sage error mRefContext

[alhafidzhamdan]

Hi HMF team,

I'm running sage in an LSF cluster. I keep getting this mRefContext is NULL error at the processALTRead stage. Screenshots:

In between these lines, there were endless lines of these:

My commands are:

Using threads = 32

Any ideas? Thanks for looking into it

Al

[charlesshale]

Is your BAM definitely sorted?

[alhafidzhamdan]

I ran this

samtools sort -@ ${THREADS} -m 2G -T ${PATIENT_ID}T -O bam ${ALIGNED_BAM_FILE_NORMAL} -o ${ALIGNED_BAM_FILE_NORMAL_SORTED}

for both tumour and normal bams and tried sage again and the same error occured.

[charlesshale]

Could you try a later version of Sage (eg v3.3) to see if it also hits this error?

Are you able to email me a small slice of the BAM so I can debug what is going on? c.shale@hartwigmedicalfoundation.nl

thanks.

[alhafidzhamdan]

Hi Charles, The original bam file was aligned using ISAAC. I re-aligned my bam using BWA and it seemed to have worked.