installation error

[circR]

Hi Sir I tried to install circtools on my PC(ubuntu 16.04) and I got the following error message. Could you help with this? Thank you

$ python3 setup.py install --verbose --user running install Requirement already satisfied: statsmodels in /home/cd/miniconda3/lib/python3.6/site-packages (0.9.0) Requirement already satisfied: patsy in /home/cd/miniconda3/lib/python3.6/site-packages (from statsmodels) (0.5.0) Requirement already satisfied: pandas in /home/cd/miniconda3/lib/python3.6/site-packages (from statsmodels) (0.23.0) Requirement already satisfied: six in /home/cd/miniconda3/lib/python3.6/site-packages (from patsy->statsmodels) (1.11.0) Requirement already satisfied: numpy>=1.4 in /home/cd/miniconda3/lib/python3.6/site-packages (from patsy->statsmodels) (1.14.3) Requirement already satisfied: python-dateutil>=2.5.0 in /home/cd/miniconda3/lib/python3.6/site-packages (from pandas->statsmodels) (2.7.3) Requirement already satisfied: pytz>=2011k in /home/cd/miniconda3/lib/python3.6/site-packages (from pandas->statsmodels) (2018.4) Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help A new version of Bioconductor is available after installing the most recent version of R; see http://bioconductor.org/install BioC_mirror: https://bioconductor.statistik.tu-dortmund.de Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15). installation path not writeable, unable to update packages: DBI, RMySQL, codetools, foreign, lattice, spatial Skipping install of 'CircTest' from a github remote, the SHA1 (2fd16602) has not changed since last install. Use force = TRUE to force installation Skipping install of 'primex' from a github remote, the SHA1 (f715f111) has not changed since last install. Use force = TRUE to force installation Cloning into 'DCC'... remote: Counting objects: 876, done. remote: Compressing objects: 100% (14/14), done. remote: Total 876 (delta 6), reused 17 (delta 4), pack-reused 857 Receiving objects: 100% (876/876), 226.95 KiB | 239.00 KiB/s, done. Resolving deltas: 100% (599/599), done. Checking connectivity... done. Traceback (most recent call last): File "setup.py", line 11, in from setuptools import setup ImportError: No module named setuptools Cloning into 'FUCHS'... remote: Counting objects: 1928, done. remote: Compressing objects: 100% (6/6), done. remote: Total 1928 (delta 2), reused 7 (delta 1), pack-reused 1920 Receiving objects: 100% (1928/1928), 36.20 MiB | 4.58 MiB/s, done. Resolving deltas: 100% (1024/1024), done. Checking connectivity... done. Traceback (most recent call last): File "setup.py", line 11, in from setuptools import setup ImportError: No module named setuptools Traceback (most recent call last): File "setup.py", line 234, in 'Documentation': 'http://docs.circ.tools' File "/home/cd/miniconda3/lib/python3.6/site-packages/setuptools/init.py", line 129, in setup return distutils.core.setup(**attrs) File "/home/cd/miniconda3/lib/python3.6/distutils/core.py", line 148, in setup dist.run_commands() File "/home/cd/miniconda3/lib/python3.6/distutils/dist.py", line 955, in run_commands self.run_command(cmd) File "/home/cd/miniconda3/lib/python3.6/distutils/dist.py", line 974, in run_command cmd_obj.run() File "setup.py", line 71, in run subprocess.check_call(["bash", "scripts/install_external.sh"]) File "/home/cd/miniconda3/lib/python3.6/subprocess.py", line 291, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '['bash', 'scripts/install_external.sh']' returned non-zero exit status 1.

[tjakobi]

Dear @circR,

it seems like you are using a conda environment which is not (yet) supported by circtools.

Checking connectivity... done.
Traceback (most recent call last):
File "setup.py", line 11, in 
from setuptools import setup
ImportError: No module named setuptools

DCC and FUCHS both need Python2 and an installed setuptools package for this Python version.

pip2 install setuptools

If that command fails due to permission errors you may try

pip2 install setuptools --user

This should install the required package. Afterwards the installation should continue normally.

[circR]

Hi Sir

Thank you very much. It worked for the installation after running the command you suggested. However, when I tried to use the primex mode, it failed again with the following message:

$ circtools primex -d test.candidates -f ../WholeGenomeFasta/genome.fa -g ../WBce235/genes.gtf Start parsing GTF file Start merging GTF file extracting flanking exons for circRNA # 1 marc-4_I_285008285638+ Traceback (most recent call last): File "/home/cd/.local/bin/circtools", line 18, in import circtools File "/home/cd/.local/lib/python3.6/site-packages/circtools/init.py", line 2, in main() File "/home/cd/.local/lib/python3.6/site-packages/circtools/circtools.py", line 31, in main CircTools() File "/home/cd/.local/lib/python3.6/site-packages/circtools/circtools.py", line 76, in init getattr(self, args.command)() File "/home/cd/.local/lib/python3.6/site-packages/circtools/circtools.py", line 329, in primex primex_instance.run_module() File "/home/cd/.local/lib/python3.6/site-packages/circtools/primex/primex.py", line 212, in run_module if current_line[3] == "not_annotated": IndexError: list index out of range

I used one candidate circRNA from DCC results as input. Any suggestions? Thank you.

[tjakobi]

Are you supplying a file name or a directory as -d parameter? -d should specify the path to the CircCoordinates file produced by DCC.

[circR]

Yes, the command is like this: $ circtools primex -d test.candidates -f ../WholeGenomeFasta/genome.fa -g ../WBce235/genes.gtf

The content of "test.candidates" is extracted from the CircCoordinates file from DCC output

Chr Start End Gene JunctionType Strand Start.End.Region OverallRegion I 285008 285638 marc-4 1 + exon-exon transcript,exon,CDS

[tjakobi]

Did you keep the tabs as column separators? circtools expects tab-separated columns in all input and output files.

[circR]

Yes, the file is tab-separated. I used DCC to predict circRNAs in C. elegans. Does this matter? Because in the -o option, it seems only mouse and human are supported.

[tjakobi]

The species shouldn't matter, circtools stumbles over an ill-formatted DCC input file.

Could you please execute the following command:

awk -F '\t' '{print $4}' test.candidates  | head

The -o option only refers to the optional BLASTING step that right now is only supported for human and mouse.

[circR]

[tjakobi]

Could you please run the edited command:

awk -F '\t' '{print $4}' test.candidates | head

[circR]

[tjakobi]

Okay, it seems you have an additional new line at the end of the test.candidates files. Could you remove that empty line and run circtools again?

[circR]

Great, it works!!! Thank you so much for your time and patience. BTW, in the results, it seems that it blasts the primers to the human genome. Is it possible to add C elegans to the blast option?

Thank you again.

[tjakobi]

Circtools employs predefined BLAST databases from the NCBI. If I can locate a specific database for C.elegans I am happy to add it, too.