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