ERROE:Phred: negative error probability -0.000000

[xixi1998815]

Hi! When I run the program using the following command：

octopus -R /home/cluster/Storage3/LB_NA/hs37d5/hs37d5.fasta
-I /home/cluster/Storage3/LB_NA/preprocess/normal.bqsr_realigned.bam /home/cluster/Storage3/LB_NA/preprocess/tumor.bqsr_realigned.bam
-N normal --somatics-only --forest $forest --threads 32 -o /home/cluster/Users/lxy/octopus.vcf

I met a problem.There is an error : Encountered a problem whilst calling 1:186276622-192997240(Phred: negative error probability -0.000000) The process stop. How can I deal with this problem.

[dancooke]

What version are you using? Are you able to provide a minimal dataset that triggers the error?

[xixi1998815]

hello!My version is octopus v0.7.4, and you can download the dataset using the following address:

https://drive.google.com/file/d/16MHCisjOIqAu9IUMcGVjA240Jrqr3BNy/view?usp=sharing

the command is :

forest="/home/cluster/Users/lxy/octopus/resources/forests/somatic.v0.7.4.forest.gz" octopus
-R /home/cluster/Storage3/LB_NA/hs37d5/hs37d5.fasta
-I /home/cluster/Storage3/LB_NA/preprocess/normal.sample.bam /home/cluster/Storage3/LB_NA/preprocess/tumor.sample.bam
-t /home/cluster/Users/lxy/octopus/region.bed
-N normal
--somatics-only
--forest $forest
--threads 4
-o /home/cluster/Users/lxy/octopus.vcf

the region.bed is: 1 156276622 299997240

the error is: [2022-05-03 11:51:05] <INFO> 1:189250253 22.9% 22m 15s 1h 15m [2022-05-03 11:51:16] <INFO> 1:190158036 23.9% 22m 26s 1h 11m [2022-05-03 11:51:22] <EROR> Encountered a problem whilst calling 1:177927401-202927401(Phred: negative error probability -0.000000) [2022-05-03 11:52:52] <INFO> 1:169811392 24.9% 24m 1s 1h 12m [2022-05-03 11:53:36] <INFO> 1:170581687 25.9% 24m 46s 1h 11m

[xixi1998815]

my version: octopus version 0.7.4 (develop 36017c2d) Target: x86_64 Linux 5.4.0-92-generic SIMD extension: AVX2 Compiler: GNU 9.4.0 Boost: 1_78

[dancooke]

Thanks for the test data but I cannot reproduce with your command line, please can you confirm that you can reproduce on the data you provided? If so, please could you add --debug to your command and send the resulting log file?

[xixi1998815]

when I add --debug to the command, this result is like that: [2022-05-19 19:11:17] <INFO> Removed 174 temporary files [2022-05-19 19:11:17] <INFO> - 100% 11m 10s - [2022-05-19 19:11:17] <EROR> A program error has occurred: [2022-05-19 19:11:17] <EROR> [2022-05-19 19:11:17] <EROR> Encountered an exception during calling 'Phred: negative error [2022-05-19 19:11:17] <EROR> probability -0.000000'. This means there is a bug and your results [2022-05-19 19:11:17] <EROR> are untrustworthy. [2022-05-19 19:11:17] <EROR> [2022-05-19 19:11:17] <EROR> To help resolve this error run in debug mode and send the log file to [2022-05-19 19:11:17] <EROR> https://github.com/luntergroup/octopus/issues. [2022-05-19 19:11:17] <INFO> ------------------------------------------------------------------------ Uploading octopus_debug.log.zip…

[xixi1998815]

octopus_debug.log.zip hello! This is the debug log.