Value error ‘g’ not in list

[MichaelSongAGradStudent]

Hello,
I’ve tried with both .bam and .mpileup files but keep getting the following error:

python3.5 Genotype_Likelihoods.py PileupList.txt
Seed is not set.
Default ploidy levels to be tested in analysis are: [1, 2, 3, 4, 5, 6]
112 files found
['FF0395.mpileup', 'FF0397.mpileup', 'FF0399.mpileup', 'FF0401.mpileup', 'FF0402.mpileup', 'FF0403.mpileup', 'FF0404.mpileup', 'FF0405.mpileup', 'FF0406.mpileup', 'FF0407.mpileup', 'FF0408.mpileup', 'FF0409.mpileup', 'FF0410.mpileup', 'FF0411.mpileup', 'FF0412.mpileup', 'FF0413.mpileup', 'FF0414.mpileup', 'FF0415.mpileup', 'FF0416.mpileup', 'FF0417.mpileup', 'FF0418.mpileup', 'FF0419.mpileup', 'FF0420.mpileup', 'FF0421.mpileup', 'FF0422.mpileup', 'FF0423.mpileup', 'FF0424.mpileup', 'FF0425.mpileup', 'FF0426.mpileup', 'FF0427.mpileup', 'FF0428.mpileup', 'FF0429.mpileup', 'FF0430.mpileup', 'FF0431.mpileup', 'FF0432.mpileup', 'FF0433.mpileup', 'FF0434.mpileup', 'FF0435.mpileup', 'FF0436.mpileup', 'FF0437.mpileup', 'FF0438.mpileup', 'FF0439.mpileup', 'FF0440.mpileup', 'FF0441.mpileup', 'FF0442.mpileup', 'FF0443.mpileup', 'FF0444.mpileup', 'FF0445.mpileup', 'FF0446.mpileup', 'FF0447.mpileup', 'FF0448.mpileup', 'FF0449.mpileup', 'FF0450.mpileup', 'FF0451.mpileup', 'FF0452.mpileup', 'FF0453.mpileup', 'FF0454.mpileup', 'FF0455.mpileup', 'FF0456.mpileup', 'FF0457.mpileup', 'FF0458.mpileup', 'FF0459.mpileup', 'FF0460.mpileup', 'FF0461.mpileup', 'FF0462.mpileup', 'FF0463.mpileup', 'FF0464.mpileup', 'FF0465.mpileup', 'FF0466.mpileup', 'FF0467.mpileup', 'FF0468.mpileup', 'FF0469.mpileup', 'FF0470.mpileup', 'FF0471.mpileup', 'FF0472.mpileup', 'FF0473.mpileup', 'FF0474.mpileup', 'FF0475.mpileup', 'FF0476.mpileup', 'FF0477.mpileup', 'FF0478.mpileup', 'FF0479.mpileup', 'FF0480.mpileup', 'FF0481.mpileup', 'FF0482.mpileup', 'FF0483.mpileup', 'FF0484.mpileup', 'FF0485.mpileup', 'FF0486.mpileup', 'FF0487.mpileup', 'FF0488.mpileup', 'FF0489.mpileup', 'FF0490.mpileup', 'FF0491.mpileup', 'FF0492.mpileup', 'FF0493.mpileup', 'FF0494.mpileup', 'FF0495.mpileup', 'FF0496.mpileup', 'FF0497.mpileup', 'FF0498.mpileup', 'FF0499.mpileup', 'FF0500.mpileup', 'FF0501.mpileup', 'FF0502.mpileup', 'FF0503.mpileup', 'FF0504.mpileup', 'FF0505.mpileup', 'FF0506.mpileup', 'FF0507.mpileup', 'FF0508.mpileup', 'FF0509.mpileup']
File type detected: mpileup
Output file is: ./FF0395.genolikes.gz
[0.0]
Traceback (most recent call last):
File "Genotype_Likelihoods.py", line 420, in
nonMajorCount = generics.calcNonMajorCounts(myReads)
File "/mnt/data/micksong/HMMploidy/generics.py", line 43, in calcNonMajorCounts
counts[alleles.index(read.base[i])]+=1
ValueError: 'g' is not in list

Any help would be appreciated.
Thanks!
Michael

[TPPSellinger]

Hello,

Havin the same error over here but :
ValueError: 'a' is not in list

Could it be some format issue in the .bam files ?

[cpouchon]

Hello,

I have exactly the same error when running on bam files:

ValueError: 'g' is not in list.

Cheers,

Charles

[fpichon]

Hello,

I have the same error with BAM files...
Best,

Fabien

EDIT: solved doing this command on my server:

sed -i "s/read.base\\[i\\]/read.base\\[i\\].upper()/g" /HMMploidy/generics.py

[SamueleSoraggi]

I think so far the best solution is from @fpichon if it can work also for others - sorry for never really solving this before, and thanks @fpichon - I have been too much on and off on this repository and drowning in too many projects... I still dream of improving the software and refreshing it with a new and better version and a documentation page...