snikumbh / seqarchr Goto Github PK

If you encounter an error similar to the one below, you probably have an older version of BiocParallel. See this issue:Bioconductor/BiocParallel#237

Error in manager$availability[[as.character(result$node)]] <- TRUE : 
  wrong args for environment subassignment
Calls: <Anonymous> ... .bploop_impl -> .collect_result -> .manager_recv -> .manager_recv
In addition: Warning message:
...
Execution halted
Error in serialize(data, node$con, xdr = FALSE) : ignoring SIGPIPE signal
Calls: <Anonymous> ... .send_to -> <Anonymous> -> sendData.SOCK0node -> serialize

As mentioned, updating BiocParallel to 1.32.5 (release version) should make the error go away!

This solution has worked on my side.

Hi, I was trying to run seqArchR for around 12k regions of 80bp using the parameters on the vignettes, setting the cores to 64. I left it running for 3 hours but did not finish, so I thought maybe there is something wrong. When I turned off parallelization, it works but runs slowly, maybe around 1-2 min for each chunk. Is this normal?

thanks for nice tool, i would be happy to get any helps regarding to BiocParallel error , I installed and ran everything according to the instruction based on the Vignettes, it comes with this error:

BiocParallel errors
1 remote errors, element index: 1
0 unevaluated and other errors
first remote error:
Error:

Thanks
Iman