Crash in Emirge amplicon

[ctSkennerton]

Rewrites the reads then dies

DONE Rewriting reads with indexes in headers at Thu Apr 18 00:12:57 2013 [0:01:21.308602]...
Number of reads (or read pairs) in input file(s): 3017638
Preallocating reads and quals in memory at Thu Apr 18 00:12:57 2013...
Traceback (most recent call last):
  File "/srv/whitlam/bio/apps/12.04/sw//emirge/0.60/bin/emirge_amplicon.py", line 1543, in <module>
    main()
  File "/srv/whitlam/bio/apps/12.04/sw//emirge/0.60/bin/emirge_amplicon.py", line 1509, in main
    rewrite_reads = not options.no_rewrite_reads)
  File "/srv/whitlam/bio/apps/12.04/sw//emirge/0.60/bin/emirge_amplicon.py", line 221, in __init__
    _emirge.populate_reads_arrays(self)
  File "_emirge_amplicon.pyx", line 525, in _emirge_amplicon.populate_reads_arrays (_emirge_amplicon.c:6577)
IndexError: Out of bounds on buffer access (axis 2)

[ishengtsai]

Hi,

Is there any update to this? I also have the same error:

Number of reads (or read pairs) in input file(s): 236531 Preallocating reads and quals in memory at Mon Mar 23 14:17:59 2015... Traceback (most recent call last): File "/Users/ishengtsai/bin/EMIRGE/emirge_amplicon.py", line 1576, in main() File "/Users/ishengtsai/bin/EMIRGE/emirge_amplicon.py", line 1542, in main rewrite_reads = not options.no_rewrite_reads) File "/Users/ishengtsai/bin/EMIRGE/emirge_amplicon.py", line 221, in init _emirge.populate_reads_arrays(self) File "_emirge_amplicon.pyx", line 525, in _emirge_amplicon.populate_reads_arrays (_emirge_amplicon.c:7016) reads[read_index, readtype_index, i] = base_alpha2int(ks_p.seq.s[i]) IndexError: Out of bounds on buffer access (axis 2)

[csmiller]

Can you post command line and verify in particular what you passed for maximum read length and what your actual maximum read length was? I can't replicate this here, but I think this is saying you have a read that is too long for what the code was expecting.

[f-heeger]

EDIT: I should have read your post carefully in the first place. The longest read in my data was indeed longer than the maximum I gave. Thanks.

Look like I have the same problem My error message is:

EMIRGE started at Fri Aug 7 16:35:16 2015 Rewriting reads with indices in headers at Fri Aug 7 16:35:16 2015... DONE Rewriting reads with indexes in headers at Fri Aug 7 16:35:19 2015 [0:00:02.404193]... Number of reads (or read pairs) in input file(s): 10000 Preallocating reads and quals in memory at Fri Aug 7 16:35:19 2015... Traceback (most recent call last): File "/usr/local/bin/emirge_amplicon.py", line 1576, in main() File "/usr/local/bin/emirge_amplicon.py", line 1542, in main rewrite_reads = not options.no_rewrite_reads) File "/usr/local/bin/emirge_amplicon.py", line 221, in init _emirge.populate_reads_arrays(self) File "_emirge_amplicon.pyx", line 525, in _emirge_amplicon.populate_reads_arrays (_emirge_amplicon.c:7033) IndexError: Out of bounds on buffer access (axis 2)

My command line was:

/usr/local/bin/emirge_amplicon.py enirge_assembly -1 CUB_S4_L001_R1_001.sub.fastq -2 CUB_S4_L001_R2_001.sub.fastq -i 550 -s 15 -f db.fasta -b db.fasta_btindex -l 300 -a 6

Any help in dealing with this would be much appreciated. You tool looks like exactly what I need.

[epruesse]

Closing due to inactivity. The issue is fixed for Emirge 2, which auto-detects the maximum read-length.