Spell error in running from bowtie index

Microbial community profiling HUMAnN
1

Human 3.9 from pipy

Ii run from the chocophlan of another sample and get the error.

I guess there is somewhere an error with the double rev.rev !!

Could not open index file …/test_humann_temp/test_bowtie2_index.rev.rev.1.bt2l

1 Like
2

This is the first I’ve heard of this error, so I don’t think it’s an issue in the normal HUMAnN workflow. What command were you executing when this happened?

3

I followed the tutorial to create one chocophlan db for the whole cohort.

  1. I run human on one sample test
  2. I used the chocophlan db of the test sample for the other runs with

--bypass-nucleotide-index --nucleotide-database test/test_humann_temp

Where the test/test_humann_temp is the output folder of the test run.
Apparently human did not find the correct bowtie db.

If I specify more explicitly:

--bypass-nucleotide-index --nucleotide-database test/test_humann_temp/test_bowtie2_index

It works.

4

Glad you figured it out!

5

I think there is still an error in the code that would be worth fixing.