Comments (3)
ok! i think i have tracked this down. To replicate (rename yaml since github won't let me upload yaml):
./scripts/write_lh_annotations.py cluster.yaml linearham_run.log --output-base path/to/out
linearham_run.log
cluster_yaml.log
issue seems to be that linearham doesn't write the actual VJ insertion for light chain insertions (like it does for heavy insertions), instead just writes a boolean if it's there:
which means that this line fails: https://github.com/matsengrp/linearham/blob/master/scripts/write_lh_annotations.py#L59
because it's resetting the deletion length without changing the insertion length:
File "./scripts/write_lh_annotations.py", line 61, in update_partis_line_with_lh_annotation
utils.add_implicit_info(glfo, partis_line, check_line_keys=debug)
File "/home/dralph/work/linearham/lib/partis/python/utils.py", line 1711, in add_implicit_info
raise Exception('naive and mature sequences different lengths %d %d for %s:\n %s\n %s' % (len(line['naive_seq']), len(line['seqs'][iseq]), ' '.join(line['unique_ids']), line['naive_seq'], line['seqs'][iseq]))
Exception: naive and mature sequences different lengths 321 322 for 0901808538749971629-igk 5827556154176009883-igk 0316148055258110569-igk 0673794353012672613-igk 5234516726189794955-igk:
GACATCCAGATGACCCAGTCTCCATCTTCTGTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGTCGGGCGAGTCAGGGTATTAGCAGCTGGTTAGCCTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTATGCTGCATCCAGTTTGCAAAGTGGGGTCCCATCAAGGTTCAGCGGCAGTGGATCTGGGACAGATTTCACTCTCACTATCAGCAGCCTGCAGCCTGAAGATTTTGCAACTTACTATTGTCAACAGGCTAACAGTTTCCCTGCACTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC
GACATCCAAATAACCCAGTCTCCATCTTCTGCGTCTCCATCTGGAGTCGACAGAGTCACCATCACTTCTCGGGCTAGTCAGGGCATTAGCAGCTGGTTAGCTTGGTATCAGCAGCAGCCAGGGCAAGCCCCTAAGCTCCTGTTCTATGCTGCATGCAGTTTGCAAAGTGGAGTCCCATCAAGGTTCAGCGGCCGTGGATCTGGGACAGATTTCACTCTCACTATCAGCAGCCTGCCGCCTGAAAATTTTGTACCTTACTATTGTCAACAGGCTAACAGGTTCCCTTGCCCTTTTGGCTAGGGGACAAATCTGGAGATCATTC
from linearham.
This seems to be written by this line: https://github.com/matsengrp/linearham/blob/master/src/PhyloHMM.cpp#L320
but I can't figure out how the value of vd_junction_insertion_samp_
gets set.
from linearham.
Well this (and this) get around the issue by looking for TRUE valued VJ insertion and figuring out what it's supposed to be, but it would be a lot better to figure out why linearham is writing the TRUE to begin with.
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Related Issues (20)
- remove dockerhub image HOT 1
- git describe crashes build HOT 1
- Do we really want to use scons? HOT 3
- NodeList object where it expected a string HOT 1
- change actions to positional argument
- make default tag on quay.io HOT 1
- Use new partis fcn add_seqs_to_line() HOT 4
- Cause of huge number of low-probability nodes HOT 6
- update readme with newer (?) output files HOT 2
- update partis + maybe add --min-cluster-size arg HOT 1
- Docker container doesn't build HOT 2
- Github Actions & Quay Container building HOT 2
- Update Master -> Main
- crash in asr/ess script HOT 7
- Inferred ancestral sequences have mutations in ambiguous regions
- Branch lengths almost all much larger than hamming distance
- Add option for less verbose output dir HOT 1
- Failed Quay build from trigger
- How to handle paired h/l data
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