racon: Illegal instruction (core dumped) racon
Hi, I got the below error when I tried to assemble genomic R genes
/var/spool/PBS/mom_priv/jobs/3178843.pbs.SC: line 39: 146216 Illegal instruction (core dumped) racon -t 8 input.fasta output.gfa1.sam output.gfa.fasta > output.racon1.fasta
source activate sra-tools
fastq-dump ERR2168704
bioawk -c fastx '{print ">"$name; print $seq}' ERR2168704.fastq > input.fasta
source activate minimap2
minimap2 -t 8 -x ava-pb \
input.fasta \
input.fasta | gzip -1 > output.paf.gz
source activate miniasm
miniasm -Rc2 -f \
input.fasta \
output.paf.gz > output.gfa
awk '/^S/{print ">"$2"\n"$3}' output.gfa | fold > output.gfa.fasta
# Correction 1
source activate minimap2
minimap2 -t 8 -ax map-pb \
output.gfa.fasta \
input.fasta > output.gfa1.sam
source activate racon
racon -t 8 \
input.fasta \
output.gfa1.sam \
output.gfa.fasta > output.racon1.fasta
# Correction 2
source activate minimap2
minimap2 -t 8 -ax map-pb \
output.racon1.fasta \
input.fasta > output.gfa2.sam
source activate racon
racon -t 8 \
input.fasta \
output.gfa2.sam \
output.racon1.fasta > output.racon2.fasta
[M::mm_idx_gen::35.606*1.65] collected minimizers
[M::mm_idx_gen::39.729*2.26] sorted minimizers
[M::main::39.729*2.26] loaded/built the index for 469719 target sequence(s)
[M::mm_mapopt_update::41.369*2.21] mid_occ = 597
[M::mm_idx_stat] kmer size: 19; skip: 5; is_hpc: 1; #seq: 469719
[M::mm_idx_stat::42.310*2.18] distinct minimizers: 101023797 (61.53% are singletons); average occurrences: 3.340; average spacing: 4.347
[M::worker_pipeline::368.045*7.04] mapped 161023 sequences
[M::worker_pipeline::621.020*6.72] mapped 159527 sequences
[M::worker_pipeline::672.753*6.24] mapped 149169 sequences
[M::main] Version: 2.10-r761
[M::main] CMD: minimap2 -t 8 -x ava-pb input.fasta input.fasta
[M::main] Real time: 673.074 sec; CPU: 4200.740 sec
[M::main] ===> Step 0: removing contained reads <===
[M::ma_hit_no_cont::278.347*1.00] dropped 855 contained reads
[M::main] ===> Step 1: reading read mappings <===
[M::ma_hit_read::576.014*1.00] read 176421820 hits; stored 90012178 hits and 375806 sequences (1248134545 bp)
[M::main] ===> Step 2: 1-pass (crude) read selection <===
[M::ma_hit_sub::591.438*1.00] 371908 query sequences remain after sub
[M::ma_hit_cut::592.852*1.00] 89672449 hits remain after cut
[M::ma_hit_flt::594.513*1.00] 89657415 hits remain after filtering; crude coverage after filtering: 83.95
[M::main] ===> Step 3: 2-pass (fine) read selection <===
[M::ma_hit_sub::599.960*1.00] 371268 query sequences remain after sub
[M::ma_hit_cut::601.356*1.00] 89535413 hits remain after cut
[M::ma_hit_contained::603.293*1.00] 18886 sequences and 177452 hits remain after containment removal
[M::main] ===> Step 4: graph cleaning <===
[M::ma_sg_gen] read 144250 arcs
[M::main] ===> Step 4.1: transitive reduction <===
[M::asg_arc_del_trans] transitively reduced 102012 arcs
[M::asg_arc_del_multi] removed 17 multi-arcs
[M::asg_arc_del_asymm] removed 5037 asymmetric arcs
[M::main] ===> Step 4.2: initial tip cutting and bubble popping <===
[M::asg_cut_tip] cut 4981 tips
[M::asg_pop_bubble] popped 327 bubbles and trimmed 160 tips
[M::main] ===> Step 4.3: cutting short overlaps (3 rounds in total) <===
[M::asg_arc_del_multi] removed 0 multi-arcs
[M::asg_arc_del_asymm] removed 6 asymmetric arcs
[M::asg_arc_del_short] removed 6 short overlaps
[M::asg_cut_tip] cut 462 tips
[M::asg_pop_bubble] popped 59 bubbles and trimmed 33 tips
[M::asg_arc_del_multi] removed 0 multi-arcs
[M::asg_arc_del_asymm] removed 39 asymmetric arcs
[M::asg_arc_del_short] removed 45 short overlaps
[M::asg_cut_tip] cut 172 tips
[M::asg_pop_bubble] popped 54 bubbles and trimmed 14 tips
[M::asg_arc_del_multi] removed 0 multi-arcs
[M::asg_arc_del_asymm] removed 73 asymmetric arcs
[M::asg_arc_del_short] removed 95 short overlaps
[M::asg_cut_tip] cut 95 tips
[M::asg_pop_bubble] popped 51 bubbles and trimmed 10 tips
[M::main] ===> Step 4.4: removing short internal sequences and bi-loops <===
[M::asg_cut_internal] cut 250 internal sequences
[M::asg_cut_biloop] cut 389 small bi-loops
[M::asg_cut_tip] cut 71 tips
[M::asg_pop_bubble] popped 33 bubbles and trimmed 21 tips
[M::main] ===> Step 4.5: aggressively cutting short overlaps <===
[M::asg_arc_del_multi] removed 0 multi-arcs
[M::asg_arc_del_asymm] removed 113 asymmetric arcs
[M::asg_arc_del_short] removed 185 short overlaps
[M::asg_cut_tip] cut 78 tips
[M::asg_pop_bubble] popped 32 bubbles and trimmed 21 tips
[M::main] ===> Step 5: generating unitigs <===
[M::main] Version: 0.2-r168-dirty
[M::main] CMD: miniasm -Rc2 -f input.fasta output.paf.gz
[M::main] Real time: 604.810 sec; CPU: 604.708 sec
[M::mm_idx_gen::0.182*0.99] collected minimizers
[M::mm_idx_gen::0.229*1.08] sorted minimizers
[M::main::0.230*1.08] loaded/built the index for 990 target sequence(s)
[M::mm_mapopt_update::0.241*1.07] mid_occ = 44
[M::mm_idx_stat] kmer size: 19; skip: 10; is_hpc: 1; #seq: 990
[M::mm_idx_stat::0.248*1.07] distinct minimizers: 541012 (92.58% are singletons); average occurrences: 1.194; average spacing: 8.030
[M::worker_pipeline::108.097*7.78] mapped 161023 sequences
[M::worker_pipeline::210.412*7.88] mapped 159527 sequences
[M::worker_pipeline::302.381*7.85] mapped 149169 sequences
[M::main] Version: 2.10-r761
[M::main] CMD: minimap2 -t 8 -ax map-pb output.gfa.fasta input.fasta
[M::main] Real time: 302.401 sec; CPU: 2373.175 sec
/var/spool/PBS/mom_priv/jobs/3178843.pbs.SC: line 39: 146216 Illegal instruction (core dumped) racon -t 8 input.fasta output.gfa1.sam output.gfa.fasta > output.racon1.fasta
[M::mm_idx_gen::0.002*1.57] collected minimizers
[M::mm_idx_gen::0.003*1.37] sorted minimizers
[M::main::0.003*1.18] loaded/built the index for 0 target sequence(s)
[M::mm_mapopt_update::0.003*1.18] mid_occ = 0
[M::mm_idx_stat] kmer size: 19; skip: 10; is_hpc: 1; #seq: 0
[M::mm_idx_stat::0.003*1.18] distinct minimizers: 0 (-nan% are singletons); average occurrences: -nan; average spacing: -nan
[M::worker_pipeline::4.009*5.12] mapped 161023 sequences
[M::worker_pipeline::5.909*6.04] mapped 159527 sequences
[M::worker_pipeline::7.427*5.91] mapped 149169 sequences
[M::main] Version: 2.10-r761
[M::main] CMD: minimap2 -t 8 -ax map-pb output.racon1.fasta input.fasta
[M::main] Real time: 7.431 sec; CPU: 43.919 sec
/var/spool/PBS/mom_priv/jobs/3178843.pbs.SC: line 51: 146264 Illegal instruction (core dumped) racon -t 8 input.fasta output.gfa2.sam output.racon1.fasta > output.racon2.fasta
What did I miss?
Thank you in advance,
Michal
About this issue
- Original URL
- State: closed
- Created 6 years ago
- Comments: 17
yes … i had reinstalled the older version and installed racon with conda (new environment) and it worked! Thanks for you help @rvaser
Have a great day!
Has been solved with
#PBS -l cpuarch=avx2