AssertionError: not all umis are the same length(!): 4 - 5

Question

[monalisa6hota]

Hello,

I am trying to run UMI-tools to remove duplicated reads based on UMI. But getting error "AssertionError: not all umis are the same length(!): 4 - 5". Can anyone suggest how to resolve this error?

I am using following command :

umi_tools dedup --stdin=filtered.bam --umi-separator=":" --log=LOGFILE  --output-stats=stats.txt  -S output.bam > OUTFILE

This is the head of my bam file:

A00609:116:H7JCGDSXY:1:2171:13937:29825 16      1       10534   255     3S96M2D21M31S   *       0       0       CGCAGTACCACCGAAATCTGTGCAGAGGAGAACGCAGCTCCGCCCTCGCGGTGCTCTCCGGGTCTGTGCTGAGGAGAACGCAACTCCGCCGTCGCAAAGGCGCCGCGCCGGCGCAGACGCCCCCATGTACTCTGCGTTGATACCACTGCTT FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF,FFFFFFFFF,FFFFFFFFFFFFFFFFFF:FFFF:FF:FFFFFFF:FFFFFFF:FFFFF:FFFF  NH:i:1  HI:i:1  AS:i:103        nM:i:3  RE:A:I  xf:i:0  li:i:0  CR:Z:CCGTGAGAGAACGCGT   CY:Z::FF:F:FF:FFF,F:F   CB:Z:CCGTGAGAGAACGCGT-1 UR:Z:TTTTCCGCACTT       UY:ZG:Z:cells:0:1:H7JCGDSXY:1

I am getting following error:

Traceback (most recent call last):
  File "/home/ubuntu/miniconda3/bin/umi_tools", line 11, in <module>
    sys.exit(main())
  File "/home/ubuntu/miniconda3/lib/python3.8/site-packages/umi_tools/umi_tools.py", line 61, in main
    module.main(sys.argv)
  File "/home/ubuntu/miniconda3/lib/python3.8/site-packages/umi_tools/dedup.py", line 329, in main
    reads, umis, umi_counts = processor(
  File "/home/ubuntu/miniconda3/lib/python3.8/site-packages/umi_tools/network.py", line 419, in __call__
    clusters = self.UMIClusterer(counts, threshold)
  File "/home/ubuntu/miniconda3/lib/python3.8/site-packages/umi_tools/network.py", line 367, in __call__
    assert max(len_umis) == min(len_umis), (
AssertionError: not all umis are the same length(!):  4 - 5

[zx8754]

Posted at GitHub and answered by the developers:

• https://github.com/CGATOxford/UMI-tools/issues/461