souporcell
souporcell copied to clipboard
troublet issue possible involving RUST (thread 'main' panicked)
I'm using the most recent (e.g. two days ago) singularity container and getting the following error (repeated here from trying to run just the troublet part in isolation)
% singularity exec /gstore/scratch/u/garfield/souporcell/souporcell_latest.sif troublet -a SAM24416638/alt.mtx -r SAM24416638/ref.mtx --clusters SAM24416638/clusters_tmp.tsv > clusters.tsv
thread 'main' panicked at 'index out of bounds: the len is 0 but the index is 91639', src/main.rs:328:22
note: run with `RUST_BACKTRACE=1` environment variable to display a backtrace
Not really sure what to check (and stack exchange is down!). Suggestions most welcome.
Actually, looking at the inputs, the issue may be upstream -- the file clusters_tmp.tsv
is empty and the log says
total loci used 23808
thread 6 iteration 0 done with -inf, best so far -inf
thread 0 iteration 0 done with -inf, best so far -inf
thread 5 iteration 0 done with -inf, best so far -inf
thread 4 iteration 0 done with -inf, best so far -inf
.
.
.
thread 5 iteration 12 done with -inf, best so far -inf
thread 2 iteration 14 done with -inf, best so far -inf
thread 3 iteration 13 done with -inf, best so far -inf
thread 1 iteration 14 done with -inf, best so far -inf
thread 5 iteration 13 done with -inf, best so far -inf
thread 4 iteration 14 done with -inf, best so far -inf
thread 3 iteration 14 done with -inf, best so far -inf
thread 5 iteration 14 done with -inf, best so far -inf
best total log probability = -inf
Attempting to call soupercell upstream leads to:
% singularity exec souporcell_latest.sif souporcell -h
/.singularity.d/actions/exec: 21: exec: souporcell: Permission denied
Something a bit off with my user or singularity settings?
um. im not sure. if it output that thread blah iteration blah then it ran souporcell so you should have permissions... but the -inf stuff probably is also due to a further upstream issue possibly there are very few or no variant calls? what is the alt.mtx and ref.mtx first few lines?
Ref
Singularity> head /gstore/scratch/u/garfield/souporcell//SAM24416638/ref.mtx
%%MatrixMarket matrix coordinate real general
% written by sprs
172837 1301589 9267869
1 91640 0
1 173540 1
1 263450 1
1 297056 1
1 388529 1
1 478029 1
1 630767 0
Alt
Singularity> head /gstore/scratch/u/garfield/souporcell//SAM24416638/alt.mtx
%%MatrixMarket matrix coordinate real general
% written by sprs
172837 1301589 9267869
1 91640 1
1 173540 0
1 263450 0
1 297056 0
1 388529 0
1 478029 0
1 630767 1
And since we're looking at inputs, the barcodes
Singularity> zcat /gstore/data/genomics/congee_rest_runs/62e1d915d6d7e0bd49c5722c/SAM24416638/output/cellranger_count_601/bf95be34-17b0-4ca5-b2cc-1dfe8bc4a34a/call-run_cellranger_count/shard-0/execution/LIB5456729_SAM24416638/outs/raw_feature_bc_matrix/barcodes.tsv.gz | head
AAACCCAAGAAACACT-1
AAACCCAAGAAACCCA-1
AAACCCAAGAAACTCA-1
AAACCCAAGAAAGAAC-1
AAACCCAAGAAAGCGA-1
AAACCCAAGAACAAGG-1
AAACCCAAGAACACCA-1
AAACCCAAGAACAGGA-1
AAACCCAAGAACCTCC-1
AAACCCAAGAACCTTT-1
(and indeed, was not a permissions thing in the end...I am just bad with singularity)
You should use the filtered barcodes not the raw barcodes file. Only use barcodes that contain cells
I think that should fix it
Is there a facepalm emoji I can be awarded?
I'll give it a go from the start again and close this ticket if it works (as I also expect it will...)