Error: libc++abi.dylib: terminating with uncaught exception of type std::out_of_range: basic_string #55
Description
- OS: OS X
- Command:
bcalm -in "hg38/hg38.fna" -out "hg38/hg38.bc31.fa" -kmer-size "31" -nb-cores "1" -abundance-min 1 - Dataset: http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz
BCALM 2, git commit c8ac60252fa0b2abf511f7363cff7c4342dac2ee
setting storage type to hdf5
[Approximating frequencies of minimizers ] 100 % elapsed: 0 min 10 sec remaining: 0 min 0 sec cpu: 99.8 % mem: [6721, 6721, 0] MB
[DSK: Collecting stats on hg38 ] 100 % elapsed: 0 min 14 sec remaining: 0 min 0 sec cpu: 99.9 % mem: [1049, 1107, 0] MB
[DSK: nb solid kmers found : 2503985560 ] 100 % elapsed: 9 min 8 sec remaining: 0 min 0 sec cpu: 94.2 % mem: [1584, 8561, 0] MB
bcalm_algo params, prefix:hg38/hg38.bc31.fa.unitigs.fa k:31 a:1 minsize:10 threads:1 mintype:1
DSK used 1 passes and 3 partitions
prior to queues allocation 15:44:10 memory [current, maxRSS]: [1593, 0] MB
Starting BCALM2 15:44:10 memory [current, maxRSS]: [1593, 0] MB
[Iterating DSK partitions ] 0 % elapsed: 0 min 0 sec remaining: 0 min 0 sec
Iterated 887340388 kmers, among them 143140847 were doubled
In this superbucket (containing 242671 active minimizers), sum of time spent in lambda's: 1475479.9 msecs
longest lambda: 610.8 msecs
tot time of best scheduling of lambdas: 1475479.9 msecs
best theoretical speedup: 2415.7x
Done with partition 0 16:18:30 memory [current, maxRSS]: [25559, 0] MB
Iterated 903788377 kmers, among them 123275495 were doubled
Loaded 40462618 doubled kmers for partition 1
In this superbucket (containing 59110 active minimizers), [0/1873]
sum of time spent in lambda's: 1558374.0 msecs
longest lambda: 1442.2 msecs
tot time of best scheduling of lambdas: 1558374.0 msecs
best theoretical speedup: 1080.6x
Done with partition 1 16:55:08 memory [current, maxRSS]: [15037, 0] MB
[Iterating DSK partitions ] 33.3 % elapsed: 70 min 58 sec remaining: 141 min 55 sec
Iterated 712856795 kmers, among them 126149961 were doubled
Loaded 70376914 doubled kmers for partition 2
In this superbucket (containing 198005 active minimizers),
sum of time spent in lambda's: 2675057.4 msecs
longest lambda: 1654.8 msecs
tot time of best scheduling of lambdas: 2675057.4 msecs
best theoretical speedup: 1616.5x
Done with partition 2 17:47:00 memory [current, maxRSS]: [21140, 0] MB
[Iterating DSK partitions ] 100 % elapsed: 122 min 50 sec remaining: 0 min 0 sec
Number of sequences in glue: 431789853
Number of pre-tips removed : 0
Buckets compaction and gluing : 7369.8 secs
Within that,
creating buckets from superbuckets: 1659.4 secs
bucket compaction (wall-clock during threads): 5710.3 secs
within all bucket compaction threads,
adding nodes to subgraphs: 1570.5 secs
subgraphs constructions and compactions: 1722.2 secs
compacted nodes redistribution: 2416.1 secs
Sum of CPU times for bucket compactions: 7368.2 secs
Discrepancy between sum of fine-grained timings and total wallclock of buckets compactions step: 1.5 secs
BCALM total wallclock (excl kmer counting): 7369.9 secs
Maximum number of kmers in a subgraph: 62422
Performance of compaction step:
Wallclock time spent in parallel section : 5710.3 secs
Best theoretical speedup in parallel section : 1676.8x
Best theor. speedup in parallel section using 1 threads : 1.0x
Sum of longest bucket compaction for each sb : 3.7 secs
Sum of best scheduling for each sb : 5708.9 secs
Done with all compactions 17:47:00 memory [current, maxRSS]: [21131, 0] MB
bglue_algo params, prefix:hg38/hg38.bc31.fa.unitigs.fa k:31 threads:1
Starting bglue with 1 threads 17:47:02 memory [current, maxRSS]: [ 88, 0] MB
number of sequences to be glued: 431789853 17:47:02 memory [current, maxRSS]: [ 88, 0] MB
libc++abi.dylib: terminating with uncaught exception of type std::out_of_range: basic_string
/bin/bash: line 1: 18662 Abort trap: 6 bcalm -in "hg38/hg38.fna" -out "hg38/hg38.bc31.fa" -kmer-size "31" -nb-cores "1" -abundance-min 1