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Thread terminated abnormally for ESPRESSO_Q #49

Closed shiny-prize closed 4 months ago

shiny-prize commented 4 months ago

Hello while running my nanopore data by ESPRESSO_Q, there are some errors.

My command is like below : perl /data/Storage_DAS02/home2/shinsy/.conda/pkgs/espresso-1.4.0-hdfd78af_0/bin/ESPRESSO_Q.pl -A ../reference/gencode.v21.annotation.gtf -L cancer_samples.tsv.updated -V cancer_compatible_isoform.tsv

Thread 5 terminated abnormally: call for /data/Storage_DAS02/home2/shinsy/.conda/envs/espresso/bin/perl /data/Storage_DAS02/home2/shinsy/.conda/pkgs/espresso-1.4.0-hdfd78af_0/bin/ESPRESSO_Q_Thread.pm ./thread_shared_arguments.tmp ./thread_chr11_arguments.tmp exited with return_code: 9 Exiting due to error in worker thread Perl exited with active threads: 4 running and unjoined 0 finished and unjoined 0 running and detached

Thank you for your help.

EricKutschera commented 4 months ago

Can you post the full output from the command? The error message is Thread 5 terminated abnormally. Usually there is another error message printed out before that one which gives a reason. Another possibility is that the thread ran out of memory. You could try watching the memory usage in htop when ESPRESSO is running to see how much memory it's using

shiny-prize commented 4 months ago

Thank you for your attention. Actually, I just solved the problem by using just only one thread. Maybe it could be a problem for our computer sever or etc.