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cbg-ethz / PredictHaplo

This software aims at reconstructing haplotypes from next-generation sequencing data.
GNU General Public License v3.0
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lib error? #29

Open antoine4ucsd opened 2 years ago

antoine4ucsd commented 2 years ago

Hello I am trying to use predicthaplo on HIV sam files. I am using a Mac bookpro last gen. I tried first with conda but got a segmentation error:

predicthaplo --sam /Volumes/SILVER/_condesa_wgs/input/set14/169132_S26.sam.gz --reference ./reference/HXB2_noLTRs.fasta 
Configuration:
  prefix = predicthaplo_output/ph_
  cons = ./reference/HXB2_noLTRs.fasta
  visualization_level = 1
  FASTAreads = /Volumes/SILVER/_condesa_wgs/input/set14/169132_S26.sam.gz
  have_true_haplotypes = 1
  FASTAhaplos = 
  do_local_Analysis = 1
Segmentation fault: 11

after reading some comments, I tried with the github version but still get errors:

predicthaplo --sam./input/167792_S30.tmp.sam --reference ./reference/HXB2_noLTR.fasta 
Configuration:
  prefix = predicthaplo_output/ph_
  cons = ./reference/HXB2_noLTR.fasta
  visualization_level = 1
  FASTAreads =./input/167792_S30.tmp.sam
  have_true_haplotypes = 1
  FASTAhaplos = 
  do_local_Analysis = 1
Warning: 0.5% of the reads were discarded because they are unpaired.
Warning: 30.0% of the read pairs were discarded because the sequence is too short. The flag "--min_length" can be used to configure the minimum length.
Warning: 0.1% of the read pairs were discarded because the gap fraction is too high. The flag "--max_gap_fraction" can be used to configure the maximum gap fraction.
After parsing the reads in file./input/167792_S30.tmp.sam: average read length= 482.784 28387
First read considered in the analysis starts at position 1. Last read ends at position 5321
There are 28387 reads
Median of read lengths: 498.000
Local window size: 348
Minimum overlap of reads to local analysis windows: 295
Reconstruction starts at position 1 and stops at position 40
Local analysis in window from 175 to 40
libc++abi: terminating with uncaught exception of type std::length_error: vector
Abort trap: 6

any suggestions? thank you!

DrYak commented 2 years ago

Hello, currently predicthaplo is temporarily developper-less as the previous dev now left, and we haven't managed to find somebody available.

In the mean time, could you send an example of the data that makes predict haplo crash? That would help who ever the next dev is to better debug your problem.