Question: Detecting Clusters Of Anomalously Mapped Pairs With Svdetect On Galaxy
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gravatar for antomarto84
4.7 years ago by
antomarto840 wrote:

Hi everyone. I'm trying to use SVDetect tool on Galaxy. I already got about 58 milion abnormal mapped pairs. Next I need to detect clusters of anomalously mapped pairs, but I get the following error:

Use of uninitialized value $cmap_file in concatenation (.) or string at /home/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/bzeitouni/svdetect/091714bd75a0/svdetect/SVDetect_r0.8b_galaxy/svdetect/SVDetect_run_parallel.pl line 721. Use of uninitialized value $cmap_file in concatenation (.) or string at /home/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/bzeitouni/svdetect/091714bd75a0/svdetect/SVDetect_r0.8b_galaxy/svdetect/SVDetect_run_parallel.pl line 721. /home/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/bzeitouni/svdetect/091714bd75a0/svdetect/SVDetect_r0.8b_galaxy/svdetect/SVDetect_run_parallel.pl: can't open :No such file or directory

Does anybody know how to deal with it?

Thanks in advance

• 1.1k views
ADD COMMENTlink written 4.7 years ago by antomarto840

cross posted on SE: http://seqanswers.com/forums/showthread.php?t=41487

ADD REPLYlink written 4.7 years ago by Pierre Lindenbaum114k
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