search

CAFS-bioinformatics / LR_Gapcloser

use long sequenced reads to close gaps in assemblies
GNU General Public License v3.0
35 stars 0 forks source link

Illegal division by zero and use of unintialized value error #7

Open apn83 opened 5 years ago

apn83 commented 5 years ago

Hi, I tried LRgapcloser with my pacbio Long reads data. The process did end sucessfully and I was able to see gapclosed.fasta file in iteration-3 folder. But I also got, 1.5Gb of log file with two kinds of lines:

Illegal division by zero at /sw/csi/lr_gapcloser/github_commit_156381a/el7.5_binary/LR_Gapcloser/src/coverage_calculator.pl line 29, line 87. Use of uninitialized value $seg[5] in pattern match (m//) at /sw/csi/lr_gapcloser/github_commit_156381a/el7.5_binary/LR_Gapcloser/src/coverage_calculator.pl line 16, line 85.

perl version is use is 5.26.1

What is the solution for this ?

Thanks in advance.

conchoecia commented 5 years ago

I am having the same issue in commit 156381a Update README.md

ViriatoII commented 4 years ago

The code that generates the error in the bottom. It has 0 documentation. I'm not a perl coder, so I can't fix it. But I detected which variables are problematic.

48 $seg[16] =~ s/XA:Z://; 49 @seg_x = split /;/,$seg[16]; ... 51 my $nn = @seg_x; 52 for (my $ii=0;$ii<$nn;$ii++) { 53 @seg_x2 = split /,/,$seg_x[$ii]; 54 @ref23 = ($seg_x2[2] =~ /(\d+)[DP]/g); 55 @read3 = ($seg_x2[2] =~ /^(\d+)[HS]/); 56 @totl3 = ($seg_x2[2] =~ /(\d+)[SH]/g); # This is probably already 0 57 @cover3 = ($seg_x2[2] =~ /(\d+)M/g); # This is probably already 0 58 @ref13 = ($seg_x2[2] =~ /(\d+)I/g); # This is probably already 0 59 my $SH = &sum(@totl3); 60 my $M = &sum(@cover3); 61 my $I = &sum(@ref13); 62 $read3 = &sum(@read3); 63 $ref_jian3 = $SH+$I; 64 $ref_jia3 = &sum(@ref23); 65 $sum3 = $SH+$M+$I; # These 3 variables must be 0 already 66 $match3 = $M+$I; 67 $ratio3 = $match3/$sum3; # <- Error is here. sum3 is 0.

jzohren commented 3 years ago

I also came across the same issue. Has anyone been able to find a fix for it?