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Re: [Seqan-dev] Fatal Error in Banded Chain Alignment Traceback

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Thanks Rene,

My query, reference, and canonical alignment from BLASR (the PacBio-specific aligner) attached.

I also noticed that the seeds it's chaining with chainGlobalAlignment() are way off the diagonal, which may be related - details below: 

"""
Query #1 - m130404_014004_sidney_c100506902550000001823076808221337_s1_p0/5779/0_10397
Finished finding seeds
Seeds: 1939
Finishing chaining seeds
Chain: 44
Seed<Simple, TConfig>(7688, 57, 7706, 75, lower diag = 7631, upper diag = 7631) Length: 18
Seed<Simple, TConfig>(7707, 94, 7722, 109, lower diag = 7613, upper diag = 7613) Length: 15
Seed<Simple, TConfig>(7933, 111, 7946, 124, lower diag = 7822, upper diag = 7822) Length: 13
Seed<Simple, TConfig>(7949, 130, 7965, 146, lower diag = 7819, upper diag = 7819) Length: 16
Seed<Simple, TConfig>(8065, 299, 8078, 312, lower diag = 7766, upper diag = 7766) Length: 13
Seed<Simple, TConfig>(8109, 314, 8126, 331, lower diag = 7795, upper diag = 7795) Length: 17
Seed<Simple, TConfig>(8169, 363, 8181, 375, lower diag = 7806, upper diag = 7806) Length: 12
Seed<Simple, TConfig>(8208, 381, 8222, 395, lower diag = 7827, upper diag = 7827) Length: 14
Seed<Simple, TConfig>(8222, 402, 8234, 414, lower diag = 7820, upper diag = 7820) Length: 12
Seed<Simple, TConfig>(8287, 446, 8304, 463, lower diag = 7841, upper diag = 7841) Length: 17
Seed<Simple, TConfig>(8304, 466, 8316, 478, lower diag = 7838, upper diag = 7838) Length: 12
Seed<Simple, TConfig>(8326, 748, 8338, 760, lower diag = 7578, upper diag = 7578) Length: 12
Seed<Simple, TConfig>(8354, 761, 8366, 773, lower diag = 7593, upper diag = 7593) Length: 12
Seed<Simple, TConfig>(8426, 801, 8438, 813, lower diag = 7625, upper diag = 7625) Length: 12
Seed<Simple, TConfig>(8702, 2291, 8721, 2310, lower diag = 6411, upper diag = 6411) Length: 19
Seed<Simple, TConfig>(8769, 2314, 8781, 2326, lower diag = 6455, upper diag = 6455) Length: 12
Seed<Simple, TConfig>(8794, 2387, 8806, 2399, lower diag = 6407, upper diag = 6407) Length: 12
Seed<Simple, TConfig>(8835, 2400, 8847, 2412, lower diag = 6435, upper diag = 6435) Length: 12
Seed<Simple, TConfig>(9162, 2650, 9174, 2662, lower diag = 6512, upper diag = 6512) Length: 12
Seed<Simple, TConfig>(9184, 2676, 9196, 2688, lower diag = 6508, upper diag = 6508) Length: 12
Seed<Simple, TConfig>(9196, 2736, 9208, 2748, lower diag = 6460, upper diag = 6460) Length: 12
Seed<Simple, TConfig>(9223, 2818, 9235, 2830, lower diag = 6405, upper diag = 6405) Length: 12
Seed<Simple, TConfig>(9251, 2844, 9267, 2860, lower diag = 6407, upper diag = 6407) Length: 16
Seed<Simple, TConfig>(9294, 2871, 9308, 2885, lower diag = 6423, upper diag = 6423) Length: 14
Seed<Simple, TConfig>(9314, 2891, 9327, 2904, lower diag = 6423, upper diag = 6423) Length: 13
Seed<Simple, TConfig>(9432, 2976, 9447, 2991, lower diag = 6456, upper diag = 6456) Length: 15
Seed<Simple, TConfig>(9515, 2992, 9527, 3004, lower diag = 6523, upper diag = 6523) Length: 12
Seed<Simple, TConfig>(9675, 3385, 9701, 3411, lower diag = 6290, upper diag = 6290) Length: 26
Seed<Simple, TConfig>(9724, 3414, 9736, 3426, lower diag = 6310, upper diag = 6310) Length: 12
Seed<Simple, TConfig>(9791, 3571, 9804, 3584, lower diag = 6220, upper diag = 6220) Length: 13
Seed<Simple, TConfig>(9805, 3596, 9817, 3608, lower diag = 6209, upper diag = 6209) Length: 12
Seed<Simple, TConfig>(9818, 4915, 9830, 4927, lower diag = 4903, upper diag = 4903) Length: 12
Seed<Simple, TConfig>(9842, 4939, 9854, 4951, lower diag = 4903, upper diag = 4903) Length: 12
Seed<Simple, TConfig>(9873, 5045, 9885, 5057, lower diag = 4828, upper diag = 4828) Length: 12
Seed<Simple, TConfig>(9886, 5077, 9898, 5089, lower diag = 4809, upper diag = 4809) Length: 12
Seed<Simple, TConfig>(9943, 5242, 9955, 5254, lower diag = 4701, upper diag = 4701) Length: 12
Seed<Simple, TConfig>(9957, 5385, 9969, 5397, lower diag = 4572, upper diag = 4572) Length: 12
Seed<Simple, TConfig>(9994, 5423, 10006, 5435, lower diag = 4571, upper diag = 4571) Length: 12
Seed<Simple, TConfig>(10062, 7096, 10074, 7108, lower diag = 2966, upper diag = 2966) Length: 12
Seed<Simple, TConfig>(10102, 7109, 10114, 7121, lower diag = 2993, upper diag = 2993) Length: 12
Seed<Simple, TConfig>(10156, 7131, 10178, 7153, lower diag = 3025, upper diag = 3025) Length: 22
Seed<Simple, TConfig>(10277, 7354, 10299, 7376, lower diag = 2923, upper diag = 2923) Length: 22
Seed<Simple, TConfig>(10299, 7378, 10313, 7392, lower diag = 2921, upper diag = 2921) Length: 14
Seed<Simple, TConfig>(10371, 7400, 10385, 7414, lower diag = 2971, upper diag = 2971) Length: 14
"""

-Brett

On Sun, Nov 16, 2014 at 2:57 AM, Rahn, René <rene.maerker@fu-berlin.de> wrote:
Hey Brett, 

It could have multiple reasons. 
In general, it means that there was a traceback path from a seed or a gap, that couldn’t be connected with one of the so far generated traceback paths. Note, that the traceback is computed incrementally to reduce the space requirements. 
If you could send me a simple text file containing the seeds of the seed chain (one seed per row using the <<-operator), that is input to the banded chain alignment function, I could have a look at it and fix the problem. 
Also, I opened an issue in github: https://github.com/seqan/seqan/issues/699, for tracking the issue.


Kind regards, 

René Rahn

On 16 Nov 2014, at 04:17, Brett Bowman <bnbowman@gmail.com> wrote:

I'm trying to build a tool with SeqAn to quickly align some PacBio data, using "bandedChainAlignment", but I'm consistently getting a crash during the trace-back step.  The generation of the Seeds (SuffixArray) and the finding of the base SeedChain works fine, but the final step of turning that into an alignment doesn't appear to work.  

Suggestions?

Error Log:
"""
bbowman@localhost:~/git/SRSLI$ ./src/C++/srsli test/data/query/ecoli_5p_sample.fastq test/data/reference/ecoliK12_5p_assembly.fasta 
Query 0
Finished finding seeds
Finishing chaining seeds
Starting alignment of sequences
/usr/include/seqan/seeds/banded_chain_alignment_traceback.h:195 Assertion failed : isGlued == true was: 0 != 1 (Fatal error while trying to connect trace backs: No glue point available!)
Aborted (core dumped)
"""

-Brett
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---

René Rahn
Ph.D. Student
--------------------------------
--------------------------------
Institute of Computer Science
Algorithmic Bioinformatics (ABI)
--------------------------------
Freie Universität Berlin
Takustraße 9
14195 Berlin
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