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Teichlab / tracer

TraCeR - reconstruction of T cell receptor sequences from single-cell RNAseq data
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tracer 0.6 test fails in summarise stage: #84

Closed hkoohy closed 5 years ago

hkoohy commented 5 years ago

Hi Mike, I have installed tracer 0.6 in an virenv and have been trying to get it run. But the test function fails at summarise stage. The following is the error that i didnt find it very informative. I have additionally tested with a few in-house cells, it again fails at the summarise stage. In the filtered_TCRAB_summary directory, I see recombinants.txt, reconstructed lengths (both pdf and txt) and TCR_summary files but nothing more whereas I was expecting to see some information about clones and clonotypes. The command I have been using is :: python tracer test -p 2 -c $HOME/tracer_v6/tracer-0.6.0/tracer.conf --no_networks or python tracer summarise ${out_dir} -c $HOME/tracer_v6/tracer-0.6.0/tracer.conf -s Hsap --no_networks

I appreciate if you could please point us what we do wrong.

here is the error I get:

Filtering by read count

Traceback (most recent call last): File "tracer", line 21, in launch() File "/t1-home/molimm2/haskoohy/tracer_v6/tracer-0.6.0/tracerlib/launcher.py", line 43, in launch Task().run() File "/t1-home/molimm2/haskoohy/tracer_v6/tracer-0.6.0/tracerlib/tasks.py", line 1212, in run loci=['A', 'B'], species='Mmus').run() File "/t1-home/molimm2/haskoohy/tracer_v6/tracer-0.6.0/tracerlib/tasks.py", line 1060, in run network_colours) File "/t1-home/molimm2/haskoohy/tracer_v6/tracer-0.6.0/tracerlib/tracer_func.py", line 797, in draw_network_from_cells cells, False, "box", dot, neato, receptor, loci, network_colours) File "/t1-home/molimm2/haskoohy/tracer_v6/tracer-0.6.0/tracerlib/tracer_func.py", line 753, in make_cell_network_from_dna to_remove = [n for n in deg if deg[n] == 0] File "/t1-home/molimm2/haskoohy/tracer_v6/tracer-0.6.0/tracerlib/tracer_func.py", line 753, in to_remove = [n for n in deg if deg[n] == 0] File "/t1-home/molimm2/haskoohy/tracer_env/lib/python3.6/site-packages/networkx/classes/reportviews.py", line 507, in getitem nbrs = self._succ[n] KeyError: (<tracerlib.core.Cell object at 0x7f4250c73c88>, 2)

mstubb commented 5 years ago

Hi Hashem,

What version of Networkx do you have installed? Tracer doesn't work with v2 so you'll need v1.11 and I think that's what's causing this problem.

Probably also best to download the latest version from the Master branch than use v0.6 just in case that helps.

Let me know if that doesn't fix it.

Cheers,

Mike

On 1 Feb 2019, at 10:12, hkoohy notifications@github.com wrote:

Hi Mike, I have installed tracer 0.6 in an virenv and have been trying to get it run. But the test function fails at summarise stage. The following is the error that i didnt find it very informative. I have additionally tested with a few in-house cells, it again fails at the summarise stage. In the filtered_TCRAB_summary directory, I see recombinants.txt, reconstructed lengths (both pdf and txt) and TCR_summary files but nothing more whereas I was expecting to see some information about clones and clonotypes. The command I have been using is :: python tracer test -p 2 -c $HOME/tracer_v6/tracer-0.6.0/tracer.conf --no_networks or python tracer summarise ${out_dir} -c $HOME/tracer_v6/tracer-0.6.0/tracer.conf -s Hsap --no_networks

I appreciate if you could please point us what we do wrong.

here is the error I get:

Filtering by read count

Traceback (most recent call last): File "tracer", line 21, in launch() File "/t1-home/molimm2/haskoohy/tracer_v6/tracer-0.6.0/tracerlib/launcher.py", line 43, in launch Task().run() File "/t1-home/molimm2/haskoohy/tracer_v6/tracer-0.6.0/tracerlib/tasks.py", line 1212, in run loci=['A', 'B'], species='Mmus').run() File "/t1-home/molimm2/haskoohy/tracer_v6/tracer-0.6.0/tracerlib/tasks.py", line 1060, in run network_colours) File "/t1-home/molimm2/haskoohy/tracer_v6/tracer-0.6.0/tracerlib/tracer_func.py", line 797, in draw_network_from_cells cells, False, "box", dot, neato, receptor, loci, network_colours) File "/t1-home/molimm2/haskoohy/tracer_v6/tracer-0.6.0/tracerlib/tracer_func.py", line 753, in make_cell_network_from_dna to_remove = [n for n in deg if deg[n] == 0] File "/t1-home/molimm2/haskoohy/tracer_v6/tracer-0.6.0/tracerlib/tracer_func.py", line 753, in to_remove = [n for n in deg if deg[n] == 0] File "/t1-home/molimm2/haskoohy/tracer_env/lib/python3.6/site-packages/networkx/classes/reportviews.py", line 507, in getitem nbrs = self._succ[n] KeyError: (<tracerlib.core.Cell object at 0x7f4250c73c88>, 2)

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hkoohy commented 5 years ago

thanks Mike for very quick response. You suggestion makes perfect sense as I don't think my current Networkx is v1.11. Also thank your for suggesting which version to use. Will give it ago. Cheers Hashem

hkoohy commented 5 years ago

Hi Mike, I can confirm that the problem is solved in case you want to close this issue. Once again thank you so much for your quick support.

mstubb commented 5 years ago

Great! Glad it's working.