# StrainPhlAn Tutorial Error

**URL:** <https://forum.biobakery.org/t/strainphlan-tutorial-error/7401>\
**Category:** StrainPhlAn\
**Created:** [August 25, 2024, 4:13am UTC](https://forum.biobakery.org/t/strainphlan-tutorial-error/7401 "2024-08-25T04:13:23Z")\
**Posts on this page:** 1\
**Page:** 1

<div class="post-metadata">

**Author:** ![cliffbueno](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/cliffbueno/32/2992_2.png) [@cliffbueno](https://forum.biobakery.org/u/cliffbueno)\
**Post date:** [August 25, 2024, 4:13am UTC](https://forum.biobakery.org/t/strainphlan-tutorial-error/7401/1 "2024-08-25T04:13:23Z")

</div>

Hello,  
I was running the StrainPhlAn tutorial. Things were working fine until I got to the consensus markers step.  
I ran the code:

```auto
sample2markers.py -i sams/*.sam.bz2 -o consensus_markers -n 8

```

And it yielded the following message. Let me know if you have ideas for troubleshooting.

Sat Aug 24 19:53:36 2024: Start samples to markers execution  
Sat Aug 24 19:53:36 2024: Creating temporary directory…  
Sat Aug 24 19:53:36 2024: Done.  
Sat Aug 24 19:53:36 2024: Filtering SAM files…  
Sat Aug 24 19:54:01 2024: Done.  
Sat Aug 24 19:54:01 2024: Converting input files…  
Sat Aug 24 19:54:01 2024: Converting samples to BAM format…  
Sat Aug 24 19:54:01 2024: Done.  
Sat Aug 24 19:54:01 2024: Sorting BAM samples…  
Sat Aug 24 19:54:01 2024: Done.  
Sat Aug 24 19:54:01 2024: Indexing BAM samples…  
Sat Aug 24 19:54:01 2024: Done.  
Sat Aug 24 19:54:01 2024: Done.  
Sat Aug 24 19:54:01 2024: Getting consensus markers from samples…  
Sat Aug 24 19:54:01 2024: Processing sample: consensus\_markers/tmpx5ykqzag/SRS\*.bam  
Sat Aug 24 19:54:01 2024: Loading the bam file and extracting information…  
Traceback (most recent call last):  
File “/projects/clbd1748/software/anaconda/envs/mpa/bin/sample2markers.py”, line 10, in   
sys.exit(main())  
File “/projects/clbd1748/software/anaconda/envs/mpa/lib/python3.7/site-packages/metaphlan/utils/sample2markers.py”, line 399, in main  
sampletomarkers.run\_sample2markers()  
File “/projects/clbd1748/software/anaconda/envs/mpa/lib/python3.7/site-packages/metaphlan/utils/sample2markers.py”, line 281, in run\_sample2markers  
filtered=‘\_filtered’ if len(self.clades) \> 0 else ‘’)  
File “/projects/clbd1748/software/anaconda/envs/mpa/lib/python3.7/site-packages/metaphlan/utils/sample2markers.py”, line 119, in build\_consensus\_markers  
results = self.get\_consensuses\_for\_sample(i)  
File “/projects/clbd1748/software/anaconda/envs/mpa/lib/python3.7/site-packages/metaphlan/utils/sample2markers.py”, line 141, in get\_consensuses\_for\_sample  
sam\_file = pysam.AlignmentFile(input\_bam)  
File “pysam/libcalignmentfile.pyx”, line 742, in pysam.libcalignmentfile.AlignmentFile. **cinit**  
File “pysam/libcalignmentfile.pyx”, line 991, in pysam.libcalignmentfile.AlignmentFile.\_open  
ValueError: file has no sequences defined (mode=‘r’) - is it SAM/BAM format? Consider opening with check\_sq=False

I’m running MetaPhlAn version 4.0.6 (1 Mar 2023).  
Thanks,  
Cliff