hi,

please help me with this obstacle :(

with this syntax I tried to map my reads on my indexed genome

[izadi@lbox200 bin]$ **mapper.pl clean.fq -e -p Aspergillus_fumigatus -s reads_collapsed.fa -t reads_collapsed_vs_genome.arf -v**

but 

parsing fastq to fasta format

discarding short reads

mapping reads to genome index

trimming unmapped nts in the 3' ends

Log file for this run is in mapper_logs and called mapper.log_2598

Mapping statistics

#desc	total	mapped	unmapped	%mapped	%unmapped

Use of uninitialized value $count2 in subtraction (-) at ./mapper.pl line 708, <IN> line 2451201.

Use of uninitialized value $count in subtraction (-) at ./mapper.pl line 708, <IN> line 2451201.

total: Use of uninitialized value $count in print at ./mapper.pl line 708, <IN> line 2451201.

Use of uninitialized value $count2 in print at ./mapper.pl line 708, <IN> line 2451201.

	0	Use of uninitialized value $count in division (/) at ./mapper.pl line 709, <IN> line 2451201.

Use of uninitialized value $count2 in division (/) at ./mapper.pl line 709, <IN> line 2451201.

Illegal division by zero at ./mapper.pl line 709, <IN> line 2451201.

[izadi@lbox200 bin]$ 
[izadi@lbox200 bin]$ mapper.pl clean.fq -e -h -m -v -p Aspergillus_fumigatus -s sample.fa -t Sample.arf