We are getting below error with the Miseq fastq data as per below
figaro -i test -o figaro_out -a 295 -f 18 -r 19
Forward read length: 295
Reverse read length: 295
multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File "/scratch/gencore/conda3/envs/figaro/lib/python3.7/multiprocessing/pool.py", line 121, in worker
result = (True, func(*args, **kwds))
File "/scratch/gencore/conda3/envs/figaro/lib/python3.7/multiprocessing/pool.py", line 44, in mapstar
return list(map(*args))
File "/scratch/gencore/conda3/envs/figaro/lib/python3.7/site-packages/figaro/expectedErrorCurve.py", line 97, in calculateAverageExpectedError
percentileExpectedError = makeExpectedErrorPercentileArrayForFastq(fastq.filePath, self.subsample, self.percentile, self.primerLength)
File "/scratch/gencore/conda3/envs/figaro/lib/python3.7/site-packages/figaro/expectedErrorCurve.py", line 109, in makeExpectedErrorPercentileArrayForFastq
expectedErrorMatrix = fastqAnalysis.buildExpectedErrorMatrix(path, subsample=subsample, leftTrim=primerLength)
File "/scratch/gencore/conda3/envs/figaro/lib/python3.7/site-packages/figaro/fastqAnalysis.py", line 37, in buildExpectedErrorMatrix
return numpy.array(expectedErrorMatrix, dataType, order='F')
ValueError: setting an array element with a sequence. The requested array has an inhomogeneous shape after 1 dimensions. The detected shape was (36340,) + inhomogeneous part.
"""
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/scratch/gencore/conda3/envs/figaro/bin/figaro", line 8, in <module>
sys.exit(main())
File "/scratch/gencore/conda3/envs/figaro/lib/python3.7/site-packages/figaro/figaro.py", line 210, in main
resultTable, forwardCurve, reverseCurve = trimParameterPrediction.performAnalysisLite(parameters.inputDirectory.value, parameters.minimumCombinedReadLength.value, subsample = parameters.subsample.value, percentile = parameters.percentile.value, forwardPrimerLength=parameters.forwardPrimerLength.value, reversePrimerLength=parameters.reversePrimerLength.value, namingStandardAlias=fileNamingStandard)
File "/scratch/gencore/conda3/envs/figaro/lib/python3.7/site-packages/figaro/trimParameterPrediction.py", line 453, in performAnalysisLite
forwardCurve, reverseCurve = expectedErrorCurve.calculateExpectedErrorCurvesForFastqList(fastqList, subsample=subsample, percentile=percentile, makePNG=makeExpectedErrorPlots, forwardPrimerLength=forwardPrimerLength, reversePrimerLength=reversePrimerLength)
File "/scratch/gencore/conda3/envs/figaro/lib/python3.7/site-packages/figaro/expectedErrorCurve.py", line 175, in calculateExpectedErrorCurvesForFastqList
forwardExpectedErrorArray = makeExpectedErrorPercentileArrayForFastqList(forwardFastqs, subsample, percentile, forwardPrimerLength)
File "/scratch/gencore/conda3/envs/figaro/lib/python3.7/site-packages/figaro/expectedErrorCurve.py", line 122, in makeExpectedErrorPercentileArrayForFastqList
expectedErrorReturns = easyMultiprocessing.parallelProcessRunner(parallelAgent.calculateAverageExpectedError, fastqList)
File "/scratch/gencore/conda3/envs/figaro/lib/python3.7/site-packages/figaro/easyMultiprocessing.py", line 68, in parallelProcessRunner
return mapper(processor, itemsToProcess, chunkSize)
File "/scratch/gencore/conda3/envs/figaro/lib/python3.7/multiprocessing/pool.py", line 268, in map
return self._map_async(func, iterable, mapstar, chunksize).get()
File "/scratch/gencore/conda3/envs/figaro/lib/python3.7/multiprocessing/pool.py", line 657, in get
raise self._value
ValueError: setting an array element with a sequence. The requested array has an inhomogeneous shape after 1 dimensions. The detected shape was (36340,) + inhomogeneous part.
Hi,
We are getting below error with the Miseq fastq data as per below
Please advise.
Thanks jay