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NabaviLab / CNV-Sim

Copy Number Variations (CNV) Simulator
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CNVsim/Wessim Index Error #2

Closed nskelkar closed 8 years ago

nskelkar commented 8 years ago

Hello, I am running CNVsim with the default settings and I am experiencing this error. Traceback (most recent call last): File "sub_wessim1.py", line 818, in main(sys.argv[1:]) File "__sub_wessim1.py", line 177, in main gcVector = getFragmentUniform(abdlist, seqlist, last, isize, 1000, bind) File "sub_wessim1.py", line 275, in getFragmentUniform seq = seqlist[ind][1] IndexError: list index out of range

I have checked to see if my reference and targets are the same format (chr1 vs 1) and still experience this issue. Thank you

abdelrahmanhosny commented 8 years ago

Hi @nskelkar Do your reference and target files contain more than one chromosome?

nskelkar commented 8 years ago

Yeah they do contain more than one chromosome. Is that an issue?

abdelrahmanhosny commented 8 years ago

Yes, read issue #1 for more info. The resolution is to divide your simulation (manually) for each chromosome. That is, run the simulation on chr1.fa and chr1-targets.bed separately from other chromosomes. Do so with other chromosomes as well.

abdelrahmanhosny commented 8 years ago

Replicated issue (refer to #1). Closing.