FileNotFoundError: [Errno 2] No such file or directory: 'circos'

[ericgonzalezs]

Hi,

I created a python virtual environment with python3.11, and I installed
biopython
circos
pandas
numpy
With pip install.

I am running the program like this:

p2c.py H1_MojtabaGaps.paf ANN1372_H1_H2_hap1.reviewed.chr_assembled.fasta VIGUIERA_H1_H2.reviewed.chr_assembled.fasta VIGUIERA_H1_H2.reviewed.chr_assembled.fasta.bed PLOT_RESULTS

I am having the next error.

Query: /lustre07/scratch/egonza02/ASSEMBLIES/SCAFFOLDING/CPU_MODE/MAKE_FASTAS/SECOND_TRY/VIGUIERA_G_AFTER_REVIEW/VISUALIZE/ANN1372_H1_H2_hap1.reviewed.chr_assembled.fasta
Reference: /lustre07/scratch/egonza02/ASSEMBLIES/SCAFFOLDING/CPU_MODE/MAKE_FASTAS/SECOND_TRY/VIGUIERA_G_AFTER_REVIEW/VISUALIZE/VIGUIERA_H1_H2.reviewed.chr_assembled.fasta
Targets: /lustre07/scratch/egonza02/ASSEMBLIES/SCAFFOLDING/CPU_MODE/MAKE_FASTAS/SECOND_TRY/VIGUIERA_G_AFTER_REVIEW/VISUALIZE/VIGUIERA_H1_H2.reviewed.chr_assembled.fasta.bed
PAF: /lustre07/scratch/egonza02/ASSEMBLIES/SCAFFOLDING/CPU_MODE/MAKE_FASTAS/SECOND_TRY/VIGUIERA_G_AFTER_REVIEW/VISUALIZE/H1_MojtabaGaps.paf
Outdir: /lustre07/scratch/egonza02/ASSEMBLIES/SCAFFOLDING/CPU_MODE/MAKE_FASTAS/SECOND_TRY/VIGUIERA_G_AFTER_REVIEW/VISUALIZE/PLOT_RESULTS
Templates: /lustre07/scratch/egonza02/SOFTWARE/CircosAlignmentPlotter/CircosAlignmentPlotter/templates
Copying files...
Building karyotype.txt...
Building links.txt...
Building highlights.txt...
Adding samtools formatted coverage...
Adding circos formatted coverage...
Running circos in /lustre07/scratch/egonza02/ASSEMBLIES/SCAFFOLDING/CPU_MODE/MAKE_FASTAS/SECOND_TRY/VIGUIERA_G_AFTER_REVIEW/VISUALIZE/PLOT_RESULTS
Traceback (most recent call last):
File "/home/egonza02/scratch/SOFTWARE/CircosAlignmentPlotter/CircosAlignmentPlotter/p2c.py", line 473, in
main()
File "/home/egonza02/scratch/SOFTWARE/CircosAlignmentPlotter/CircosAlignmentPlotter/p2c.py", line 470, in main
plotPAF(dAlns, iFH.outdir, iFH.templates, iFH.query, iFH.reference, correspondance, min_len, contigs_lengths, targets_to_plot, bed=iFH.bed, scov=iFH.scov, ccov=iFH.ccov, snps=iFH.snps)
File "/home/egonza02/scratch/SOFTWARE/CircosAlignmentPlotter/CircosAlignmentPlotter/p2c.py", line 410, in plotPAF
run(cmd)
File "/home/egonza02/scratch/SOFTWARE/CircosAlignmentPlotter/CircosAlignmentPlotter/p2c.py", line 415, in run
proc = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/python/3.11.2/lib/python3.11/subprocess.py", line 1024, in init
self._execute_child(args, executable, preexec_fn, close_fds,
File "/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/python/3.11.2/lib/python3.11/subprocess.py", line 1901, in _execute_child
raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'circos'

Do you know how I could solve this error?

Thanks,

Eric

[AntoineHo]

Hello,

Given the error message, I think it comes from a problem of either circos or from the python subprocess package that calls to circos.

Because this is the last step of the pipeline, you can try to run it manually by going into this directory: cd /lustre07/scratch/egonza02/ASSEMBLIES/SCAFFOLDING/CPU_MODE/MAKE_FASTAS/SECOND_TRY/VIGUIERA_G_AFTER_REVIEW/VISUALIZE/PLOT_RESULTS and just running circos, it should find the config file in the directory. (If this fails because the config file was not specified, you can also try with circos -c circos.conf).

If you still get an error, then it could be that circos is not installed in the environment or a problem with "subprocess", maybe installing another version of python (I just tried the pipeline with python 3.11.4 and it worked fine).

Best,

Antoine