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merenlab / oligotyping

Exploring microbial patterns through subtle nucleotide variation within 16S rRNA gene tag sequences of closely related taxa
GNU General Public License v2.0
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Length error #27

Closed jpearl01 closed 6 years ago

jpearl01 commented 6 years ago

Hello,

When running this command, I get this error:

$ decompose BEI_OTU_12_eefilt_subset.fasta 
Config Error: Not all reads have the same length.
$ decompose --version
Oligotyping Pipeline Version .....................................: 2.1

I was under the impression that using the MED pipeline would allow for varying length sequences, as long as they were biologically meaningful?

If I use the flag --skip-check-input-file, I end up with this error:

$ decompose --skip-check-input-file BEI_OTU_12_eefilt_subset.fasta 
Project ..........................................................: BEI_OTU_12_eefilt_subset
Run date .........................................................: 05 Jun 18 17:33:06
Library version ..................................................: 2.1
Command line .....................................................: /home/testing/.local/bin/decompose --skip-check-input-file BEI_OTU_12_eefilt_subset.fasta
Multi-threaded ...................................................: True
Extraction info output file ......................................: /home/testing/BEI_OTU_12_eefilt_subset-m0.10-A0-M0-d4/RUNINFO
Log file path ....................................................: /home/testing/BEI_OTU_12_eefilt_subset-m0.10-A0-M0-d4/RUNINFO.log
Input file .......................................................: BEI_OTU_12_eefilt_subset.fasta
Mapping file .....................................................: None
Quick (and dirty) analysis requested .............................: False
Merge homopolymer splits .........................................: False
Skip removing outliers ...........................................: False
Try to relocate outliers .........................................: False
Store topology dict ..............................................: False
Skip generating figures post analysis ............................: False
Min entropy for a component to be picked for decomposition .......: 0.0965
Perform entropy normalization heuristics .........................: True
Max number of discriminants to use for decomposition .............: 4
Min total abundance of oligotype in all samples ..................: 0
[05 Jun 18 17:33:06 Initializing topology] May take a while depending on the number of reads...                                                                                                                  Traceback (most recent call last):
  File "/home/testing/.local/bin/decompose", line 42, in <module>
    decomposer.decompose()
  File "/home/testing/.local/lib/python2.7/site-packages/Oligotyping/lib/decomposer.py", line 304, in decompose
    self._init_topology()
  File "/home/testing/.local/lib/python2.7/site-packages/Oligotyping/lib/decomposer.py", line 220, in _init_topology
    self.root = self.topology.add_new_node('root', reads, root = True)
  File "/home/testing/.local/lib/python2.7/site-packages/Oligotyping/lib/topology.py", line 71, in add_new_node
    node.refresh()
  File "/home/testing/.local/lib/python2.7/site-packages/Oligotyping/lib/topology.py", line 375, in refresh
    self.do_entropy()
  File "/home/testing/.local/lib/python2.7/site-packages/Oligotyping/lib/topology.py", line 334, in do_entropy
    column = ''.join([read.seq[position] * read.frequency for read in self.reads])
IndexError: string index out of range

Any ideas on how to fix that?

Thanks, ~josh

meren commented 6 years ago

You could use o-pad-with-gaps if the variation is meaningful across your sequences.