Strainphlan sample2markers.py AttributeError: 'NoneType' object has no attribute 'reference_free_consensus'

Microbial community profiling StrainPhlAn
1

There seem to be a problem with running sample2markers on one of my sam files whereas it runs fine on all the others. Would you happen to know what is the problem or how to interpret the error message?

Run fine on samples such as:

image
image1255×260 10.6 KB

Throws an error when running on this particular file:

image
image1282×900 69.6 KB

Using the latest metaphlan database.

Thanks!

2

Hi @Jeffrey_Chiu
If seems there is some kind of problem with the sam file or the bam file conversion. Was the MetaPhlAn profiling executed correctly for that sample? Is the sam file corrupted or with no entries?

Best,
Aitor

3

Hi Aitor,

Thanks for getting back to me. The metaphlan step seemed to run just fine. Repeated a couple of times. Is there I way to share the corresponding sam.bz2 file that I used as input and have trouble running properly.

Really not sure how to resolve this problem.

Thank you,
JC

4

Hi @Jeffrey_Chiu
Sorry for the late answer. Do you have any Dropbox / WeTransfer / Google Drive account? Or in case you don’t, is it possible for you to upload the SAM files you have problem with here Biobakery StrainPhlAn - Google Drive?

Best,
Aitor

1 Like