IndexError: Out of bounds on buffer access (axis 0)

[Kelley Núñez]

Hello,

  I have been getting this error: IndexError: Out of bounds on buffer access (axis 0).  I've read the other forums and tried moving everything to a different directory but the problem still remains. Is there another reason for this error? My output is below. Thanks anyone that can help.

imported _emirge C functions from: /home/kgwin1/packages/EMIRGE/install/lib/python2.7/site-packages/_emirge.so
Command:
/home/kgwin1/packages/EMIRGE/install/bin/emirge.py /work/kgwin1/empty/emirge_output_shawns602 -1 /work/kgwin1/empty/602_R1_R2_trim_0.05_noNs_len90_forEMIRGE.fastq -f /work/kgwin1/empty/SSURef_111_NR_tax_silva_trunc.ge1200bp.le2000bp.fixed.sorted.97.fasta -b /work/kgwin1/empty/SSU_Ref_111_db_btindex -l 142 --phred33

EMIRGE started at Tue Apr 15 10:59:00 2014
Time loading forward index: 00:00:24
Time loading mirror index: 00:00:24
[samopen] SAM header is present: 150807 sequences.
Seeded quality full-index search: 00:02:08
# reads processed: 172326
# reads with at least one reported alignment: 49969 (29.00%)
# reads that failed to align: 122357 (71.00%)
Reported 49969 alignments to 1 output stream(s)
Time searching: 00:02:56
Overall time: 00:02:56
Performing initial mapping with command:
cat  /work/kgwin1/empty/602_R1_R2_trim_0.05_noNs_len90_forEMIRGE.fastq |  bowtie --phred33-quals -t -p 1 -n 3 -l 20 -e 300 --best --sam --chunkmbs 128  /work/kgwin1/empty/SSU_Ref_111_db_btindex - | samtools view -b -S -u -F 0x0004 - > /work/kgwin1/empty/emirge_output_shawns602/initial_mapping/initial_bowtie_mapping.PE.bam
Beginning initialization at Tue Apr 15 11:01:56 2014...
Reading bam file /work/kgwin1/empty/emirge_output_shawns602/initial_mapping/initial_bowtie_mapping.PE.bam at Tue Apr 15 11:01:56 2014...
DONE Reading bam file /work/kgwin1/empty/emirge_output_shawns602/initial_mapping/initial_bowtie_mapping.PE.bam at Tue Apr 15 11:01:59 2014 [0:00:02.980176]...
DONE with initialization at Tue Apr 15 11:01:59 2014...
Starting iteration 0 at Tue Apr 15 11:01:59 2014...
Reading bam file /work/kgwin1/empty/emirge_output_shawns602/initial_mapping/initial_bowtie_mapping.PE.bam at Tue Apr 15 11:01:59 2014...
DONE Reading bam file /work/kgwin1/empty/emirge_output_shawns602/initial_mapping/initial_bowtie_mapping.PE.bam at Tue Apr 15 11:02:01 2014 [0:00:02.035173]...
Calculating likelihood (1854, 46525) for iteration 0 at Tue Apr 15 11:02:01 2014...
     Calculating Pr(N=n) for iteration 0 at Tue Apr 15 11:02:01 2014...
     DONE calculating Pr(N=n) for iteration 0 at Tue Apr 15 11:02:04 2014 [0:00:03.205593]...
Traceback (most recent call last):
  File "/home/kgwin1/packages/EMIRGE/install/bin/emirge.py", line 1697, in <module>
    main()
  File "/home/kgwin1/packages/EMIRGE/install/bin/emirge.py", line 1688, in main
    do_iterations(em, max_iter = options.iterations, save_every = options.save_every)
  File "/home/kgwin1/packages/EMIRGE/install/bin/emirge.py", line 1439, in do_iterations
    em.do_iteration(em.current_bam_filename, em.current_reference_fasta_filename)
  File "/home/kgwin1/packages/EMIRGE/install/bin/emirge.py", line 491, in do_iteration
    self.calc_likelihoods()
  File "/home/kgwin1/packages/EMIRGE/install/bin/emirge.py", line 1141, in calc_likelihoods
    lik_data)
  File "_emirge.pyx", line 130, in _emirge._calc_likelihood (_emirge.c:2580)
IndexError: Out of bounds on buffer access (axis 0) 

[ruthmi...@gmail.com]

Hi,

I have been getting a very similar error, which I will paste in below.

I was wondering whether anyone ever followed up on this? Kelley - did you work out a solution?

Thanks,

Ruth

I am calling:

emirge.py /projects4/ruth/rat_metagenomics/raw_rat/set1/cutadapt1.3/prinseq -1 HI.0931.002.Index_22.630F_R1.cutadapt.fastq.pass_CPNHBS_50_to_rn5_unmapped.fa_prinseqGOOD_1.fastq  -f /projects2/ref_databases/SILVA/v115/bowtiedb/LSURef_115_SSURef_NR99_nogaps.fasta -b /projects2/ref_databases/SILVA/v115/bowtiedb_V1/LSURef_115_SSURef_NR99_nogaps -l 100 -2 HI.0931.002.Index_22.630F_R1.cutadapt.fastq.pass_CPNHBS_50_to_rn5_unmapped.fa_prinseqGOOD_2.fastq -i 169 -s 52 --phred33

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The error I am getting is:

EMIRGE started at Tue May 13 12:33:29 2014

Time loading reference: 00:00:02

Time loading forward index: 00:00:02

Time loading mirror index: 00:00:03

[samopen] SAM header is present: 519138 sequences.

Seeded quality full-index search: 01:00:03

# reads processed: 4016220

# reads with at least one reported alignment: 2382145 (59.31%)

# reads that failed to align: 1634075 (40.69%)

Reported 2382145 paired-end alignments to 1 output stream(s)

Time searching: 01:00:10

Overall time: 01:00:10

Performing initial mapping with command:

cat  /projects4/ruth/rat_metagenomics/raw_rat/set1/cutadapt1.3/prinseq/LSUSSUremoved_bowtie2/HI.0931.002.Index_22.630F_R1.cutadapt.fastq.pass_CPNHBS_50_to_rn5_unmapped.fa_prinseqGOOD_1.fastq_to_LSUSSUrRNA_mapped_R1.fastq |  bowtie --phred33-quals -t -p 1 -n 3 -l 2

0 -e 300 --best --sam --chunkmbs 128 --minins 100 --maxins 278 /projects2/ref_databases/SILVA/v115/bowtiedb_V1/LSURef_115_SSURef_NR99_nogaps -1 - -2 /projects4/ruth/rat_metagenomics/raw_rat/set1/cutadapt1.3/prinseq/LSUSSUremoved_bowtie2/HI.0931.002.Index_22.630F_R

1.cutadapt.fastq.pass_CPNHBS_50_to_rn5_unmapped.fa_prinseqGOOD_1.fastq_to_LSUSSUrRNA_mapped_R2.fastq | samtools view -b -S -u -F 0x0004 - > /projects4/ruth/rat_metagenomics/raw_rat/set1/cutadapt1.3/prinseq/initial_mapping/initial_bowtie_mapping.PE.bam 

Beginning initialization at Tue May 13 13:33:39 2014...

Reading bam file /projects4/ruth/rat_metagenomics/raw_rat/set1/cutadapt1.3/prinseq/initial_mapping/initial_bowtie_mapping.PE.bam at Tue May 13 13:33:39 2014...

DONE Reading bam file /projects4/ruth/rat_metagenomics/raw_rat/set1/cutadapt1.3/prinseq/initial_mapping/initial_bowtie_mapping.PE.bam at Tue May 13 13:38:24 2014 [0:04:44.844242]...

DONE with initialization at Tue May 13 13:38:53 2014...

Starting iteration 0 at Tue May 13 13:38:53 2014...

Reading bam file /projects4/ruth/rat_metagenomics/raw_rat/set1/cutadapt1.3/prinseq/initial_mapping/initial_bowtie_mapping.PE.bam at Tue May 13 13:38:53 2014...

DONE Reading bam file /projects4/ruth/rat_metagenomics/raw_rat/set1/cutadapt1.3/prinseq/initial_mapping/initial_bowtie_mapping.PE.bam at Tue May 13 13:47:33 2014 [0:08:40.518353]...

Calculating likelihood (71347, 4764290) for iteration 0 at Tue May 13 13:47:35 2014...

        Calculating Pr(N=n) for iteration 0 at Tue May 13 13:47:35 2014...

Traceback (most recent call last):

  File "/usr/local/bin/emirge.py", line 1697, in <module>

    main()

  File "/usr/local/bin/emirge.py", line 1688, in main

    do_iterations(em, max_iter = options.iterations, save_every = options.save_every)

  File "/usr/local/bin/emirge.py", line 1439, in do_iterations

    em.do_iteration(em.current_bam_filename, em.current_reference_fasta_filename)

  File "/usr/local/bin/emirge.py", line 491, in do_iteration

    self.calc_likelihoods()

  File "/usr/local/bin/emirge.py", line 1099, in calc_likelihoods

    self.calc_probN()   # (handles initial iteration differently within this method)

  File "/usr/local/bin/emirge.py", line 1245, in calc_probN

    self.probN)

  File "_emirge.pyx", line 243, in _emirge._calc_probN (_emirge.c:3850)

    probN_single[pos + i, j] += qual2p_div_3[qualints_single[i]] * weight

IndexError: Out of bounds on buffer access (axis 0)

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[vinu manikandan]

Did any one found the fix for this problem? If so please do post the same