/home/yanhui/anaconda3/envs/drep/lib/python3.6/site-packages/statsmodels/tools/_testing.py:19: FutureWarning: pandas.util.testing is deprecated. Use the functions in the public API at pandas.testing instead.
  import pandas.util.testing as tm
You gave me a sam- I'm going to make it a .bam now
Converting allGenomes-vs-17119-05-01-243200068.sam to allGenomes-vs-17119-05-01-243200068.bam
samtools view -S -b allGenomes-vs-17119-05-01-243200068.sam > allGenomes-vs-17119-05-01-243200068.bam
sorting allGenomes-vs-17119-05-01-243200068.bam
samtools sort allGenomes-vs-17119-05-01-243200068.bam -o allGenomes-vs-17119-05-01-243200068.sorted.bam
[bam_sort_core] merging from 23 files and 1 in-memory blocks...
Indexing allGenomes-vs-17119-05-01-243200068.sorted.bam
samtools index allGenomes-vs-17119-05-01-243200068.sorted.bam allGenomes-vs-17119-05-01-243200068.sorted.bam.bai
***************************************************
    ..:: inStrain profile Step 1. Filter reads ::..
***************************************************

Getting read pairs: 100%|████████████████████████████████████████████████████████████████████████████████████████████████| 32943/32943 [06:26<00:00, 85.34it/s]
Making read report
/home/yanhui/anaconda3/envs/drep/lib/python3.6/site-packages/numpy/core/fromnumeric.py:3335: RuntimeWarning: Mean of empty slice.
  out=out, **kwargs)
/home/yanhui/anaconda3/envs/drep/lib/python3.6/site-packages/numpy/core/_methods.py:161: RuntimeWarning: invalid value encountered in double_scalars
  ret = ret.dtype.type(ret / rcount)