You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
Pipeline terminates prematurely while performing group by operation with data.table on file of 100745 observations in mutation_watchlist.R.
Error executing process > 'collectTables (Generate mutation frequency and collapse into regional estimates)'
Caused by:
Process `collectTables (Generate mutation frequency and collapse into regional estimates)` terminated with an error exit status (134)
Command executed:
Rscript bin/mutation_watchlist.R --concat_mutations=mutation_tables.csv --outdir=""
Command exit status:
134
Command output:
(empty)
Command error:
address 0x8d62eb8, cause 'memory not mapped'
*** caught segfault ***
address 0x8e62e08, cause 'memory not mapped'
*** caught segfault ***
address 0x8e22e0c, cause 'memory not mapped'
*** caught segfault ***
address 0x8d22e3c, cause 'memory not mapped'
address 0x8da2e2c, cause 'memory not mapped'
*** caught segfault ***
address 0x8f62f08, cause 'memory not mapped'
*** caught segfault ***
address 0x8ee2e10, cause 'memory not mapped'
Traceback:
1: forderv(firstofeachgroup)
2: `[.data.table`(dt_clean, , .(VAF = round((sum(AO)/sum(DP)), digits = 4)), by = .(LOCATION, COLLECTION_DATE, ANNO))
*** caught segfault ***
address 0x8ea2e0c, cause 'memory not mapped'
*** caught segfault ***
address 0x8fa2df4, cause 'memory not mapped'
Error: no more error handlers available (recursive errors?); invoking 'abort' restart
3: dt_clean[, .(VAF = round((sum(AO)/sum(DP)), digits = 4)), by = .(LOCATION, COLLECTION_DATE, ANNO)]
Traceback:
Traceback:
*** caught segfault ***
address 0x8c62e40, cause 'memory not mapped'
An irrecoverable exception occurred. R is aborting now ...
Error: no more error handlers available (recursive errors?); invoking 'abort' restart
*** caught segfault ***
address 0x8de2e10, cause 'memory not mapped'
Traceback:
1:
Traceback:
Execution halted
*** stack smashing detected ***: <unknown> terminated
An irrecoverable exception occurred. R is aborting now ...
Error: bad value
.command.sh: line 2: 2713426 Aborted (core dumped) Rscript bin/mutation_watchlist.R --concat_mutations=mutation_tables.csv --outdir=""
tested script outside of Nextflow in environment envs/vcf_2_table.yml and completed successfully with expected outputs
adjusting memory setting in collectTables process within nextflow.config (memory = '100 GB') did not resolve
change threads in setDTthreads() to 20 - sets the number of threads to be used in data.table functions that are parallelized, which resolved issue.
error reproduced 5 times at 80 threads.
successful completion reproduced 5 times at 60 threads.
It seems as setDTthreads decreases, probability of successful completion increases (at the cost of duration). DT threads are now set to 60 in mutation_watchlist.R. This may need to be adjusted as dataset increases.
The text was updated successfully, but these errors were encountered:
Pipeline terminates prematurely while performing group by operation with data.table on file of 100745 observations in mutation_watchlist.R.
It seems as setDTthreads decreases, probability of successful completion increases (at the cost of duration). DT threads are now set to 60 in mutation_watchlist.R. This may need to be adjusted as dataset increases.
The text was updated successfully, but these errors were encountered: