ERROR: Could not compute forward-backward algorithm!

[MelaniaAbe]

Hello Sabrina,

I was wondering whether you could advise on the following error, I used -g GRCh38_no_alt_analysis_set_GCA_000001405.15.fasta and eCLIP seq target and input bam files (for GRCH38) from encode Project and included -nt 30 -vv
ERROR:

.. 0th iteration
computeEmissionProbs()
computeStatePosteriorsFB()
ERROR: alphas_1[113][0] is -inf
f1 -inf f2 -inf f3 -inf f4 -inf
alphas_1[t-1][0] -248.933 logA[0][k] -0.00612862 this->eProbs[s][i][t][k] -inf
alphas_1[t-1][1] -300.814 logA[1][k] -0.00451315 this->eProbs[s][i][t][k] -inf
alphas_1[t-1][2] -254.545 logA[2][k] -4.87479 this->eProbs[s][i][t][k] -inf
alphas_1[t-1][3] -306.003 logA[3][k] -5.28933 this->eProbs[s][i][t][k] -inf
ERROR: alphas_1[135][0] is -inf
f1 -inf f2 -inf f3 -inf f4 -inf
alphas_1[t-1][0] -472.318 logA[0][k] -0.00612862 this->eProbs[s][i][t][k] -inf
alphas_1[t-1][1] -521.849 logA[1][k] -0.00451315 this->eProbs[s][i][t][k] -inf
alphas_1[t-1][2] -478.063 logA[2][k] -4.87479 this->eProbs[s][i][t][k] -inf
alphas_1[t-1][3] -527.182 logA[3][k] -5.28933 this->eProbs[s][i][t][k] -inf
ERROR: Could not compute forward-backward algorithm!

Any input is appreciated!
Best,
Mel

[tjdrnjsqpf]

I have the same problem.

[skrakau]

Hi Mel,

was the eCLIP data a full dataset, or just a small test dataset? And which command did you use exactly to run PureCLIP?

I am sorry, currently I do not have time to check PureCLIP on your data, but you could send me your log files and I can have a look.

[MelaniaAbe]

Hi Sabrina,

I am not sure what you mean by full dataset? I used sorted bam files (basically I first sorted the bam files from Encode Project webpage). And I used the command as :

pureclip -g hg19.fasta -i sorted.bam -bai Sorted.bai -ibam sortedInput.bam -ibai sorted.bai -o crosslinksites.bed -nt 30 -vv.

BTW, what is the best way to send you the log files, personal email?

Thank you so much!

[skrakau]

Sorry for the late reply. Yes, just drop me an email and I will try to have a look.