Error - invalid start byte - Metaphlan3

Hello,
We have been processing through the steps in metaphlan 3 and most of our samples produce results that we understand. But sometimes we get an error stream (in bowtie) that looks like this (see below). It ends in the traceback with an invalid start byte error. There wasn’t a corresponding error encountered when we ran through the kneaddata steps. And a visual inspection of the kneaddata files doesn’t raise any red flags.

  1. is this at all familiar?
  2. what do we need to do to avoid this error in our processing of metaphlan 3?

Thanks so much
Scot Zens
— start of Error message -----------------------------------------------------------------
Use of uninitialized value $bt2_args[2] in join or string at /HOME/miniconda3/bin/bowtie2 line 423.
Use of uninitialized value bt2_args[3] in join or string at /HOME/miniconda3/bin/bowtie2 line 423. Use of uninitialized value [2] in string eq at /HOME/miniconda3/bin/bowtie2 line 360.
Use of uninitialized value $
[3] in string eq at /HOME/miniconda3/bin/bowtie2 line 360.
Use of uninitialized value in exists at /HOME/miniconda3/bin/bowtie2 line 81.
Use of uninitialized value in exists at /HOME/miniconda3/bin/bowtie2 line 81.
Use of uninitialized value $bt2_args[2] in join or string at /HOME/miniconda3/bin/bowtie2 line 459.
Use of uninitialized value $bt2_args[3] in join or string at /HOME/miniconda3/bin/bowtie2 line 459.
Traceback (most recent call last):
File “/HOME/miniconda3/bin/read_fastx.py”, line 10, in
sys.exit(main())
File “/HOME/miniconda3/lib/python3.8/site-packages/metaphlan/utils/read_fastx.py”, line 155, in main
nreads += read_and_write_raw(f, opened=False, min_len=min_len)
File “/HOME/miniconda3/lib/python3.8/site-packages/metaphlan/utils/read_fastx.py”, line 119, in read_and_write_raw
nreads = read_and_write_raw_int(inf, min_len=min_len)
File “/HOME/miniconda3/lib/python3.8/site-packages/metaphlan/utils/read_fastx.py”, line 64, in read_and_write_raw_int
l = fd.readline()
File “/HOME/miniconda3/lib/python3.8/codecs.py”, line 322, in decode
(result, consumed) = self._buffer_decode(data, self.errors, final)
UnicodeDecodeError: ‘utf-8’ codec can’t decode byte 0x8b in position 1: invalid start byte
— end of Error message -----------------------------------------------------------------

About the “Use of uninitialized value” warnings, see [Warnings] MetaPhlAn version 3.0 · Issue #101 · biobakery/MetaPhlAn (github.com), it does not affect the analysis.

For the UnicodeDecodeError, can you paste here the command line you used?