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Hi, I need some help with running oncoanalyzer2.1....
# oncoanalyser
s
Hi, I need some help with running oncoanalyzer2.1.0. After dealing with this issue I was able to run the 2.0.0 version successfully. I am now trying to run 2.1.0, starting from the redux bam files which were created as output from 2.0.0. Somehow I keep getting this error within samtools within TEAL_prep: 
htsjdk.samtools.util.RuntimeIOException: IOException seeking to unmapped reads
and have no clue how to solve this. Attached you can find my .nextflow.log and .command.log files. For the issues that I had with 2.0.0, where 
/local
wasn’t getting bound to the singularity image, the issue also always occured in samtools, so I am unsure whether this might also have something to do with it? I would appreciate any help!
.command.log.nextflow.log
r
Hi Sophie, thanks for your question! It seems your 
.command.log
seems to come from a 2.1.0 run with the TEAL issue but your 
.nextflow.log
seems to come from a 2.0.0 run without TEAL and the ORANGE step crashing because it's missing the CUPPA input which can't be generated when the virusinterpreter step is skipped like in your command
Not sure if this was intentional or if you wanted to share the 
.nextflow.log
from the failed 2.1.0 run with the TEAL issue ? Let me know ! 🙂
s
Ah sorry. I uploaded the wrong .nextflow.log. I will fix that
But it basically says the same as the .command.log file….
r
seems the bam file(s) is/are corrupted - can you run a 
samtools quickcheck -v <path/to/file>
command on it to see if it actually is ?
👍 1
you could potentially get away w/ regenerating the index (
samtools index
)
s
The redux.bam files seem to be fine…
r
and you've set your info column to 
redux_bam
in your samplesheet, correct ?
s
Yes
r
My guess is that the pipeline is trying to access a position in your bam, using "an" index file that's not there - could you try reindexing one bam and seeing if that works ?
s
I will do this and let you know how it went. But shouldn’t the 2.0.0 have crashed then too? These are the redux files which were generated by oncoanalyzer two weeks ago and worked fine for all other downstream steps…
r
yeah that's really strange - those files aren't empty, correct ?
s
No, they are not…
r
well, 2.0.0 didn't have teal in it but theoretically it could've
s
I think it is strange that it is again failing at the samtools steps (as it did for esvee and bwa-mem2….)
This time they should be correct
.nextflow.log.command.log
r
is this with reindexed bams ?
s
No, not yet
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