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Teichlab / tracer

TraCeR - reconstruction of T cell receptor sequences from single-cell RNAseq data
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Running "tracer test -p 1 -c tracer.config" problem with dot #86

Closed solyris closed 5 years ago

solyris commented 5 years ago

Hi,

I am testing the tracer run on the test data and hit the error below which is just after the quantifying by kallisto stage. It seems like my version of dot is not supporting "-T pdf" in particular, may I know which version of Graphviz is supporting that? Or what option can I use to by-pass this without damage to the downstream analysis?

Regards Solyris

Filtering by read count

Format: "pdf" not recognized. Use one of: canon cmap cmapx cmapx_np dot dot_json eps fig gv imap imap_np ismap json json0 mp pic plain plain-ext pov ps ps2 svg svgz tk vml vmlz xdot xdot1.2 xdot1.4 xdot_json Traceback (most recent call last): File "/usr/local/bin/tracer", line 11, in load_entry_point('tracer==0.5', 'console_scripts', 'tracer')() File "/usr/local/lib/python2.7/dist-packages/tracer-0.5-py2.7.egg/tracerlib/launcher.py", line 43, in launch Task().run() File "/usr/local/lib/python2.7/dist-packages/tracer-0.5-py2.7.egg/tracerlib/tasks.py", line 1230, in run loci=['A', 'B'], species='Mmus').run() File "/usr/local/lib/python2.7/dist-packages/tracer-0.5-py2.7.egg/tracerlib/tasks.py", line 1078, in run network_colours) File "/usr/local/lib/python2.7/dist-packages/tracer-0.5-py2.7.egg/tracerlib/tracer_func.py", line 831, in draw_network_from_cells subprocess.check_call(command) File "/usr/lib/python2.7/subprocess.py", line 190, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '['/usr/local/bin/dot', '-Gsplines=true', '-Goverlap=false', '-Gsep=0.4', '-o', '/home/ubuntu/software/tracer-master/test_data/results/filtered_TCRAB_summary/clonotype_network_with_identifiers.pdf', '-T', 'pdf', '/home/ubuntu/software/tracer-master/test_data/results/filtered_TCRAB_summary/clonotype_network_with_identifiers.dot']' returned non-zero exit status 1

mstubb commented 5 years ago

Hi,

Sorry, I don't know which specific graphviz versions support PDF.

You can use tracer test -g svg to get svg output or use any of the other options from the list in the error message. Or use tracer test --no_networks to stop it attempting to draw networks.

Best,

Mike