diffSplice Error #179
Comments
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Hi,
you have -nan 6, but this options reads a proportion between 0 and 1
It might be that the option is not working and you have cases that are all
nan?
Best
Eduardo
…On Tue, 9 Jan 2024 at 18:17, liuyh99 ***@***.***> wrote:
Hello!
When running diffSplice,I got this error:
Calculating differential analysis between conditions: CCA_TE1 and
CCA_no_TE1 ERROR:__main__:Unknown error: (<class 'ZeroDivisionError'>,
ZeroDivisionError('float division by zero'), <traceback object at
0x7f87b1972880>)
my programe is:
{suppa} diffSplice --method empirical --input {ioe_event} --psi {te_psi}
{unte_psi} --tpm {te_exp} {unte_exp} --area 1000 -nan 6 --lower-bound 0.05
-gc -o {output_prefix}
The files as follow:
{ioe_event}/cat -A CCA.supp25.all.events.ioe |head -10 :
seqname^Igene_id^Ievent_id^Ialternative_transcripts^Itotal_transcripts$
chr10^IENSG00000187134.14^IENSG00000187134.14;A3:chr10:4963528-4965914:4963528-4966010:+^IENST00000380872.9^I93:1203|0ae78ee1-e985-4615-8b90-f56422daa188,ENST00000380872.9$
chr10^IENSG00000134453.16^IENSG00000134453.16;A3:chr10:6105097-6106141:6105097-6106144:+^IENST00000379888.9^IENST00000379888.9,106:1706|bf4ab9d7-5ed6-4ead-a91e-1f6e1e81606a$
chr10^IENSG00000123240.17^IENSG00000123240.17;A3:chr10:13116340-13118888:13116340-13118906:+^I105:3618|896806bc-0beb-494c-a953-7fef7f703bf6,ENST00000378757.6^I90:2460|07cb8d2b-b6d1-423f-bbae-1ed34bc4120c,105:3618|896806bc-0beb-494c-a953-7fef7f703bf6,ENST00000378757.6$
{unte_psi}/cat -A CCA_no_TE1.psi |head -10:
CCA4^ICCA10^ICCA12^ICCA9^ICCA8^ICCA1$
ENSG00000000419.14;A3:chr20:50940955-50942031:50940933-50942031:-^I0.1492537313432836^I0.030612244897959183^I0.012048192771084338^I0.08928571428571433^I0.0^I0.06837606837606837$
ENSG00000000419.14;A5:chr20:50940933-50941105:50940933-50941129:-^I0.018518518518518517^I0.027777777777777776^I0.0^I0.0^I0.05263157894736842^I0.07042253521126761$
ENSG00000000419.14;SE:chr20:50936262-50940865:50940933-50942031:-^I0.8507462686567164^I0.8260869565217391^I0.9111111111111112^I0.8793103448275862^I0.8153846153846154^I0.8582677165354331$
{te_psi}/cat -A CCA_TE1.psi |head -10:
CCA5^ICCA7^ICCA3^ICCA11^ICCA6^ICCA2$
ENSG00000000419.14;A3:chr20:50940955-50942031:50940933-50942031:-^I0.05109489051094891^I0.04819277108433735^I0.109375^I0.05797101449275361^I0
.06521739130434782^I0.1$
ENSG00000000419.14;A5:chr20:50940933-50941105:50940933-50941129:-^I0.040540540540540536^I0.09090909090909093^I0.04166666666666666^I0.08163265
30612245^I0.024999999999999998^I0.14285714285714288$
ENSG00000000419.14;SE:chr20:50936262-50940865:50940933-50942031:-^I0.9027777777777778^I0.831578947368421^I0.9047619047619048^I0.9558823529411
764^I0.86^I0.8181818181818182$
{unte_exp}/cat -A CCA_no_TE1.matrix |head -10:
CCA4^ICCA10^ICCA12^ICCA9^ICCA8^ICCA1$
100:1008|80be9691-a36c-425e-9a41-79c2935fbb4d^I3.4092059213645345^I2.9080364626229036^I4.168162739364187^I7.550650180894003^I4.8592659398500615^I1.9585498113776643$
100:1017|5a3da768-e194-4171-aa2e-c068276e7dd8^I0.0^I0.4154337803747005^I0.0^I0.0^I0.0^I0.5595856603936181$
100:1017|d2f5edcf-e0d3-4d4a-b6ed-136e0c0f5d76^I2.1307537008528343^I3.5311871331849547^I4.168162739364187^I4.474459366455705^I2.5916085012533667^I5.316063773739373$
{te_exp}/cat -A CCA_TE1.matrix |head -10:
CCA5^ICCA7^ICCA3^ICCA11^ICCA6^ICCA2$
100:1008|80be9691-a36c-425e-9a41-79c2935fbb4d^I4.241449833589367^I4.715680316109029^I3.2117433194503664^I4.346638635677064^I3.406021970699541^I1.330438889615703$
100:1017|5a3da768-e194-4171-aa2e-c068276e7dd8^I0.0^I0.5658816379330833^I0.2470571784192589^I0.0^I0.30963836097268554^I0.0$
100:1017|d2f5edcf-e0d3-4d4a-b6ed-136e0c0f5d76^I1.5905436875960124^I3.3952898275985004^I1.4823430705155538^I3.259978976757799^I2.4771068877814844^I3.991316668847108$
I'm sure there is no problem about additional tab at the end of any of the
headers , and I use -nan 6 allow the occurrence of nan values.
Could you give some suggestions?
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Oh! Thank you for pointing out this issue, I changed the parameter to - nan1 to run the program, but unfortunately, I still reported this error: programe: And I do have some events where the PSI calculated in all samples is NaN, could this be the reason for this error?
I removed events that were NaN in all samples (a total of 844 events) and rerun the diffSplice program for psi that did not include all NaN, And reported this error again: Could you give some suggestions? |
|
Oh! Thank you for pointing out this issue, I changed the parameter to - nan1 to run the program, but unfortunately, I still reported this error: programe: And I do have some events where the PSI calculated in all samples is NaN, could this be the reason for this error? I removed events that were NaN in all samples (a total of 844 events) and rerun the diffSplice program for psi that did not include all NaN, And reported this error again: Could you give some suggestions? I'm very sorry for the error in the program uploaded in the previous comment. I changed the parameter to -nan1 to run the program. |
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Hi,
Please try something like -nan 0.6
E.
…On Wed, 10 Jan 2024 at 20:06, liuyh99 ***@***.***> wrote:
Oh! Thank you for pointing out this issue, I changed the parameter to -
nan1 to run the program, but unfortunately, I still reported this error:
Calculating differential analysis between conditions: CCA_TE1 and
CCA_no_TE1 ERROR:*main*:Unknown error: (<class 'ZeroDivisionError'>,
ZeroDivisionError('float division by zero'), <traceback object at
0x7f852941ec00>)
programe:
{suppa} diffSplice --method empirical --input {ioe_event} --psi {te_psi}
{unte_psi} --tpm {te_exp} {unte_exp} --area 1000 -nan 1 --lower-bound 0.05
-gc -o {output_prefix}
And I do have some events where the PSI calculated in all samples is NaN,
could this be the reason for this error?
CCA1 CCA2 CCA3 CCA4 ... CCA10 CCA11 CCA12 CCA13 ENSG00000000003.15;AF:chrX:100635746-100636191:... NaN NaN NaN NaN ... NaN NaN NaN NaN ENSG00000000419.14;A3:chr20:50940955-50942031:5... 0.068376 0.100000 0.109375 0.149254 ... 0.030612 0.057971 0.012048 0.093750 ENSG00000000419.14;A5:chr20:50940933-50941105:5... 0.070423 0.142857 0.041667 0.018519 ... 0.027778 0.081633 0.000000 0.038462
I removed events that were NaN in all samples (a total of 844 events) and
rerun the diffSplice program for psi that did not include all NaN,
still use this program:
{suppa} diffSplice --method empirical --input {ioe_event} --psi {te_psi}
{unte_psi} --tpm {te_exp} {unte_exp} --area 1000 -nan 1 --lower-bound 0.05
-gc -o {output_prefix}
And reported this error again:
Calculating differential analysis between conditions: CCA_TE3 and
CCA_no_TE3 ERROR:*main*:Unknown error: (<class 'ZeroDivisionError'>,
ZeroDivisionError('float division by zero'), <traceback object at
0x7fdf14696200>)
Could you give some suggestions?
If you need my files, I can send them to you by email.
Thank you.
I'm very sorry for the error in the program uploaded in the previous
comment. I changed the parameter to -nan1 to run the program.
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Hi,
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Thanks for trying that.
Another possibility is that the method runs out of events in some range of
the expression values. You could consider varying the --area value
E.
…On Thu, 11 Jan 2024 at 12:45, liuyh99 ***@***.***> wrote:
Hi,
I just tried -nan 0.6, and still got this error
Calculating differential analysis between conditions: CCA_TE3 and
CCA_no_TE3 ERROR:__main__:Unknown error: (<class 'ZeroDivisionError'>,
ZeroDivisionError('float division by zero'), <traceback object at
0x7ffba6ed2640>)
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Hello!
When running
diffSplice,I got this error:Calculating differential analysis between conditions: CCA_TE1 and CCA_no_TE1 ERROR:__main__:Unknown error: (<class 'ZeroDivisionError'>, ZeroDivisionError('float division by zero'), <traceback object at 0x7f87b1972880>)my programe is:
{suppa} diffSplice --method empirical --input {ioe_event} --psi {te_psi} {unte_psi} --tpm {te_exp} {unte_exp} --area 1000 -nan 6 --lower-bound 0.05 -gc -o {output_prefix}The files as follow:
{ioe_event}/cat -A CCA.supp25.all.events.ioe |head -10 :
seqname^Igene_id^Ievent_id^Ialternative_transcripts^Itotal_transcripts$ chr10^IENSG00000187134.14^IENSG00000187134.14;A3:chr10:4963528-4965914:4963528-4966010:+^IENST00000380872.9^I93:1203|0ae78ee1-e985-4615-8b90-f56422daa188,ENST00000380872.9$ chr10^IENSG00000134453.16^IENSG00000134453.16;A3:chr10:6105097-6106141:6105097-6106144:+^IENST00000379888.9^IENST00000379888.9,106:1706|bf4ab9d7-5ed6-4ead-a91e-1f6e1e81606a$ chr10^IENSG00000123240.17^IENSG00000123240.17;A3:chr10:13116340-13118888:13116340-13118906:+^I105:3618|896806bc-0beb-494c-a953-7fef7f703bf6,ENST00000378757.6^I90:2460|07cb8d2b-b6d1-423f-bbae-1ed34bc4120c,105:3618|896806bc-0beb-494c-a953-7fef7f703bf6,ENST00000378757.6${unte_psi}/cat -A CCA_no_TE1.psi |head -10:
CCA4^ICCA10^ICCA12^ICCA9^ICCA8^ICCA1$ ENSG00000000419.14;A3:chr20:50940955-50942031:50940933-50942031:-^I0.1492537313432836^I0.030612244897959183^I0.012048192771084338^I0.08928571428571433^I0.0^I0.06837606837606837$ ENSG00000000419.14;A5:chr20:50940933-50941105:50940933-50941129:-^I0.018518518518518517^I0.027777777777777776^I0.0^I0.0^I0.05263157894736842^I0.07042253521126761$ ENSG00000000419.14;SE:chr20:50936262-50940865:50940933-50942031:-^I0.8507462686567164^I0.8260869565217391^I0.9111111111111112^I0.8793103448275862^I0.8153846153846154^I0.8582677165354331${te_psi}/cat -A CCA_TE1.psi |head -10:
CCA5^ICCA7^ICCA3^ICCA11^ICCA6^ICCA2$ ENSG00000000419.14;A3:chr20:50940955-50942031:50940933-50942031:-^I0.05109489051094891^I0.04819277108433735^I0.109375^I0.05797101449275361^I0 .06521739130434782^I0.1$ ENSG00000000419.14;A5:chr20:50940933-50941105:50940933-50941129:-^I0.040540540540540536^I0.09090909090909093^I0.04166666666666666^I0.08163265 30612245^I0.024999999999999998^I0.14285714285714288$ ENSG00000000419.14;SE:chr20:50936262-50940865:50940933-50942031:-^I0.9027777777777778^I0.831578947368421^I0.9047619047619048^I0.9558823529411 764^I0.86^I0.8181818181818182${unte_exp}/cat -A CCA_no_TE1.matrix |head -10:
CCA4^ICCA10^ICCA12^ICCA9^ICCA8^ICCA1$ 100:1008|80be9691-a36c-425e-9a41-79c2935fbb4d^I3.4092059213645345^I2.9080364626229036^I4.168162739364187^I7.550650180894003^I4.8592659398500615^I1.9585498113776643$ 100:1017|5a3da768-e194-4171-aa2e-c068276e7dd8^I0.0^I0.4154337803747005^I0.0^I0.0^I0.0^I0.5595856603936181$ 100:1017|d2f5edcf-e0d3-4d4a-b6ed-136e0c0f5d76^I2.1307537008528343^I3.5311871331849547^I4.168162739364187^I4.474459366455705^I2.5916085012533667^I5.316063773739373${te_exp}/cat -A CCA_TE1.matrix |head -10:
CCA5^ICCA7^ICCA3^ICCA11^ICCA6^ICCA2$ 100:1008|80be9691-a36c-425e-9a41-79c2935fbb4d^I4.241449833589367^I4.715680316109029^I3.2117433194503664^I4.346638635677064^I3.406021970699541^I1.330438889615703$ 100:1017|5a3da768-e194-4171-aa2e-c068276e7dd8^I0.0^I0.5658816379330833^I0.2470571784192589^I0.0^I0.30963836097268554^I0.0$ 100:1017|d2f5edcf-e0d3-4d4a-b6ed-136e0c0f5d76^I1.5905436875960124^I3.3952898275985004^I1.4823430705155538^I3.259978976757799^I2.4771068877814844^I3.991316668847108$I'm sure there is no problem about additional tab at the end of any of the headers , and I use
-nan 6allow the occurrence of nan values.Could you give some suggestions?
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