Cannot evaluate ONT real data (UnicodeDecodeError)

[Shen-Jing]

Hi!

To evaluate raw reads quality, I use raw reads as uncorrected reads & corrected reads at the same time.

• Data: https://www.genoscope.cns.fr/externe/nas/datasets/MinION/ecoli/Ecoli_LomanAll2D.fa.gz

My progress:

• command

python3 -m elector -threads 4 -uncorrected /mnt/d/Data/Ecoli_LomanAll2D.fasta -reference reproduce_manuscript_results/references/Ecoli.fasta -corrected /mnt/d/Data/Ecoli_LomanAll2D.fasta -output Ecoli_ONT_real -remap -assemble -simu
lator real

• progress

- Means that a large amount of reads has been handled: 10000
/mnt/d/tools/ELECTOR/elector/../bin/masterSplitter Ecoli_ONT_real/reference_sorted_duplicated.fa Ecoli_ONT_real/uncorrected_sorted_duplicated.fa Ecoli_ONT_real/corrected_sorted.fa Ecoli_ONT_real/out1 Ecoli_ONT_real/out2 Ecoli_ONT_real/
out3 7 200 10000 0.1 Ecoli_ONT_real
10000 200 50
--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------/mnt/d/tools/ELECTOR/elector/../bin
/masterSplitter Ecoli_ONT_real/reference_sorted_duplicated.fa Ecoli_ONT_real/uncorrected_sorted_duplicated.fa Ecoli_ONT_real/corrected_sorted.fa Ecoli_ONT_real/out1 Ecoli_ONT_real/out2 Ecoli_ONT_real/out3 7 200 10000 0.1 Ecoli_ONT_real
10000 200 50
--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------/mnt/d/tools/ELECTOR/elector/../bin
/masterSplitter Ecoli_ONT_real/reference_sorted_duplicated.fa Ecoli_ONT_real/uncorrected_sorted_duplicated.fa Ecoli_ONT_real/corrected_sorted.fa Ecoli_ONT_real/out1 Ecoli_ONT_real/out2 Ecoli_ONT_real/out3 7 200 10000 0.1 Ecoli_ONT_real
10000 200 50
--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------None
Traceback (most recent call last):
  File "/usr/lib/python3.8/runpy.py", line 194, in _run_module_as_main
    return _run_code(code, main_globals, None,
  File "/usr/lib/python3.8/runpy.py", line 87, in _run_code
    exec(code, run_globals)
  File "/mnt/d/tools/ELECTOR/elector/__main__.py", line 167, in <module>
    main()
  File "/mnt/d/tools/ELECTOR/elector/__main__.py", line 141, in main
    nbReads, throughput, precision, recall, correctBaseRate, errorRate, smallReads, wronglyCorReads, percentGCRef, percentGCCorr, numberSplit, meanMissing, numberExtended, meanExtension, minLength, indelsubsUncorr, indelsubsCorr , trun
cated, ratioHomopolymer = computeStats.outputRecallPrecision(sortedCorrectedFileName, outputDirPath, logFile, smallReads, wronglyCorReads, reportedHomopolThreshold, size_corrected_read_threshold, readSizeDistribution, clipsNb, 0, 0, so
ft)
  File "/mnt/d/tools/ELECTOR/elector/computeStats.py", line 208, in outputRecallPrecision
    readsToSplit = getSplit(outDir + "/msa.fa")
  File "/mnt/d/tools/ELECTOR/elector/computeStats.py", line 47, in getSplit
    lines = subprocess.check_output(['bash','-c', cmdGrep]).decode('ascii')
UnicodeDecodeError: 'ascii' codec can't decode byte 0xc2 in position 7351: ordinal not in range(128)

Sorry, I would like to ask what I did wrong. 😥

Thank you.

Jing