HI
I downloaded the latest version of the tool and got some error. I will be glad if you help me figure out the errors.
command used
/usr/bin/time -f "%M %U" perl `pwd`/tools/gnumaps/scripts/
gnumaps.pl --genome `pwd`/ref/allchr.fa --pair_1 `pwd`/simulated_data/sim_end1.fastq --pair_2 `pwd`/simulated_data/sim_end2.fastq --adaptor AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG --adaptor2 AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT --read_type dna --phred_offset 64 --nt_conv bs --skip_blat 1 --debug 1 --pileup 1 -outdir `pwd`/runs/simulated_data/gnumap/
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GNUMAP_PIPELINE(v0.1)
-
http://jlab.bu.edu-
cjh...@bu.edu-running at /data2/bsi/staff_analysis/m078940/TRACE-RRBS/tools/gnumaps
Tue Jan 7 14:30:20 CST 2014
-elapsed time: 0.0
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In progress ...
sh: line 2: /data2/bsi/staff_analysis/m078940/TRACE-RRBS/tools/gnumaps/dep/gnumap_MPI_opt/bin/gnumap-stl: No such file or directory
sh: line 2: /data2/bsi/staff_analysis/m078940/TRACE-RRBS/tools/gnumaps/dep/gnumap_MPI_opt/bin/gnumap-stl: No such file or directory
Can't exec "/data2/bsi/staff_analysis/m078940/TRACE-RRBS/tools/gnumaps/dep/blat/faToTwoBit": No such file or directory at /data2/bsi/staff_analysis/m078940/TRACE-RRBS/tools/gnumaps/scripts/
gnumaps.pl line 434.
sh: line 2: /data2/bsi/staff_analysis/m078940/TRACE-RRBS/tools/gnumaps/dep/gnumap_MPI_opt/bin/gnumap-stl: No such file or directory
sh: line 2: /data2/bsi/staff_analysis/m078940/TRACE-RRBS/tools/gnumaps/dep/gnumap_MPI_opt/bin/gnumap-stl: No such file or directory
sh: line 2: /data2/bsi/staff_analysis/m078940/TRACE-RRBS/tools/gnumaps/dep/gnumap_MPI_opt/bin/gnumap-stl: No such file or directory
sh: line 2: /data2/bsi/staff_analysis/m078940/TRACE-RRBS/tools/gnumaps/dep/gnumap_MPI_opt/bin/gnumap-stl: No such file or directory
it is looking for gnumap-stl command which is not available, is there something wrong with my installation.
Thanks
Saurabh