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 $count2 in division (/) at ./mapper.pl line 709, <in> line 2451201.
Illegal division by zero at ./mapper.pl line 709, <in> line 2451201.
[izadi@lbox200 bin]$
