marginAlign & marginCaller errors

[amnaniamin]

Hi,

I'm using Ubuntu 16.04 LTS on virtualbox. I got the following error when running marginAlign for Nanopore reads.

---JOBTREE SLAVE OUTPUT LOG--- Traceback (most recent call last): File "/home/ewc/marginAlign/submodules/jobTree/src/jobTreeSlave.py", line 271, in main defaultMemory=defaultMemory, defaultCpu=defaultCpu, depth=depth) File "/home/ewc/marginAlign/submodules/jobTree/scriptTree/stack.py", line 153, in execute self.target.run() File "/home/ewc/marginAlign/src/margin/mappers/last.py", line 35, in run Last.run(self) File "/home/ewc/marginAlign/src/margin/mappers/last.py", line 19, in run for name, seq, quals in fastqRead(self.readFastqFile): File "/home/ewc/marginAlign/submodules/sonLib/bioio.py", line 769, in fastqRead raise RuntimeError("Got a qual value out of range %s (range is 33 to 126)" % i) RuntimeError: Got a qual value out of range 13 (range is 33 to 126) Exiting the slave because of a failed job on host ewc-VirtualBox Due to failure we are reducing the remaining retry count of job /media/sf_MinION_Pipeline/jobTree/jobs/job to 0 We have set the default memory of the failed job to 2147483648.0 bytes

Then, I also got the following error when running marginCaller for SAM file (aligned using BWA-MEM).

---JOBTREE SLAVE OUTPUT LOG--- Traceback (most recent call last): File "/home/ewc/marginAlign/submodules/jobTree/src/jobTreeSlave.py", line 271, in main defaultMemory=defaultMemory, defaultCpu=defaultCpu, depth=depth) File "/home/ewc/marginAlign/submodules/jobTree/scriptTree/stack.py", line 153, in execute self.target.run() File "/home/ewc/marginAlign/submodules/jobTree/scriptTree/target.py", line 197, in run func(*((self,) + tuple(self.args)), *self.kwargs) File "/home/ewc/marginAlign/src/margin/marginCallerLib.py", line 211, in variantCallSamFileTargetFn evolutionarySubstitutionMatrix, errorSubstitutionMatrix) File "/home/ewc/marginAlign/src/margin/marginCallerLib.py", line 89, in calcBasePosteriorProbs observedBase))baseObservations[observedBase], BASES)), BASES) File "/home/ewc/marginAlign/src/margin/marginCallerLib.py", line 86, in math.log(getProb(evolutionarySubstitionMatrix, refBase.upper(), missingBase)) + File "/home/ewc/marginAlign/src/margin/marginCallerLib.py", line 79, in getProb return subMatrix[(start, end)] KeyError: ('N', 'A') Exiting the slave because of a failed job on host ewc-VirtualBox Due to failure we are reducing the remaining retry count of job /media/sf_MinION_Pipeline/jobTree/jobs/job to 0 We have set the default memory of the failed job to 2147483648 bytes ount of job /media/sf_MinION_Pipeline/jobTree/jobs/job to 0 We have set the default memory of the failed job to 2147483648 bytes

What should i do to solve the issues?

Thanks.

[mitenjain]

For issue 1, how was the fastq file generated? If you could send a test example to miten@soe.ucsc.edu, I can try reproducing the issue at our end and push a fix.

Issue 2 seems to have arisen due to the presence of "N" in the reference fasta file. If you replace the "N"s in the file and re-run, ti should work. I need to put in a workaround for this (WIP).

Apologies for the hassle. -Miten & Benedict

[mitenjain]

Hi there, just checking in if this issue is resolved for you?

[maximus-sci]

Hello,

I'm getting the first error that the OP posted:

raise RuntimeError("Got a qual value out of range %s (range is 33 to 126)" % i)
RuntimeError: Got a qual value out of range 13 (range is 33 to 126)

What does this error mean? I can email one of the fasta files to someone if that will help...

[mitenjain]

A MWE would help. Could you email it to miten@soe.ucsc.edu?