sqmreads2tables.py AssertionError

[CarlosNavr]

Hi everyone.

Ive been using the sqmreads2tables.py without problems, but when I run that command on this project and I get the following error:

[csmgrmgr@login211-1 METALGENsalivas]$ sqmreads2tables.py SQMrun61 SQMrun61.tables
Traceback (most recent call last):
File "/opt/cesga/system/software/Core/squeezemeta/1.7.0/bin/sqmreads2tables.py", line 407, in main(parse_args())
File "/opt/cesga/system/software/Core/squeezemeta/1.7.0/bin/sqmreads2tables.py", line 247, in main assert read not in read_fun[method]
AssertionError

Apparently, there were no problems when running the sqm_longreads pipeline, and I ve re-run this project twice, but the same error still occurs. Ive checked for duplicated sequences but it seems there are not duplicates.

Thank you in advance.

[fpusan]

Let's see if this is the case.

1. Edit the file /opt/cesga/system/software/Core/squeezemeta/1.7.0/bin/sqmreads2tables.py
2. Replace line 247

   SqueezeMeta/utils/sqmreads2tables.py

   Line 247 in ff69605

   assert read not in read_fun[method]

   
   by

   if read in read_fun[method]:
       print(read)
       assert False

3. Search for this read name in your input files, let me know if it actually appears only once

[CarlosNavr]

It seems it's duplicated in one of the input files. Gonna re-run again and see if it works now.

Thank you very much!

[fpusan]

So was the duplication an error on your part, or did the sequencer (MinION, I suppose) output the same read name in two different runs?

If the latter, I should probably change that assertion to a warning