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Specific srp seems to cause metadata download to freeze #218

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nasjr08 opened this issue May 10, 2024 · 0 comments
Open

Specific srp seems to cause metadata download to freeze #218

nasjr08 opened this issue May 10, 2024 · 0 comments
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@nasjr08
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nasjr08 commented May 10, 2024

I ran the following code:

pysradb metadata --detailed SRP131661

And I neither got an error message nor an output.

Running the following does work however:
pysradb metadata SRP131661

When I retrieve the srx files using the srp-to-srx command and use them instead, I notice that up until the 28th SRX id, the command works fine.

Including the 29th SRX ID leads to the same problem as above.
Excluding the 29th ID but running the rest also causes a timeout.
Including the 1-28 + the last SRX ID causes the output to have 2638 rows with the majority not belonging to the study of interest. I have attached the four files to demonstrate what I mean.

This is really odd behaviour. What is the explanation for this?

srp-to-srx 1-28&46.txt
srp-to-srx.txt
output_metadata_detailed.txt
get_metadata_detailed.txt

UPDATE: I ran with 4 srx now ( SRX3607048, SRX3791765, SRX3791771, SRX3791772) and again, I get over 1900 rows. all but the last 4 have an experiment_accession of SRX3607048. Ag
liver_samples_metadata_detailed.txt
ain, results appear to be very odd.

selected_samples_metadata_detailed.txt

@nasjr08 nasjr08 added the bug Something isn't working label May 10, 2024
@nasjr08 nasjr08 changed the title Specific srx seems to cause metadata download to freeze Specific srp seems to cause metadata download to freeze May 10, 2024
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