"IndexError: list index out of range" in AltAnalyze

[bigcit...@gmail.com]

I am an intern at the National Eye Institute and we are analyzing mouse retina for alternative splicing. When I run AltAnalyze on our samples, it gets near completion then gives an "IndexError: list index out of range" error and quits. 

When I run the program, I choose RNASeq, Mus musculus, RNA-seq aligned read counts; Process RNA-seq reads; named "gMixMouse", files have names such as "062pf_21-WT-1ug__junction.bed" and "062pf_21-WT-1ug__exon.bed", and the folder containing these is what I use for the BED containing folder and the output directory; all other options I leave default except for using "All groups" instead of pairwise comparison.

---

Processing exon/junction coordinates sequentially by chromosome...

* * * * * * * * * * * * * * * * * * * * * * user coordinates imported/processed

Importing read counts from coordinate data...

639710 junction read counts present for Unknown

Normalizing junction expression (RPKM analogue - 60nt length)... finished

854052 exon read counts present for Unknown

Normalizing exon expression (RPKM)... finished

RPKM normalization complete

Imported Junction Statistics:

     683 junctions found in Ensembl/UCSC and 639023 are novel

     8942 trans-splicing junctions found (two aligning Ensembl genes)

     221524 junctions where neither splice-site aligned to a gene

Imported Exon Statistics:

     5547 exons where neither aligned to a gene

User databases and read counts written to: /Users/perezsl/Desktop/Development/Junctions/ExpressionInput

...RNA-seq import completed in 6096 seconds

Beginning to Process the Mm RNASeq dataset

22659 Ensembl GO/pathway annotations imported in 3 seconds

37681 constitutive genes and 1302923 junction IDs imported out of 1303836 lines.

Exon data imported in 25 seconds

Reorganizing expression data into comparison groups for export to down-stream splicing analysis software

Exon data imported in 122 seconds

Exon data imported in 0 seconds

Pairwise comparisons for AltAnalyze exported...

998219 expression and 0 detection p-value filtered junction IDs out of 1302923

998219 junction IDs after detection p-value and expression filtering.

Exon data imported in 11 seconds

Exon data imported in 16 seconds

597848 junction IDs imported with expression values

Steady-state data exported to /Users/perezsl/Desktop/Development/Junctions/ExpressionInput/exp.gMixMouse-steady-state.txt

Reorganizing expression data into comparison groups for export to down-stream splicing analysis software

Exon data imported in 118 seconds

Exon data imported in 1 seconds

Pairwise comparisons for AltAnalyze exported...

Reorganizing expression data into comparison groups for export to down-stream splicing analysis software

Exon data imported in 155 seconds

Exon data imported in 1 seconds

Pairwise comparisons for AltAnalyze exported...

Processing the expression file: /Users/perezsl/Desktop/Development/Junctions/ExpressionInput/counts.gMixMouse-steady-state.txt

14328 IDs imported...beginning to calculate statistics for all group comparisons

Processing the expression file: /Users/perezsl/Desktop/Development/Junctions/ExpressionInput/exp.gMixMouse-steady-state.txt

14328 IDs imported...beginning to calculate statistics for all group comparisons

* * * * * * * * * * * * * * * * * * * * Ensembl-Affymetrix relationships imported

37682 Ensembl Biotypes and 37 housekeeping genes.

Full Dataset with statistics: DATASET-gMixMouse.txt written

Traceback (most recent call last):

  File "/Applications/AltAnalyze/AltAnalyze.app/Contents/Resources/AltAnalyze.py", line 4753, in AltAnalyzeSetup

  File "/Applications/AltAnalyze/AltAnalyze.app/Contents/Resources/AltAnalyze.py", line 4383, in __init__

  File "/Applications/AltAnalyze/AltAnalyze.app/Contents/Resources/AltAnalyze.py", line 5030, in AltAnalyzeMain

  File "ExpressionBuilder.pyc", line 937, in remoteExpressionBuilder

  File "ExpressionBuilder.pyc", line 162, in calculate_expression_measures

  File "ExpressionBuilder.pyc", line 303, in exportDataForGenMAPP

  File "ExpressionBuilder.pyc", line 296, in importSystemCodes

IndexError: list index out of range

...exiting AltAnalyze due to unexpected error

---

The junction files I am using were converted from some Genomatix expression files, so the error may be in my conversion, but I am not extremely familiar with AltAnalyze so I want to make sure I am running it correctly.

Excerpt from a junction.bed file:

chrY 235931 236277 Junc000000016 14 + 235931 236277 255,0,0 2 62,47 0,299

chrY 236345 236980 Junc000000017 13 + 236345 236980 255,0,0 2 55,58 0,577

chrY 237002 246935 Junc000000018 8 + 237002 246935 255,0,0 2 54,44 0,9889

chrY 237014 246927 Junc000000019 1 + 237014 246927 255,0,0 2 42,32 0,9881

chrY 246766 246924 Junc000000020 1 + 246766 246924 255,0,0 2 41,33 0,125

chrY 246993 247138 Junc000000021 1 + 246993 247138 255,0,0 2 36,38 0,107

chrY 246970 247182 Junc000000022 6 + 246970 247182 255,0,0 2 59,53 0,159

chrY 247237 250504 Junc000000023 5 + 247237 250504 255,0,0 2 55,36 0,3231

Exceprt from an exon.bed file:

chr1 134214314 134221529 ENSMUSG00000009772:I2.1_ 0 + 19 1182 7215 0.1638254

chr1 25158374 25168536 ENSMUSG00000033569:I29.1_ 0 - 11 467 10162 0.0459555

chr1 33541654 33568860 ENSMUSG00000026134:I11.1_ 0 - 12 817 27206 0.0300301

chr1 58718307 58723670 ENSMUSG00000047528:I11.1_ 0 - 4 304 5363 0.0566847

chr1 8353715 8404283 ENSMUSG00000025909:I24.1_ 0 - 15 1067 50568 0.0211003

chr1 109051351 109051988 ENSMUSG00000073602:I8.1_ 0 - 0 0 637 0.0000000

chr1 75496750 75498246 ENSMUSG00000026211:I4.1_ 0 - 6 388 1496 0.2593583

If anyone has any idea what could be going wrong, I would greatly appreciate your help.

[Nathan Salomonis]

Greetings,

Looks like one of your original program configuration files was somehow damaged or modified. The program crashes because it is importing one of the lines from this file (should be two columns and less or more found). I have attached the original that you can replace in the folder AltAnalyze_v.2.0.6/Config. 

As a side note, the latest version of AltAnalyze is now out and has a number of new analyses available. 

Best,

Nathan

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