Unexpected phred quality scores with perfect reads

[lcoombe]

Hello all,

As we discussed via Slack, I found that the phred quality scores when outputting perfect reads appear to vary as expected for when simulating error reads, instead of having the max phred quality score (as you'd expect for perfect reads).

Using NanoSim 3.1.0, an example command:

simulator.py genome -c /projects/btl/datasets/hprc/HG01243/nanopore/nanosim/training -o celegans-perfect-test -n 4 --perfect --fastq -t16 -rg celegansN2_referencegenome.fna -b guppy 

Note that I also got an error when I didn't specify -b, which was also unexpected as I they are perfect reads, so wouldn't need to have a basecaller to simulate homopolymers. from.

An example of a resulting simulated read with unexpected phred qualities:

@gi|453232348|ref|NC-003282_9826629_perfect_0_F_0_6095_0
CGAGATAAAGGTATGCTGGAAAACGTTAAAATTTGATTTAATTTATTATTTTCAGAGCGCGGAGTTGTCTGGGAGGAAACAATTATTCTGATGAGCAAGAACATCAAACAGGCCTTCCTATCGGCAACAATTCCTAATGCTAGACAGTTTGCACGTTAGTTTTTCAATCGTTGATCTGATTTACTTAAAATATTTTTAACTTCAGAATGGGTCGCCAGCATCAAGCAACAACCAGTTAACGTGGTTTACACAGACTATCGTCCAACTCCTCTCCAACACTGGATATATCCAGTAGGTGGAGAAGGAATGTATGAAGTGGTTAATGTGAAGGTAACTATTTAAATAACAATTTTAAAATTCTACAAATTTCGAATTCAGGGTGAATTCCGCGAAGACAAATTCAGAGACGCGATGAGCGGATTGGCAACAGCTGGAGATTCTGCCGGAAGTTTCAATAAAAGAAGAACTGGTGGAGGAACTCAAGGAGATTCAAACGTTCTCAAAATTATTCGATCAGTGGCTTCCAATGATGGCCTTAACTGTATCGTTTTCTCATTTTCGCGAAAAGAATGCGAGTCGTATGCTATAAGTTTGAAAGATATGGATTTCAATAAAGATCACGAAAAAGGAATGGTCAAATCGGTTTATGAGAGTGCGATTGCGCAATTATCACCTGAAGACCAAAAACTTCCACAGATTTTGAACGTTGGTTTTCGTTTTCAACAAAACTCGTGAAAAATTTTAAAATTTCAGATTCTTCCACTACTTCGCCGTGGAATCGGTGTCCATCACTCTGGATTGATGCCAATTTTGAAAGAAACAATTGAAATTCTATTCGGAGAGGGTCTTGTAAAAGTCTTGTTTGCCACTGAAACATTCTCAATGGGTCTCAACATGCCTGCTCGAACTGTTGTTTTCACTTCAGCTCGTAAATTTGATGGCAGTGATAACCGATATATCACGTCAGGAGAATACATTCAAATGGCTGGAAGAGCTGGAAGACGTGGAAAAGATGATAGAGGAACTGTTATTCTTATGGTCGACTCTGCAATGTCTGCTGATGATGCGAAACAAATTATTAAGGTGCTACCATTATTTCAGATCAAAATGGACCAGTGTGACATGTTCTCGTAATTTTTCTCCTCAAAATCTTGTGATAAACTATAAAAAAATATTTTCTGAATCTGTAAAATAACTTTTATTCAATTTGGAACAACTGAAAAGTGGTCCAACATTGTCCTAAAGTTGAAAAATGCCCGAAAAAAATATTTTGAGCACTTTTTCTAGTTGTTCAAACTGAAATAAAAGTTTTTTTGGGATACAGATAATGTTTTCCTATATTTGATCATAAAATGTTGATTAAAAATATTGGAAAACATGCCACACTAGCCCATTTCGAGGAATTACTGTTTCAGATTTAAATCTGTGCTCTTATAGACGCTTCTTTCATATTTACTTTTTCCAGGGTGCTACTGATCCACTGAATTCGCAATTTCGTCTCACCTATAACATGGTTCTCAATTTAATGAGAGTTGAAGGAATGGCTGTTTCATGGATTATCAATAACAGTTTTCATCAATTCCAAAGCTATGCTAAAATTCCTGAAATCGATAAAAGTAGTTTATTCAATTTTTTAGATCAATTAATTTCAGTTTCTAATTTCAGAATGCGTGCAGGTTGAACGAAAGATTGCTTCATTCAATTTCCCATGGGAAAATGAAATGCGCACTTTGGTAGATCTTCAAGATCAATTGGAGGCAACTCGTCAAAGAATTATTCAAATTCAACGAGAACCCAAATATATTGTCGGTTTTCTTCACGCGGGACGCCTTTTCAAGGTGAATTTTAGAAAAATGTTCCATCTGTGTAATGAATATTTTTCCTAATTTAGGTAAAATCCGGTGATCGTGATTTCAAATGGGGAATTTTGAATCAATTCAAAAAAGAACAGAATCCAGACGACCGCAATGATCAAATGTAAGAATTTTGTTCATAATAAGGGTGTCGTCGTAAAATTTCCGATTTTTCCGGTGTTTTAGTCAGCTTTAGATTAGGAAAAAAATTAAACATTTTATCAAAATGTAAAACACAAGAAAACCTTCGATTTTTGGTTAAAAAATATAATACAAGAAATGGCCAAAATTTAAGAATGTTTTTGAAATATCAGAAAATCGAGATGCGAAAATCGATTTTTTTGAAAAAAAAAATTCTGGTACCACTTTGAATATAAATTCCAGTTATCTGTGTGACATGATGATTGCAATTAACACAGAAGGTCGATTTGATCCAACAAATCCCGCAACTCTTGTTCCTGGATTCGATTTGCCAAAGGTACGAATTTTAATATTATCATTTTTTTACAAAAAAACCCTTTCAGCGTCGCTGGATTCGTGTGCCTATGACCATCGATAGAATCACTGCAATTTCTGCTGTTCGCCTCAAAGTTCCAGCAGATATTGATAAGCCAGATGGACAAATGCGTCTTGACGGTATGATGGCTGCAGCTACAAAGCGATTTGGCAATCAAATTCCATTATTGGACCCCATTCAGGATATGGAAGTACGTTTTAATAACAAAGTAGATGAGAATAGTAGATTTTTTTGGAAATTTTAGTTTTTGCCAATTTATTGCAACTGATTTATAGCTCTTTTCATAAAATGTAGTATTACGTTTTTTAGATCAAAACCGTGGAAATGAAGGAACTGATTGCACGCGAGAAAAGCTTGGAAGGACGATTGGAGACACATTCAATGACAAAGCGTGATAATATGAAAGATCTCAAAAAACAATTTGAACAGAAACAAGACGCTGTGAAAGAATTAAATGCTTTGAAAGCCGAAAGAAAAAGTGTACAAAGTACATTGCATTTGGAAGAATTAAACAATAGAAAACGTGTTCTCAGAAGACTTGGTTATCTGGGAAACGATGATGCTCTTGTTCTTAAGGTAATTTCAAGGTTTTGAATAAAGATGCTCAATTGTTTTTTCAGGGATCCGTTGCCTGTGAATTATCCGCTTCAGATGAGTTGATCTTGACAGAAATGCTCTTGAAAGGAATTTTCAATACGCTTGATGTCGCTCAAACGGCTGCTCTACTCTCGTGTTTCGTGTTCCAAGACAAATGTGCAGCTCCGAAGTTGGCAACAGAACTTCAGACATGTCTCAGTGAACTTCATGTTGGTTTTAGTTGAAATAATTGAAGTAATTAGAAATGTTTTGCAGGAACAAGCTAGAAATGTGGCGAAGGTATCAAATGAATGTAAAATGGAAGTTATGGAGGACAAGTATGTCAGTAGTTTCAATCCTGGACTCATGGATGTCGTATATCAATGGGTTAACGGAGCTACGTTCAGTGAAATTGTCAAGACTACGGATGTTTTTGAAGGTATTTGTTTTTTTTTTCCATTCTAGATTACTAGATTACTAAAAAAAAGTTCAAAATCGCTCCTTCGGGGCTAAAATAGGAGGATATGAAATTTTACAATATAGCTTTCAAAATTTGACAATTACTTGCGGAAAAAAGTTTTCTGAATACAGAGATAGAAATAAAAAGTTTTGTGTTCTAGATTTGTATTCGGACATTTTTGGAATTGATCAAAAGCTAAAAAAAAGCACTTTAAAAAGAAGTTTGGCAATTTTCCAAAATTTCTGGAGTGCCTGAAATCCCCACTGACTCAATAAAATTCAATGTTCAGGCTCAATCATTCGAACCTTGCGACGGCTGGAAGAAGTTCTACGTGAGATGATCAACGCCGCCAAGGCTTTAGCGAATAAGGAGTTGGAGCAAAAGTTCGAAGATGCTCGAAAGAATTTGAAGAGAGATATTGTTTTCGCTGCATCTCTCTATCTATAATTTAATCGTTTTTAAATATTTTTATTTGTTGTTACTTCCCGGCATTACAGTATTCTGAAAGTCCCCATTTCTTTATGCTTTGTAATTCCTTGTTGTTTTAAGTTTATTTGGAAATTCATTAAAGTTTTGAAAACAATTGTTCACAAACGAATTAAGAAGAAGTAATTAAGTATGTTTAAAATTCCTAAACAAAGGAGGAACGACTCGAGTTTTGCAAAAGGAAATGACTTGAAGAGAATTTCGATGTTCCACTTTTATCCCGTGAACTTCTTTCCAGTGATCCACTGAAACTAAAAGATCTTCAAGACAAAATCTTCCAACAACTTCAGTTTTTGGATTCATTCATAAATTAGGATCCAAGGACATTACGGTCACTCCTACTGGCGGAGCACCAGAAAAGTTGGGCAAATACTGTTTTACTACTTGATCTTTTACTACGCATCTCTTTTACTACAGGATCTCTTTTACTACGGAATCTCTTTTACTACGAATTCCACATCTAGATCTTTTACTACAATCGGCTCTTTTACTACGGAATCTCTTTTACTACGGTTTACCAACATAGCTCTTTTACTACAGTACGAAAATTTTCAATTTAAGAATTAAATTTTCAACAACATTATGCCGGCAAACACTCATTGACTACCTTCTCATTGACTACCTTTGCTCATTGACTACCTTTTGCTCATTGACTACCTTTGCTAATTGACTACCTTCAAATGCTCTTTGACTACCTCTATCTAATAAAATTTTCCAAAATTTTTTTTGAAAACTTTTCAAAATTTGATCAGAAAAAGGCAATGTTTGTAGTTTTTCTAGTTTGGATGTTCTGCACACGATTGCAGACGAAAACCTGAGGTTTAGTAGAACACCTAAGCTCAAAAAACGCACTCACTTCGGATGCTGATATCTCCGTGGAAAAATTTTTTATGACAAAGTGATCAACTACAAAGTTGTTTATCTTAATCTAAAGTACAACTTTGTAGTTAATCGTTTTTTATCAAAAAATTTGTTGGTTGAGATATGAACAGAAAAAGAAGAAGAAAATACAAGCATGAAGGTGCCGAACTTTACACAACTTTATCTCGACCAACAAATTTTTTGATAAAAAACAATCAACTACAAAGTTGTACTTTAGATTAAGATAAACAACTTTGTAGTTGATCACTTTGTCATAAAAAATTTTTCCACGGAGATATCAGCATCCGAAGTGAGTGCGTTTTTTGAGCTTAGGTGTTCTACTAAACCTCAGGTTTTCGTCTGCAATCGTGTGCAGAACATCCAAACTAGAAAAACTACAAACATTGCATTTTTCTGATCAAATTTTGAAAAGTTTTCAAAAAAAATTTTGGAAAATTTTATTAGATAGAGGTAGTCAAAGAGCATTTGAAGGTAGTCAATTAGCAAAGGTAGTCAATGAGCAAAAGGTAGTCAATGAGCAAAGGTAGTCAATGAGAAGGTAGTCAATGAGTGTTTGCCGGCATAATGTTGTTGAAAATTTAATTCTTAAATTGAAAATTTTCGTACTGTAGTAAAAGAGCTATGTTGGTAAACCGTAGTAAAAGAGATTCCGTAGTAAAAGATCCAATTGTAGTAAAAGATCTAGATGTGGAATTCGTAGTGAAAGAGATTCCGTAGTAAAAAAGATGCGTAGTAAAAGATCAAGTAGTAAAACAGTATTTGCCGAAAAGTTGTCATTCGCTGTAACACCATTTGTTGTTAGAAATTTTTGTATATCTCGAATACTGTTACAAATACAAAAAAGATTTCACTACATTTTTCTGAATAATAGATTTTTTAAATGAAATTTCTTCAAATTTATGCCGGAAAATGAAGTTCAAGCGGTCCTCAAACAGAATCGGCTTTAACCTTGACGCTCTCCCACATTTTGTGTTCAAATTGATACAAAAGCACCAAAGTTGGTTCGTTTTAAAAACTGAAAAGTTCAAAACCAAAAAAACAAGGAACATTTAAAACTATTTATTGAAAAAAGTCAATAAAGGCTCTATGGGTTGTACTCAATTGGAAGGTTCTTGCGACGAACCATACCGTCTCCCTGGAACCATTCACGACGGAATTGTTTGGCAGCGCCATCCGGGGTGTTGGTCCACTCAACAGTGATACGGTCGTTGTTGGAGTTATGAGAACTCTATGAAGATTATGGAAAAATCTGTCCAATTTATAGCAAGCTTCTTATCTTTGTCCTAGATCTTTGCTCTAGATACGTCACGTAAAGTTCAAA
+
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