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TraCeR - reconstruction of T cell receptor sequences from single-cell RNAseq data
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tracer breaks down after kallisto #59

Closed tiagobrc closed 5 years ago

tiagobrc commented 6 years ago

I could not verify the reason for this error. This is the test run of tracer. Just after kallisto, this strange error popped.

##Quantifying with Kallisto##

[quant] fragment length distribution will be estimated from the data
[index] k-mer length: 31
[index] number of targets: 63,852
[index] number of k-mers: 72,966,044
[index] number of equivalence classes: 194,076
[quant] running in paired-end mode
[quant] will process pair 1: /home/tiago/programs/tracer/test_data/cell1_1.fastq
                             /home/tiago/programs/tracer/test_data/cell1_2.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 1,135 reads, 1,044 reads pseudoaligned
[quant] estimated average fragment length: 148.91
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 52 rounds

##Filtering by read count##
Traceback (most recent call last):
  File "/home/tiago/bin/tracer", line 21, in <module>
    launch()
  File "/home/tiago/programs/tracer/tracerlib/launcher.py", line 43, in launch
    Task().run()
  File "/home/tiago/programs/tracer/tracerlib/tasks.py", line 1207, in run
    loci=['A', 'B'], species='Mmus').run()
  File "/home/tiago/programs/tracer/tracerlib/tasks.py", line 1055, in run
    network_colours)
  File "/home/tiago/programs/tracer/tracerlib/tracer_func.py", line 787, in draw_network_from_cells
    cells, False, "box", dot, neato, receptor, loci, network_colours)
  File "/home/tiago/programs/tracer/tracerlib/tracer_func.py", line 743, in make_cell_network_from_dna
    to_remove = [n for n in deg if deg[n] == 0]
  File "/home/tiago/programs/tracer/tracerlib/tracer_func.py", line 743, in <listcomp>
    to_remove = [n for n in deg if deg[n] == 0]
  File "/home/tiago/anaconda3/lib/python3.6/site-packages/networkx/classes/reportviews.py", line 502, in __getitem__
    nbrs = self._succ[n]
KeyError: (<tracerlib.core.Cell object at 0x7f955250c470>, 0)

Do you have any thoughts about this?

idalind commented 6 years ago

Hi, Exactly which command did you run, and what was your memory limit?

mstubb commented 6 years ago

Hi @tiagobrc, have you managed to resolve this?

We're happy to help if you can let us know some more details.

Thanks!

Mike

cramirezs commented 6 years ago

Hello,

I have what I think is the same error. It appears after running the summarise step. Could you help me with this?

tracer summarise results/ -s Hsap --config /mnt/BioHome/ciro/bin/tracer-master/tracer.conf -i

My memory limit in the cluster.json file is 10GB. The full error is:

/mnt/BioHome/ciro/bin/miniconda3/lib/python3.6/site-packages/matplotlib/axes/_axes.py:6462: UserWarning: The 'normed' kwarg is deprecated, and has been replaced by the 'density' kwarg.
  warnings.warn("The 'normed' kwarg is deprecated, and has been "
/mnt/BioHome/ciro/bin/miniconda3/lib/python3.6/site-packages/matplotlib/axes/_axes.py:6462: UserWarning: The 'normed' kwarg is deprecated, and has been replaced by the 'density' kwarg.
  warnings.warn("The 'normed' kwarg is deprecated, and has been "
Traceback (most recent call last):
  File "/mnt/BioHome/ciro/bin/tracer-master/tracer", line 21, in <module>
    launch()
  File "/mnt/BioHome/ciro/bin/tracer-master/tracerlib/launcher.py", line 43, in launch
    Task().run()
  File "/mnt/BioHome/ciro/bin/tracer-master/tracerlib/tasks.py", line 1009, in run
    network_colours)
  File "/mnt/BioHome/ciro/bin/tracer-master/tracerlib/tracer_func.py", line 783, in draw_network_from_cells
    cells, False, "box", dot, neato, receptor, loci, network_colours)
  File "/mnt/BioHome/ciro/bin/tracer-master/tracerlib/tracer_func.py", line 739, in make_cell_network_from_dna
    to_remove = [n for n in deg if deg[n] == 0]
  File "/mnt/BioHome/ciro/bin/tracer-master/tracerlib/tracer_func.py", line 739, in <listcomp>
    to_remove = [n for n in deg if deg[n] == 0]
  File "/mnt/BioHome/ciro/bin/miniconda3/lib/python3.6/site-packages/networkx/classes/reportviews.py", line 507, in __getitem__
    nbrs = self._succ[n]
KeyError: (<tracerlib.core.Cell object at 0x7f917a5af160>, 4)

Thank you very much, Ciro

tiagobrc commented 5 years ago

Hi @tiagobrc, have you managed to resolve this?

We're happy to help if you can let us know some more details.

Thanks!

Mike

Hi! I am so sorry for the late follow-up. I will be testing this again soon and report here.

lchong commented 5 years ago

I'm having the same issue when running the test from within the tracer directory (./tracer test --config_file tracer.conf).

At the stage of filtering by read counts:

##Filtering by read count##
/projects/clc/usr/anaconda/5.1.0/lib/python3.6/site-packages/matplotlib/axes/_axes.py:6462: UserWarning: The 'normed' kwarg is deprecated, and has been replaced by the 'density' kwarg.
  warnings.warn("The 'normed' kwarg is deprecated, and has been "
Traceback (most recent call last):
  File "./tracer", line 21, in <module>
    launch()
  File "/projects/clc/usr/tracer/tracer-0.6.0/tracerlib/launcher.py", line 43, in launch
    Task().run()
  File "/projects/clc/usr/tracer/tracer-0.6.0/tracerlib/tasks.py", line 1212, in run
    loci=['A', 'B'], species='Mmus').run()
  File "/projects/clc/usr/tracer/tracer-0.6.0/tracerlib/tasks.py", line 1060, in run
    network_colours)
  File "/projects/clc/usr/tracer/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 "/projects/clc/usr/tracer/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 "/projects/clc/usr/tracer/tracer-0.6.0/tracerlib/tracer_func.py", line 753, in <listcomp>
    to_remove = [n for n in deg if deg[n] == 0]
  File "/projects/clc/usr/anaconda/5.1.0/lib/python3.6/site-packages/networkx/classes/reportviews.py", line 507, in __getitem__
    nbrs = self._succ[n]
KeyError: (<tracerlib.core.Cell object at 0x7f41b1a09a58>, 2)

My config file specifies the location of the tools (all installed with anaconda) and the references, I haven't altered anything else. I'm running the test on centos6. Let me know what other details I can provide.

mstubb commented 5 years ago

Hi,

Can you try this with the latest version from the master branch of the repo. It looks like you're using release 0.6.0 but it's possible we've altered something in the meantime.

Also, which version of the NetworkX package are you using?

Best,

Mike

lchong commented 5 years ago

Hi Mike,

I tried with the most recent version and get the same error. I'm using version 2.1 of NetworkX:

[lchong@n104 current]$ python
Python 3.6.3 |Anaconda custom (64-bit)| (default, Nov  9 2017, 00:19:18)
[GCC 7.2.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import networkx
>>> networkx.__version__
'2.1'
mstubb commented 5 years ago

Please can you try with NetworkX v1.11?

v2 made some breaking changes so we specify v1.11 in https://github.com/Teichlab/tracer/blob/master/requirements.txt

Let me know if that helps.

Mike

On 8 Nov 2018, at 00:23, Lauren Chong notifications@github.com wrote:

Hi Mike,

I tried with the most recent version and get the same error. I'm using version 2.1 of NetworkX:

[lchong@n104 current]$ python Python 3.6.3 |Anaconda custom (64-bit)| (default, Nov 9 2017, 00:19:18) [GCC 7.2.0] on linux Type "help", "copyright", "credits" or "license" for more information.

import networkx networkx.version '2.1' — You are receiving this because you commented. Reply to this email directly, view it on GitHub, or mute the thread.

lchong commented 5 years ago

Hi Mike,

That seems to have done the trick, I'm able to generate the test data results now.

Thank you!

mstubb commented 5 years ago

Great!