mwykes
commented
4 years ago Hi @ccbruels, Illegal instruction messages typically occur when racon is compiled on a CPU which supports a certain instruction set and then used on another (typically older) CPU which does not support that instruction set. This has affected racon users before. How did you install pomoxis? If you install pomoxis with make install, we use the -mno-avx2 flags to compile racon to try to avoid this. If you did install with make install, I would recommend removing completely your pomoxis repo, recloning and running a fresh make install on the oldest node on your cluster.
Hi, I've tried to run several versions of pomoxis (the info is from v. 0.3.2), on a linux compute cluster in an sbatch script. The command I use is: mini_assemble -i $READS -t 30. Any thoughts on what might be going wrong?
The output files are: total 10485624 20 Feb 20 16:38 racon_1_1.fa.gz 10701156352 Feb 20 16:38 core.57211 123399808 Feb 20 16:30 reads2contigs_1_1.paf.gz 56765084 Feb 20 16:28 reads.gfa.fa.gz 2182392876 Feb 20 15:29 reads.fa.gz
Everything seems to run fine, then I get this info before the error: [M::main] CMD: minimap2 -K 500M -t 30 reads.gfa.fa.gz reads.fa.gz [M::main] Real time: 137.471 sec; CPU: 2542.682 sec; Peak RSS: 2.415 GB [racon::Polisher::initialize] loaded target sequences 3.306026 s [racon::Polisher::initialize] loaded sequences 126.045216 s [racon::Polisher::initialize] loaded overlaps 11.698260 s [racon::Polisher::initialize] aligning overlaps [=====> ] 66.562001 s [racon::Polisher::initialize] aligning overlaps [==========> ] 109.589898 s [racon::Polisher::initialize] aligning overlaps [================> ] 150.993377 s [racon::Polisher::initialize] aligning overlaps [====================] 192.331360 s [racon::Polisher::initialize] transformed data into windows 6.027842 s /apps/pomoxis/0.3.2/bin/mini_assemble: line 206: 57211 Illegal instruction (core dumped) racon ${BASERACON OPTS} ${ADDRACONOPTS} -w ${MOD_WINDOW_LEN} -t ${THREADS} -q -1 ${SHUFREADS} ${READS2TIGS} ${SCAFFOLD} 57212 Done | gzip -1 > ${NEWSCAF}