Old script from clinical_epps "2. Calculate Aliquot Volume" in micro causing very high sample volumes

[AbiDalby]

Lims Issue

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Work Flow: Microbial WGS v7
Protocol: CG002 - Normalization of microbial samples for sequencing v2
Step: CG002 - Normalization of microbial samples for sequencing

Description:

It was discovered during nex250313_2 MWx normalisation step for sequencing that the calculated sample volume needed can sometimes be very high. In this case over 500 uL. The target concentration required for the normalisation was 2.5 nM and the sample ACC17120A31 has a concentration close to that, at 2.51 nM.

The EPP used is "2. Calculate Aliquot Volume" with bash -c "/home/glsai/miniconda3/envs/epp_master/bin/aliquot_sequencing_microbial.py --pid {processLuid}"

After looking at the script, it seems it is almost entirely hard-coded and that the buffer volume needs to be a minimum of 2.0 uL. This then leads to the sample volume scaling up in response to samples that are very close to the target final concentration.

The script even specifies that the sample volume is 10 uL (if the concentration is below the target final concentration) or 5 uL. But overrides in the case that the buffer volume is under 2.0 uL and re-calculates the sample volume needed due to this.

See here

We need to look further into this, as this could explain why we often have sequencing issues, many top-ups and many over-sequenced samples for micro.

Here is a LIMS issue for the transfer of the microbial normalization scripts from clinical epps to cg_lims