Psiblast: Stop After Checkpoint?

Question

[pascal]

Hi,

I'm using psiblast 2.2.25+ to generate PSSMs for PSIPred, and I noticed that even after writing to the checkpoint file, it takes a while (feels like half the run time) before exiting, even though I don't need any output beyond that. Running with:

psiblast -db $DB -out_pssm $PSSM -num_iterations 3 -num_alignments 0 -out /dev/null < $QUERY

Are there some other parameters to prevent further calculations? (I'd also like to print the PSSM to STDOUT, and I don't like its ASN.1 format either ­— could I use the API to customize this? I haven't found any examples…)

Edit: looked at the source and it turns out the checkpoint file is written after every iteration (except the first, i.e. two times for me), so the time I thought nothing happened was actually the last iteration. It does exit immediately after writing the last checkpoint.

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Also I'm getting a warning: "Composition-based score adjustment conditioned on sequence properties and unconditional composition-based score adjustment is not supported with PSSMs, resetting to default value of standard composition-based statistics", can I shut this up by setting -comp_based_stats? (but I don't give it, so it's resetting it from default to default?!)

Answer 1

[Arjen Ten Have]

I would not worry about the warning. Read ALtschuls paper on Composition-based score adjustment and you will understand that these are just incompatible. There is nothing more to it and PSI-Blast automatically corrects.....