Error pyomo

[ktroule]

Hi.

I'm trying to use OptiType, but I get some warnings and errors. I assume that is related to pyomo, but not sure how can I solve it. Downgrade the version? I'm using version 5.2

WARNING: Constant objective detected, replacing with a placeholder to prevent solver failure.
ERROR: Expecting 's' row after 'c' rows
WARNING: Solver does not support multi-threading. Please change the config file accordingly. Falling back to single-threading.
WARNING: Constant objective detected, replacing with a placeholder to prevent solver failure.
ERROR: Expecting 's' row after 'c' rows
Traceback (most recent call last):
  File "/home/.local/lib/python3.5/site-packages/pyomo/solvers/plugins/solvers/GLPK.py", line 351, in process_soln_file
    raise ValueError("Expecting 's' row after 'c' rows")
ValueError: Expecting 's' row after 'c' rows

Thanks for your time.

[b-schubert]

There are multiple things going on:

1. You are using GLPK as a solver, which does not support multithreading. I suggest changing the config file to threads=1 in the ILP section, or (in my opinion better solution) switch to CBC, which is also an open source solver but faster and supports multithreading.

2. It seems that the set covering problem OptiType is solving has a trivial solution (probably 0). This could be due to no reads mapping to any of the HLA alleles, or only one remaining column is left after problem reduction.

Could you run OptiType with verbosity on and post the output?

[ktroule]

I've downgraded pyomo to 4.3.X and it seems to be working. Or at leas it is no giving any error, just some warnings such.

Warning: Constant objective detected, replacing with a placeholder to prevent solver failure. Once its over I'll check you solutions, but I think threads were set as 1. I'll also try CBC instead of pyomo.

Thanks

[b-schubert]

It still would help us to see the verbose output of OptiType to find out whats going wrong..

Warning: Constant objective detected, replacing with a placeholder to prevent solver failure

This error here tells you that something major is going wrong! The files that you want to infer the HLA type from probably do not contain any reads that map to the HLA locus.

[ktroule]

Sure, as soon as I can I'll show you the verbose output.

Thanks for your time.

[ktroule]

Hi once.

Im trying to run optitype to show you the verbose output (it seems to be working now).

But I'm facing a new problem, I've aligned samples using tophat2 with the reference hla rna provided by you. Then fished those bam file into fastq. These fastq weight less than 100mb. But when running optitype the memory usage rises above 100GB (my ram is ~96GB). Any clue on what I might be doing wrong (I know this is related to razers3).

Thanks

[andras86]

That sounds very strange. Could you share the fished fastq files with me?

[ktroule]

Yes. Its a paired end experiment, treated in tophat2 as single end.

[ktroule]

https://drive.google.com/open?id=0B5bhJHovPxMKaHF5N3FsaGZKWXc

Forward and reverse after separately aligned with tophat2 and fished with bam2fq.

[ktroule]

Any news? Thanks