Circle-Map
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iprada
WARNING: Could not compute the probability for the mate interval priors
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.
Dear Zhang,
Which version of Circle-Map are you using?
- Also, If you run it without seqtk does it work?
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.
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.
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
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.
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.
dear @iprada, I'm having the same issue with Circle-Map. Is there a way to solve this problem?
Best regards. Michele
dear @iprada I have the similar issues, which has stuck me for a long time. It would be great if you can provide a way to solve it.
Best regards, Phaedo
Hi @iprada @zhang919,
I recently encountered the same issue. Is there a solution for it? Thanks!
Best, Haiqi
