Error running pantera script

Ojwang-Biot commented 2 months ago

Good evening. I am trying to run pantera using the test.gfa file provided. The following is the command I have tried

pantera -g test.gfa -c 10 -o te_library

However, I am getting the following error several times

cat: 'consen*.fa': No such file or directory
Error in nchar(seq) : 
  cannot coerce type 'closure' to vector of type 'character'
Calls: [ -> [.data.table -> eval -> eval -> nchar -> nchar
In addition: Warning messages:
1: In mclapply(rev(zones), process_zone, mc.preschedule = FALSE, mc.cores = opt$cores) :
  148 function calls resulted in an error
2: File '/tmp/RtmpOO0M6C/file1a7c6430d7cd' has size 0. Returning a NULL data.table. 
3: File '/tmp/RtmpOO0M6C/file1a7c1292a3ae' has size 0. Returning a NULL data.table. 
Execution halted

Please help

piosierra commented 2 months ago

Hi, can you try again without using the -c parameter? If that doesn't work, can you try with -c 2? Also, how much memory do you have available?

Ojwang-Biot commented 2 months ago

Hi, I have 16gb of memory. I have tried the option you’ve suggested and still getting the same error.

Kind regards Paul

On Wed, 11 Sep 2024 at 09:51 Pío Sierra @.***> wrote:

Hi, can you try again without using the -c parameter? If that doesn't work, can you try with -c 2? Also, how much memory do you have available?

— Reply to this email directly, view it on GitHub https://github.com/piosierra/pantera/issues/3#issuecomment-2342804054, or unsubscribe https://github.com/notifications/unsubscribe-auth/A3ZJVQ452QATR5DMWUXZHFDZV7R7XAVCNFSM6AAAAABN67R53CVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGNBSHAYDIMBVGQ . You are receiving this because you authored the thread.Message ID: @.***>

piosierra commented 2 months ago

Confirmed that the issue was a corrupt installation of CellaRepertorium, and that it can be installed with the current (3.19) version of Bioconductor.

piosierra / pantera

Error running pantera script #3