    return "chr" . $chrNumToLetter{$chr};
  }
  else {
    my $msg = "Error: unrecognized chromosome: $chr";
    say $msg;
    exit(1);
  }
}