WARNING: Could not compute the probability for the mate interval priors

zhang919 commented 4 years ago

Dear, I am using Circle-map to predict ecDNA，My data is download from SRA (for example, https://www.ncbi.nlm.nih.gov/sra/?term=SRR9089606). I firstly downsample this data to about 10X by seqtk like this: seqtk sample -2 -s606 {input.r1} 103333333 | gzip -c > {output.out1} seqtk sample -2 -s606 {input.r2} 103333333 | gzip -c > {output.out2} But at the finally step, Circle-Map Realign report so many warnings like this:

UserWarning: WARNING: Could not compute the probability for the mate interval priors [['chr4', 63670302, 63670344, 'DR', 'R', '0.999999'], ['chr4', 63670302, 63670344, 'DR', 'R', '0.999999']] due to the following error cannot convert float NaN to integer

You can download and review my pipline written by snakemake from https://send.firefox.com/download/ae3406fc3df56d2a/#MvYyGhVOUUgspILl8UWUAQ , and could you please give me some advises about this problem, thanks for your attention and kindly help. Best. Zhang.

iprada commented 4 years ago

Dear Zhang,

Which version of Circle-Map are you using?

Also, If you run it without seqtk does it work?

zhang919 commented 4 years ago

Dear @iprada, Thanks for your reply and patient advice. I recheck and sure I am using the lastest version installed from conda version=1.1.4, and this is my envirment:

> # Name                    Version                   Build  Channel
> _libgcc_mutex             0.1                 conda_forge    conda-forge
> _openmp_mutex             4.5                       0_gnu    conda-forge
> alsa-lib                  1.1.5             h516909a_1002    conda-forge
> bedtools                  2.29.2               hc088bd4_0    bioconda
> biopython                 1.76             py37h516909a_0    conda-forge
> bwa                       0.7.17               hed695b0_7    bioconda
> bz2file                   0.98                       py_0    conda-forge
> bzip2                     1.0.8                h516909a_2    conda-forge
> ca-certificates           2020.4.5.1           hecc5488_0    conda-forge
> certifi                   2020.4.5.1       py37hc8dfbb8_0    conda-forge
> circle-map                1.1.4                      py_0    bioconda
> curl                      7.69.1               h33f0ec9_0    conda-forge
> cutadapt                  1.18             py37h14c3975_1    bioconda
> edlib                     1.2.3                h2d50403_1    bioconda
> fastqc                    0.11.9                        0    bioconda
> font-ttf-dejavu-sans-mono 2.37                 hab24e00_0    conda-forge
> fontconfig                2.13.1            h86ecdb6_1001    conda-forge
> freetype                  2.10.1               he06d7ca_0    conda-forge
> giflib                    5.2.1                h516909a_2    conda-forge
> htslib                    1.9                  ha228f0b_7    bioconda
> icu                       64.2                 he1b5a44_1    conda-forge
> jpeg                      9c                h14c3975_1001    conda-forge
> krb5                      1.17.1               h2fd8d38_0    conda-forge
> lcms2                     2.9                  hbd6801e_1    conda-forge
> ld_impl_linux-64          2.34                 h53a641e_0    conda-forge
> libblas                   3.8.0               14_openblas    conda-forge
> libcblas                  3.8.0               14_openblas    conda-forge
> libcurl                   7.69.1               hf7181ac_0    conda-forge
> libdeflate                1.0                  h14c3975_1    bioconda
> libedit                   3.1.20170329      hf8c457e_1001    conda-forge
> libffi                    3.2.1             he1b5a44_1007    conda-forge
> libgcc-ng                 9.2.0                h24d8f2e_2    conda-forge
> libgfortran-ng            7.3.0                hdf63c60_5    conda-forge
> libgomp                   9.2.0                h24d8f2e_2    conda-forge
> libiconv                  1.15              h516909a_1006    conda-forge
> liblapack                 3.8.0               14_openblas    conda-forge
> libllvm8                  8.0.1                hc9558a2_0    conda-forge
> libopenblas               0.3.7                h5ec1e0e_6    conda-forge
> libpng                    1.6.37               hed695b0_1    conda-forge
> libssh2                   1.8.2                h22169c7_2    conda-forge
> libstdcxx-ng              9.2.0                hdf63c60_2    conda-forge
> libtiff                   4.1.0                hc7e4089_6    conda-forge
> libuuid                   2.32.1            h14c3975_1000    conda-forge
> libwebp-base              1.1.0                h516909a_3    conda-forge
> libxcb                    1.13              h14c3975_1002    conda-forge
> libxml2                   2.9.10               hee79883_0    conda-forge
> llvmlite                  0.31.0           py37h5202443_1    conda-forge
> lz4-c                     1.9.2                he1b5a44_0    conda-forge
> ncurses                   6.1               hf484d3e_1002    conda-forge
> numba                     0.48.0           py37hb3f55d8_0    conda-forge
> numpy                     1.18.1           py37h8960a57_1    conda-forge
> openjdk                   11.0.1            h600c080_1018    conda-forge
> openssl                   1.1.1g               h516909a_0    conda-forge
> pandas                    1.0.3            py37h0da4684_1    conda-forge
> perl                      5.26.2               h14c3975_7    genomedk
> pigz                      2.3.4                hed695b0_1    conda-forge
> pip                       20.1               pyh9f0ad1d_0    conda-forge
> pthread-stubs             0.4               h14c3975_1001    conda-forge
> pybedtools                0.8.1            py37he513fc3_0    bioconda
> pysam                     0.15.3           py37hda2845c_1    bioconda
> python                    3.7.6           h8356626_5_cpython    conda-forge
> python-dateutil           2.8.1                      py_0    conda-forge
> python-edlib              1.3.8.post1      py37hc9558a2_0    bioconda
> python_abi                3.7                     1_cp37m    conda-forge
> pytz                      2020.1             pyh9f0ad1d_0    conda-forge
> readline                  8.0                  hf8c457e_0    conda-forge
> samtools                  1.9                 h10a08f8_12    bioconda
> scipy                     1.4.1            py37ha3d9a3c_3    conda-forge
> seqtk                     1.3                  hed695b0_2    bioconda
> setuptools                46.1.3           py37hc8dfbb8_0    conda-forge
> six                       1.14.0                     py_1    conda-forge
> sqlite                    3.30.1               hcee41ef_0    conda-forge
> tk                        8.6.10               hed695b0_0    conda-forge
> tqdm                      4.45.0             pyh9f0ad1d_1    conda-forge
> trim-galore               0.6.5                         0    bioconda
> wheel                     0.34.2                     py_1    conda-forge
> xopen                     0.7.3                      py_0    bioconda
> xorg-fixesproto           5.0               h14c3975_1002    conda-forge
> xorg-inputproto           2.3.2             h14c3975_1002    conda-forge
> xorg-kbproto              1.0.7             h14c3975_1002    conda-forge
> xorg-libx11               1.6.9                h516909a_0    conda-forge
> xorg-libxau               1.0.9                h14c3975_0    conda-forge
> xorg-libxdmcp             1.1.3                h516909a_0    conda-forge
> xorg-libxext              1.3.4                h516909a_0    conda-forge
> xorg-libxfixes            5.0.3             h516909a_1004    conda-forge
> xorg-libxi                1.7.10               h516909a_0    conda-forge
> xorg-libxrender           0.9.10            h516909a_1002    conda-forge
> xorg-libxtst              1.2.3             h516909a_1002    conda-forge
> xorg-recordproto          1.14.2            h516909a_1002    conda-forge
> xorg-renderproto          0.11.1            h14c3975_1002    conda-forge
> xorg-xextproto            7.3.0             h14c3975_1002    conda-forge
> xorg-xproto               7.0.31            h14c3975_1007    conda-forge
> xz                        5.2.5                h516909a_0    conda-forge
> zlib                      1.2.11            h516909a_1006    conda-forge
> zstd                      1.4.4                h6597ccf_3    conda-forge

I am working on alignment with raw data without downsample to eliminate possible seqtk errors，As soon as I have the results, I will post them here.

zhang919 commented 4 years ago

Dear @iprada, I have run circle-map without seqtk, but it looks like not work. I also see many warning like this:

/home/user/miniconda3/envs/trim/lib/python3.7/site-packages/circlemap/utils.py:728: UserWarning: WARNING: Could not compute the probability for the mate interval priors [['chr6', 5256485, 5256516, 'DR', 'L', '0.999999'], ['chr6', 5256485, 5256516, 'DR', 'L', '0.999999']] due to the following error cannot convert float NaN to integer Skipping intervals

and finally the program will output a empty "my_unknown_circle.bed" file.

iprada commented 4 years ago

Dear Zhang,

Thanks a lot for the report. Could you please tell me which sample produced the issue? Was it sample SRR9089606? or was it all of them?

I will try to reproduce the error to see what went wrong, and fix the issue.

I have to admit that I am very busy at this moment. So the timeline for the fix will take around 2 weeks.

Best,

Iñigo

zhang919 commented 4 years ago

Dear @iprada ， Thank you for your quick response, you are right , I am currently using the data saved on the SRA to verify some results，so you can download this data from https://www.ncbi.nlm.nih.gov/sra?LinkName=bioproject_sra_all&from_uid=504942 . Thank you for your attention to this issue in your busy schedule. Best. Zhang.

iprada commented 4 years ago

Dear @zhang919

I wrote you a mail. Did you receive it?

zhang919 commented 4 years ago

Dear @iprada, I'm sorry to ignore your mail because outlook puted your mail to unimportant mail folder along with a lot of advertising mails automatically. Unfortunately, because I haven't seen your email for a long time and we no longer plan to use cloud servers as an alternative means to work, I cleaned the disk to free up space afterday morning (;´༎ຶД༎ຶ`) . So I just spent some time to reproduce the bug again. Now you can access via the information I have sent to you. Thanks for your attention. Best. Zhang.

iprada commented 4 years ago

No worries, and no harm done. I just wrote you a mail :)