Error running Masurca in the background: how to rectify memory allocation error
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5.7 years ago
VBer ▴ 200

I tried running MaSuRCA for a genome of size 1.278 gbp using the following command:

 nohup bash assemble.sh &

To make sure that the process runs even after the terminal closes. However I am getting the following error:

 [Fri Mar 22 12:19:13 IST 2019] Processing pe library reads
 [Fri Mar 22 12:54:44 IST 2019] Average PE read length 100
 [Fri Mar 22 12:54:45 IST 2019] Using kmer size of 67 for the graph
 [Fri Mar 22 12:54:45 IST 2019] MIN_Q_CHAR: 33
 [Fri Mar 22 12:54:45 IST 2019] Creating mer database for Quorum

 terminate called after throwing an instance of 'std::runtime_error'

 what():  Can't allocate memory for atomic_bits_array

 assemble.sh: line 95: 32713 Broken pipe  awk '{print substr($0,1,200)}' Ae.renamed.fastq
 32714 Aborted                 (core dumped) | quorum_create_database -t 16 -s $JF_SIZE -b 7 -m 24 -q          $((MIN_Q_CHAR + 5)) -o quorum_mer_db.jf.tmp /dev/stdin

 [Fri Mar 22 12:57:08 IST 2019] Error correct PE
   assemble.sh: line 102: 32749 Aborted                 (core dumped) quorum_error_correct_reads -q           
   $(($MIN_Q_CHAR + 40)) --contaminant=/opt/masurca/MaSuRCA-3.3.1/bin/../share/adapter.jf -m 1 -s 1 -g 1 -a 3 -t 16 -w 10 -e 3 -M quorum_mer_db.jf Ae.renamed.fastq --no-discard -o pe.cor.tmp --verbose > quorum.err 2>&1

 [Fri Mar 22 12:57:09 IST 2019] Error correction of PE reads failed. Check pe.cor.log.

I understand that there seems to be some problem with allocating memory. My JF hash size is 10*genome and that ran perfectly fine without using the nohup and & commands, ie., when the process was not running in the background.

I want to know how to rectify this error. Thank you.

Assembly genome • 1.3k views
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