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View Code? Open in Web Editor NEWNextflow pipeline for pathogen surveillance in wastewater
License: GNU General Public License v3.0
Nextflow pipeline for pathogen surveillance in wastewater
License: GNU General Public License v3.0
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=""
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.
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