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christophertbrown / iRep

scripts for estimating bacteria replication rates based on population genome copy number variation
MIT License
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bPTR output shows no coverage and calculated PTR #23

Closed sv1714 closed 6 years ago

sv1714 commented 6 years ago

Hi! I've been trying to use bPTR but when I run it I get this error.

This is the code I run: bPTR -f sequence.fna -s barcode132_clonal_sort.sam -o test.bPTR.tsv -plot test.bPTR.pdf -m coverage

And this is the warning it gives me: /Users/sv/anaconda2/envs/iRep/lib/python3.6/site-packages/mkl_fft/_numpy_fft.py:1044: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use arr[tuple(seq)] instead of arr[seq]. In the future this will be interpreted as an array index, arr[np.array(seq)], which will result either in an error or a different result. output = mkl_fft.rfftn_numpy(a, s, axes) /Users/sv/anaconda2/envs/iRep/lib/python3.6/site-packages/mkl_fft/_numpy_fft.py:1044: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use arr[tuple(seq)] instead of arr[seq]. In the future this will be interpreted as an array index, arr[np.array(seq)], which will result either in an error or a different result. output = mkl_fft.rfftn_numpy(a, s, axes)

It still gives me an output but it's missing the coverage and consensus Ori and Ter.
test.bPTR.pdf

Any help would be much appreciated. Thanks!

christophertbrown commented 6 years ago

Hi,

Not sure about this. Could there be an issue with the reads and/or mapping that would result in no coverage? Are the reads paired and do they map accurately to the genome (i.e. without mismatches)?

Chris

On Aug 7, 2018, at 1:59 PM, sv1714 notifications@github.com wrote:

Hi! I've been trying to use bPTR but when I run it I get this error.

This is the code I run: bPTR -f sequence.fna -s barcode132_clonal_sort.sam -o test.bPTR.tsv -plot test.bPTR.pdf -m coverage

And this is the warning it gives me: /Users/sv/anaconda2/envs/iRep/lib/python3.6/site-packages/mkl_fft/_numpy_fft.py:1044: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use arr[tuple(seq)] instead of arr[seq]. In the future this will be interpreted as an array index, arr[np.array(seq)], which will result either in an error or a different result. output = mkl_fft.rfftn_numpy(a, s, axes) /Users/sv/anaconda2/envs/iRep/lib/python3.6/site-packages/mkl_fft/_numpy_fft.py:1044: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use arr[tuple(seq)] instead of arr[seq]. In the future this will be interpreted as an array index, arr[np.array(seq)], which will result either in an error or a different result. output = mkl_fft.rfftn_numpy(a, s, axes)

It still gives me an output but it's missing the coverage and consensus Ori and Ter. test.bPTR.pdf

Any help would be much appreciated. Thanks!

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sv1714 commented 6 years ago

Hello,

Sorry forgot to close this, I think this is because I was using the output of breseq which doesn't align as paired reads so I've had to redo my alignment with bowtie2.

Thanks Chris!

christophertbrown commented 6 years ago

Not aligning as paired reads would definitely be a problem. Thanks for the update! Hopefully re-mapping with Bowtie2 will solve the problem.

On Aug 15, 2018, at 5:42 PM, sv1714 notifications@github.com wrote:

Hello,

Sorry forgot to close this, I think this is because I was using the output of breseq which doesn't align as paired reads so I've had to redo my alignment with bowtie2.

Thanks Chris!

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