ERROE:Phred: negative error probability -0.000000
xixi1998815 opened this issue · comments
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.
What version are you using? Are you able to provide a minimal dataset that triggers the error?
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] 1:189250253 22.9% 22m 15s 1h 15m
[2022-05-03 11:51:16] 1:190158036 23.9% 22m 26s 1h 11m
[2022-05-03 11:51:22] Encountered a problem whilst calling 1:177927401-202927401(Phred: negative error probability -0.000000)
[2022-05-03 11:52:52] 1:169811392 24.9% 24m 1s 1h 12m
[2022-05-03 11:53:36] 1:170581687 25.9% 24m 46s 1h 11m
my version:
octopus version 0.7.4 (develop 36017c2)
Target: x86_64 Linux 5.4.0-92-generic
SIMD extension: AVX2
Compiler: GNU 9.4.0
Boost: 1_78
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?
when I add --debug to the command, this result is like that:
[2022-05-19 19:11:17] Removed 174 temporary files
[2022-05-19 19:11:17] - 100% 11m 10s -
[2022-05-19 19:11:17] A program error has occurred:
[2022-05-19 19:11:17]
[2022-05-19 19:11:17] Encountered an exception during calling 'Phred: negative error
[2022-05-19 19:11:17] probability -0.000000'. This means there is a bug and your results
[2022-05-19 19:11:17] are untrustworthy.
[2022-05-19 19:11:17]
[2022-05-19 19:11:17] To help resolve this error run in debug mode and send the log file to
[2022-05-19 19:11:17] https://github.com/luntergroup/octopus/issues.
[2022-05-19 19:11:17] ------------------------------------------------------------------------
Uploading octopus_debug.log.zip…
octopus_debug.log.zip
hello!
This is the debug log.