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OverflowError: Cannot convert float infinity to integer #38
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The last time this happened there was a problem with the users files. Could you please post the output of (My guess is that your files are not tab-separated.) On Thursday, September 8, 2016, Carlos Guzman notifications@github.com
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And if this is not it, I will probably be able to find the bug right away if you could send me the files privately through dropbox or something. |
Head of treatment bed:
Head of Input bed:
I can send the files to you via dropbox if you still need them. They're encode files. Specifically ENCSR000DLY and it's associated control. I used bamtobed from bedtools to generate these bed files so i'm not entirely sure why they wouldn't be tab separated to begin with. |
I was able to reproduce this; it happens when there is no "chr" in the sed "s/^/chr/" treatment.bed > ucsc_treatment.bed Thanks for reporting. I will support encode style chromo names soon, but do On Fri, Sep 9, 2016 at 4:55 PM, Carlos Guzman notifications@github.com
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Great! Thank you! |
All of zebrafish genome contigs are not called ~ "^chr". |
Thanks for the feedback! I agree that epic should handle gencode genome names, but I do not see how to handle arbitrary strings. The problem is that I have a lookup table for each supported genome:
I need to match the chromosome names in the user's bed files to the chromosome names in the lookup table. If the names are arbitrary strings I do not see how to do it. Also, contigs (are those non-canonical chromosome parts?) are not supported because they would mess with mappability and total genome length. Of course if the contig length is <<< genome length, this should not matter much. Edit: I think the only problem with arbitrary names for chromosomes is that I cannot remove reads that are shifted outside of the chromosome boundaries, which is a minor issue. I'll think about whether I should add a Edit2: Also, the built-in chromosome names are there to save time; without them, I would need another pass through the data to fetch the chromosome names. This is because to make each core work with one chromosome, I need to know which chromosomes are in the data. Of course Edit3: With non-canonical genome names, the bigwigs created by epic won't be viewable in the UCSC genome browser. |
@balwierz In |
Command used:
Resulting error:
Any ideas?
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