#1 Could not open at /home/ashwin/DistMap_v1.0/bin/DataProcess.pm line 171.

[Anonymous]

Originally created by: ashwinun...@griffithuni.edu.au

What steps will reproduce the problem?
1.Tried to run Distmap referring to the manual. This is what I used

DistMap_v1.0/distmap --reference-fasta datasets/WholeGenome/genome.fa --reference-index-archive datasets/indexed_genome/refarch.tgz --input "datasets/synthetic_sample1.fq.gz,datasets/synthetic_sample2.fq.gz" --mapper bwa --mapper-path bwa-0.5.8c/bwa --picard-mergesamfiles-jar picard-tools-1.99/MergeSamFiles.jar --picard-sortsam-jar picard-tools-1.99/SortSam.jar --mapper-args "-o 1 -n 0.01 -l 200 -e 12 -dd 12" --output-format sam --output /home/ashwin/distmap_output/ --hadoop-home /usr/lib/hadoop-0.20-mapreduce/

What is the expected output? What do you see instead?
Earlier it was getting past second step and I was having errors at the 3rd step. Now I am having trouble getting past the second step itself.

This is what I am getting..

=======================================================================
Step2: Converting FASTQ into tab seperated file
             and creating archieve to upload into HDFS system
=======================================================================

Started at:  24/09/2013 19:8:54 Tuesday
Writng fastq files into tab text file
Use of uninitialized value $_ in concatenation (.) or string at /home/ashwin/DistMap_v1.0/bin/DataProcess.pm line 171.
could not open  at /home/ashwin/DistMap_v1.0/bin/DataProcess.pm line 171.

What version of the product are you using? On what operating system?
I am using DistMap V1.0 . Operating System is CentOs 6.2.

Please provide any additional information below.
I have set up a one-node cluster using Cloudera Hadoop (CDH4). I think Hadoop is working alright as i managed to get an indexed genome using Distmap on the same system.

Thanks

[Anonymous]

Originally posted by: sangeeth... (code.google.com)@gmail.com

Do you have any updates on this issue? how did you resolve this? I am facing the same problem.