Deion of the bug I'm preprocessing some samples using the Si

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Singularity - C call correction local variable referenced before assignment about dandelion HOT 4 CLOSED

chrish935 commented on August 17, 2024

Singularity - C call correction local variable referenced before assignment

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Comments (4)

zktuong commented on August 17, 2024

thanks @chrish935 for finding this bug!

I've added a fix at #325 which hopefully solves this. i will try and build a singularity image and ask you to try it and see if it corrects your error.

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zktuong commented on August 17, 2024

can you try with:

singularity pull library://kt16/default/sc-dandelion:dev

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chrish935 commented on August 17, 2024

That looks like it fixed the problem, but it also started to complain a lot when quantifying mutations, which I don't recall it doing before (see below; error was printed to the console twice per sample). It doesn't seem to cause any real issues though as the resultant .tsv files all have the mu_count & mu_freq columns.

Code:

singularity run -B "$PWD" ../sc-dandelion_dev.sif dandelion-preprocess \
    --filter_to_high_confidence \
    --file_prefix "all" \
    --meta d14__meta.csv

Error:

finished: saving DataFrame at d14_1/dandelion/all_contig_dandelion.tsv
 (0:00:28)
Quantifying mutations
R[write to console]: Error: package or namespace load failed for ‘shazam’:
 .onAttach failed in attachNamespace() for 'shazam', details:
  call: file(con, "r")
  error: cannot open the connection

 finished: saving DataFrame at d14_1/dandelion/all_contig_dandelion.tsv
 (0:00:08)
Quantifying mutations
R[write to console]: Error: package or namespace load failed for ‘shazam’:
 .onAttach failed in attachNamespace() for 'shazam', details:
  call: file(con, "r")
  error: cannot open the connection