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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.
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Could not retrieve index file error #124

Open johannesnicolaus opened 2 years ago

johannesnicolaus commented 2 years ago

Hi, I just ran the pipeline and got the following errors:

[E::idx_find_and_load] Could not retrieve index file for 
'demultiplexed_matched.bam'
[E::idx_find_and_load] Could not retrieve index file for 
'annotated.bam'

Where these files are inside the temp folder.

After running the pipeline I got a bed and a tsv file which seemed ok (but I didn't get any file for stats), and the pipeline ran successfully.

Is it ok to ignore these errors?

jfnavarro commented 2 years ago

Hi!

Thanks for your message.

Those are warning messages generated during the demultiplexing and you could ignore them.

I plan on fixing that in the next release but that said, the output is not affected at all.

ps: I suggest that you use this repository instead https://github.com/jfnavarro/st_pipeline which is more up to date.

Best, Jose

johannesnicolaus commented 2 years ago

Thanks for the reply. I think I used the more up to date repository but wrongly posted an issue here.

Anyway, I'm glad it did not affect the output!

Again thanks a lot!

Cheers, Nico