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diffSplice Error

Open liuyh99 opened this issue 1 year ago • 6 comments

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?

liuyh99 avatar Jan 09 '24 07:01 liuyh99

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?

— Reply to this email directly, view it on GitHub https://github.com/comprna/SUPPA/issues/179, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADCZKB6OLQKEWA6WJSQ3HQLYNTVHNAVCNFSM6AAAAABBSTZFNGVHI2DSMVQWIX3LMV43ASLTON2WKOZSGA3TCNZWHA3TCOI . You are receiving this because you are subscribed to this thread.Message ID: @.***>

EduEyras avatar Jan 09 '24 12:01 EduEyras

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? — Reply to this email directly, view it on GitHub <#179>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADCZKB6OLQKEWA6WJSQ3HQLYNTVHNAVCNFSM6AAAAABBSTZFNGVHI2DSMVQWIX3LMV43ASLTON2WKOZSGA3TCNZWHA3TCOI . You are receiving this because you are subscribed to this thread.Message ID: @.>

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 6 --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 6 --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.

liuyh99 avatar Jan 10 '24 09:01 liuyh99

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.

liuyh99 avatar Jan 10 '24 09:01 liuyh99

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.

— Reply to this email directly, view it on GitHub https://github.com/comprna/SUPPA/issues/179#issuecomment-1884446055, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADCZKB7DZ6TRJT4OI5YCDU3YNZKXXAVCNFSM6AAAAABBSTZFNGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQOBUGQ2DMMBVGU . You are receiving this because you commented.Message ID: @.***>

EduEyras avatar Jan 10 '24 10:01 EduEyras

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>)

liuyh99 avatar Jan 11 '24 01:01 liuyh99

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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EduEyras avatar Jan 11 '24 04:01 EduEyras