search

SpatialTranscriptomicsResearch / st_pipeline

ST Pipeline contains the tools and scripts needed to process and analyze the raw files generated with the Spatial Transcriptomics method in FASTQ format.
Other
78 stars 30 forks source link

Could not retrieve index file #119

Closed MNM-TB closed 3 years ago

MNM-TB commented 3 years ago

Hi,

Thank you for great work with the ST tools! We are about to finish a ST study and are updating the tools to ensure data consistency with the latest st_pipeline. When re-running our analysis in the current version I'm experiencing a new warning message which I have not seen previously.

This is: [E::idx_find_and_load] Could not retrieve index file for '/tmp/st_pipeline_tempiex5kjya/demultiplexed_matched.bam'

And is repeated a variable number of times in different analyses. the STAR index and raw ST reads are identical to our prior runs which were error-free. only the st_pipeline and dependencies have changed.

Could you point me to where I can look for solutions to this issue?

Thank you again

/Tomas

MNM-TB commented 3 years ago

It does unfortunately appear to be related to pysam 0.16.0.1 : https://github.com/pysam-developers/pysam/issues/939

I'm evaluating a downgrade to pysam version 0.15.4 to see if this will remove the error.

MNM-TB commented 3 years ago

The downgrade to 0.15.4 through: pip3 install 'pysam==0.15.4' --force-reinstall run after the install of the stpipeline removed the error messages.