ZeroDivisionError in rMATS v4.0.02

[Shashank Sathe]

Hi,

I recently ran a test set through rMATS v4.0.02 and I am getting the following error:

"""

Running the statistical part.

Traceback (most recent call last):

  File "/projects/ps-yeolab3/shsathe/software/rMATSv4.0.2/rMATS.4.0.2/rMATS-turbo-Linux-UCS4/rMATS_P/inclusion_level.py", line 50, in <module>

    psi2=vec2psi(inc2,skp2,effective_inclusion_length,effective_skipping_length);

  File "/projects/ps-yeolab3/shsathe/software/rMATSv4.0.2/rMATS.4.0.2/rMATS-turbo-Linux-UCS4/rMATS_P/inclusion_level.py", line 30, in vec2psi

    psi.append(str(round(float(inc[i])/inclusion_length/(float(inc[i])/inclusion_length+float(skp[i])/skipping_length),3)));

ZeroDivisionError: float division by zero

Traceback (most recent call last):

  File "/projects/ps-yeolab3/shsathe/software/rMATSv4.0.2/rMATS.4.0.2/rMATS-turbo-Linux-UCS4/rMATS_P/inclusion_level.py", line 49, in <module>

    psi1=vec2psi(inc1,skp1,effective_inclusion_length,effective_skipping_length);

  File "/projects/ps-yeolab3/shsathe/software/rMATSv4.0.2/rMATS.4.0.2/rMATS-turbo-Linux-UCS4/rMATS_P/inclusion_level.py", line 30, in vec2psi

    psi.append(str(round(float(inc[i])/inclusion_length/(float(inc[i])/inclusion_length+float(skp[i])/skipping_length),3)));

ZeroDivisionError: float division by zero

Traceback (most recent call last):

  File "/projects/ps-yeolab3/shsathe/software/rMATSv4.0.2/rMATS.4.0.2/rMATS-turbo-Linux-UCS4/rMATS_P/inclusion_level.py", line 50, in <module>

    psi2=vec2psi(inc2,skp2,effective_inclusion_length,effective_skipping_length);

  File "/projects/ps-yeolab3/shsathe/software/rMATSv4.0.2/rMATS.4.0.2/rMATS-turbo-Linux-UCS4/rMATS_P/inclusion_level.py", line 30, in vec2psi

    psi.append(str(round(float(inc[i])/inclusion_length/(float(inc[i])/inclusion_length+float(skp[i])/skipping_length),3)));

ZeroDivisionError: float division by zero

The statistical part is done.

"""

Also, no FDR values are generated for the 'JCEC.txt' results. For some events, no IncLevelDifference values are generated. The JC.txt events seem to work fine.

Has this error been encountered before ?

Thank you,

Shashank

[jthom...@gmail.com]

I have also been getting this error! I've tried both ensembl and Gencode gtf files and have confirmed read lengths are all equal.

My command is:

rmats.py \

    --b1 $RMATS/b1.${COMPARISON}.txt \

    --b2 $RMATS/b2.${COMPARISON}.txt \

    --gtf $SUPPORT_FILES/annotations/$ASSEMBLY/ensembl.filtered.gtf \

    --od $RMATS/$COMPARISON \

    -t paired \

    --cstat 0.0001 \

    --nthread 8

[iti....@igib.in]

I am also getting the same error.. did you find the solution for same?

[Shihao Shen]

The issue is caused by zero read counts in both inclusion and skipping junction. No naive psi estimate and FDR will be output in this case. Can you post your JCEC.raw.input.SE.txt and JC.raw.input.SE.txt?

Thanks,

Shihao