Closed zhouxinseeu closed 3 years ago
I think you're giving summarize
an input directory that doesn't contain tracer output directories for multiple cells.
The input directory should contain all of the individual cell output directories that you made using assemble
.
For example, if /SGRNJ01/RD_dir/pipeline_test/zhouyiqi/users/zhouxin/test/newvdj_test/MusTCR1_12/
is the assemble
output for a single cell then you might want to use /SGRNJ01/RD_dir/pipeline_test/zhouyiqi/users/zhouxin/test/newvdj_test/
as the input directory for summarize
.
Hope that helps. Let me know if now.
Mike
Thank you! I have tried but it does not work:
$ /SGRNJ/Public/Software/tracer/tracer summarize -c /SGRNJ01/RD_dir/pipeline_test/zhouyiqi/unittest/tcr_fl/20201103/tracer_SGR.conf /SGRNJ01/RD_dir/pipeline_test/zhouyiqi/users/zhouxin/test/newvdj_test
Traceback (most recent call last):
File "/SGRNJ/Public/Software/tracer/tracer", line 21, in
Hi! I have another question. Should I perform split before I start assemble? Will it affect the final results? Thank you!
Please could you send me the command that you used to run assemble
.
Please could you send me the output of running ls /SGRNJ01/RD_dir/pipeline_test/zhouyiqi/users/zhouxin/test/newvdj_test/
What do you mean by "perform split"?
Thanks,
Mike
run assemble : python ./assemble.py --outdir .//MusTCR1_12/01.assemble --sample MusTCR1_12 --demultiplex_dir .//MusTCR1_12/00.demultiplex --index AACGTGAT,AAACATCG,ATGCCTAA,AGTGGTCA,ACCACTGT,ACATTGGC,CAGATCTG,CATCAAGT --species Mmus --type TCR --software tracer The index was split by ',' and each index represents one cell.
I have tried to use tracer directly, and the results are the same as above: /SGRNJ/Public/Software/tracer/tracer assemble MusTCR1_5/00.demultiplex/AAACATCG/AAACATCG_1.fq.gz MusTCR1_5/00.demultiplex/AAACATCG/AAACATCG_2.fq.gz AAACATCG ./ -c /SGRNJ01/RD_dir/pipeline_test/zhouyiqi/unittest/tcr_fl/20201103/tracer_SGR.conf -s Mmus -p 6
output: $ ls assemble.py log MusTCR1_5.sh.e314126 pycache test_vdj.py data_give MusTCR1_12 MusTCR1_5.sh.o314126 run.sh demultiplex.py MusTCR1_12.sh.e277750 MusTCR1_8 run.sh.e277616 filtered_TCRAB_summary MusTCR1_12.sh.o277750 MusTCR1_8.sh.e318300 run.sh.o277616 init.py MusTCR1_5 MusTCR1_8.sh.o318300 shell
MusTCR* are output directories: $ ls MusTCR1_5 00.demultiplex 01.assemble
$ ls MusTCR1_5/00.demultiplex/ AAACATCG ACATTGGC AGTGGTCA CAGATCTG MusTCR1_5_invalid_index.tsv stat.txt AACGTGAT ACCACTGT ATGCCTAA CATCAAGT MusTCR1_5_invalid_linker.tsv
$ ls MusTCR1_5/01.assemble/ AAACATCG AACGTGAT ACATTGGC ACCACTGT AGTGGTCA ATGCCTAA CAGATCTG CATCAAGT
$ ls MusTCR1_5/01.assemble/AAACATCG/ aligned_reads expression_quantification filtered_TCR_seqs IgBLAST_output Trinity_output unfiltered_TCR_seqs
Split means multiplexing, classifying cells by barcode(index). I use index as cell name, and when I performed assemble, the alignment rate after multiplexing are very low(~25%) in paired-end mod. Log shows that this pipeline can successfully complete without error, but there are no successful assemble results in the output.
Thank you,
Zhou Xin
------------------ Original ------------------ From: "Mike Stubbington"<notifications@github.com>; Date: Thu, Dec 10, 2020 06:35 PM To: "Teichlab/tracer"<tracer@noreply.github.com>; Cc: "zhouxinseeu"<zhouxin@singleronbio.com>; "Author"<author@noreply.github.com>; Subject: Re: [Teichlab/tracer] a ZeroDivisionError (#108)
Please could you send me the command that you used to run assemble.
Please could you send me the output of running ls /SGRNJ01/RD_dir/pipeline_test/zhouyiqi/users/zhouxin/test/newvdj_test/
What do you mean by "perform split"?
Thanks,
Mike
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Have you run summarise
with MusTCR1_5/01.assemble/
as the input directory? From your ls
outputs above, that looks like the one that contains the individual tracer output directories for each cell.
Regarding demultiplexing, tracer expects to run on input fastq files from a single cell. So, yes, you must demultiplex your reads before passing them to tracer.
Best,
Mike
Hi! I have tried the command below, and it still failed. Will tracer got an error when the successful assemble results are NONE?
$ /SGRNJ/Public/Software/tracer/tracer summarize MusTCR1_5/01.assemble/ -c /SGRNJ01/RD_dir/pipeline_test/zhouyiqi/unittest/tcr_fl/20201103/tracer_SGR.conf -p 6
/SGRNJ/Public/Software/conda_env/celescope_tracer/lib/python3.7/site-packages/seaborn/distributions.py:2551: FutureWarning: distplot
is a deprecated function and will be removed in a future version. Please adapt your code to use either displot
(a figure-level function with similar flexibility) or histplot
(an axes-level function for histograms).
warnings.warn(msg, FutureWarning)
/SGRNJ/Public/Software/conda_env/celescope_tracer/lib/python3.7/site-packages/seaborn/distributions.py:2551: FutureWarning: distplot
is a deprecated function and will be removed in a future version. Please adapt your code to use either displot
(a figure-level function with similar flexibility) or histplot
(an axes-level function for histograms).
warnings.warn(msg, FutureWarning)
Traceback (most recent call last):
File "/SGRNJ/Public/Software/tracer/tracer", line 21, in <module>
launch()
File "/SGRNJ01/Public/Software/tracer/tracerlib/launcher.py", line 43, in launch
Task().run()
File "/SGRNJ01/Public/Software/tracer/tracerlib/tasks.py", line 1078, in run
network_colours)
File "/SGRNJ01/Public/Software/tracer/tracerlib/tracer_func.py", line 817, in draw_network_from_cells
cells, False, "box", dot, neato, receptor, loci, network_colours)
File "/SGRNJ01/Public/Software/tracer/tracerlib/tracer_func.py", line 773, in make_cell_network_from_dna
to_remove = [n for n in deg if deg[n] == 0]
File "/SGRNJ01/Public/Software/tracer/tracerlib/tracer_func.py", line 773, in <listcomp>
to_remove = [n for n in deg if deg[n] == 0]
File "/Personal/zhouxin/.local/lib/python3.7/site-packages/networkx/classes/reportviews.py", line 502, in getitem
nbrs = self._succ[n]
KeyError: (<tracerlib.core.Cell object at 0x7fe1b5cfbf28>, 0)
Thank you! Zhou Xin ------------------ Original ------------------ From: "Mike Stubbington"<notifications@github.com>; Date: Fri, Dec 11, 2020 09:22 PM To: "Teichlab/tracer"<tracer@noreply.github.com>; Cc: "zhouxinseeu"<zhouxin@singleronbio.com>; "Author"<author@noreply.github.com>; Subject: Re: [Teichlab/tracer] a ZeroDivisionError (#108)
Have you run summarise with MusTCR1_5/01.assemble/ as the input directory? From your ls outputs above, that looks like the one that contains the individual tracer output directories for each cell.
Regarding demultiplexing, tracer expects to run on input fastq files from a single cell. So, yes, you must demultiplex your reads before passing them to tracer.
Best,
Mike
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This looks like a new error (which is good because it means that other things are now working)
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.
If you currently have v2.x of Networkx please try replacing it with v1.11 and re-run the summarise
command.
Best,
Mike
Hi! I used networkx==1.11 and the problem finally solved, thank you!
Best Zhou Xin ------------------ Original ------------------ From: "Mike Stubbington"<notifications@github.com>; Date: Mon, Dec 14, 2020 05:55 PM To: "Teichlab/tracer"<tracer@noreply.github.com>; Cc: "zhouxinseeu"<zhouxin@singleronbio.com>; "Author"<author@noreply.github.com>; Subject: Re: [Teichlab/tracer] a ZeroDivisionError (#108)
This looks like a new error (which is good because it means that other things are now working)
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.
If you currently have v2.x of Networkx please try replacing it with v1.11 and re-run the summarise command.
Best,
Mike
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Great! Glad you got it working.
Hi! I get an error when I run tracer summarize.
command: /SGRNJ/Public/Software/tracer/tracer summarize -c /SGRNJ01/RD_dir/pipeline_test/zhouyiqi/unittest/tcr_fl/20201103/tracer_SGR.conf /SGRNJ01/RD_dir/pipeline_test/zhouyiqi/users/zhouxin/test/newvdj_test/MusTCR1_12/
output: Traceback (most recent call last): File "/SGRNJ/Public/Software/tracer/tracer", line 21, in
launch()
File "/SGRNJ01/Public/Software/tracer/tracerlib/launcher.py", line 43, in launch
Task().run()
File "/SGRNJ01/Public/Software/tracer/tracerlib/tasks.py", line 800, in run
pc = round((count / float(total_cells)) * 100, 1)
ZeroDivisionError: float division by zero
tracer assemble were performed successfully. So I am not sure what's wrong with my pipe. Thank you.