Error using in Smalt aligner program

Question

[mh.noroozi]

Hello I want to use Smalt program to aligning paired-end nucleotide sequence reads to reference with hashing tables. I created hashing files and map reads to the reference. When I mapped reads with this command:

smalt map -c 0.6 -d 0.5 -f cigar -x -y 0.6 -l mp -o seq.cigar hash seq_1.fastq seq_2.fastq

The result of above command returns an error with this manner:

# Opening read files ...
# Reading reference sequences ...
# Reading hash table ...
# =-=-=-=-= Hash Index Stats =-=-=-=-=
# Perfect hash index.
# Word length:              13 bases
# Skip step:                13 bases
# Number of hash keys:      67108864
# Number of word positions: 562854259
# =-=-= End of Hash Index Stats =-=-=
# Processing query reads ...
[0] rmap.c:1371 ERROR: assertion failed
  when processing read No. 1874 'ERR688528.1874 FCC1MNHACXX:3:1101:8825:2830#AAGGATGC/1'

I copy reads number 1874 and previous reads:

Seq_1.fastq:
@ERR688528.1873 FCC1MNHACXX:3:1101:8920:2807#AAGGATGC/1
GATGTTCTAAAAGATTGTCATGGAACGATTCAAACTCTGCAGATTCCTCATTATTAAGGACACCAGGTACAAGACGGGAAACCGCATCAATCATAA
+
FFFFHHHHHJIIJJJJJIJIIIIIJHIGGIIJJJJIJJIJJIIJIJIJJJJJIIIIJJIJJIIIJJI@=EHEHDFFFDA?=?B@DDBBDDDDDDDD
@ERR688528.1874 FCC1MNHACXX:3:1101:8825:2830#AAGGATGC/1
GTAAGGCGCCCAGTAGATAATAGGACGCACGGATTTTTCTGATGTATTCATTGTCAACGCTCGTTTCATGAATGGTTGAGCCGTTGATCTTTACCG
+
FEFFHHGFFIIGHFCGBFHHGGJJGHIJJJIJGAHGHIIJJGHIDHHHIIJJHHFHFHFDDDD??BDCCDA@CCCAC??CCC@<BB<>CACCCDCB

Seq_2.fastq:
@ERR688528.1873 FCC1MNHACXX:3:1101:8920:2807#AAGGATGC/2
TATCTTGCTTATGAGGATGTGACTCAGAACATGGAGAAAAAGCCACGGGTGGTTTATGTGACACCGCAGGGATCCGTATTTAACCAGTCAATGGCA
+
FDFFHHHHHJJJJJIJHIIEHGJJJJJJHIGIIJIGGIJIIIIGJJHIJ@AHAHHHHHHFGGFFFDDDDDDDDDCBBBBCDC>CCCDCCCDDDDDD
@ERR688528.1874 FCC1MNHACXX:3:1101:8825:2830#AAGGATGC/2
GAGGTGCAAAATGGATCAATATGTAATAAAAGGTGGAAATCCGTTAATCGGAGATGTGGCAATCGGCGGGG
+
FADDHBFHHIJIJJGHIIIJIJJFIHBGHIIII9CFGHBDHIDGGE??FGGIJHGG@A@EGEAEHH>CB@B

I did not find any difference between reads 1873 and 1874. Please help me to solve this problem.

[GenoMax]

One possible reason @ERR688528.1874 FCC1MNHACXX:3:1101:8825:2830#AAGGATGC/2 is not the same length of corresponding R1 read. Does smalt need reads from R1/R2 to be identical length?

[Prakki Rama]

It is a bug that is fixed in 0.7.6 version. From the SMALT release history:

• fixed bug in 'smalt map -p' resulting in the "assertion failed" error message. This could occur when a read aligned across two successive sequences in the reference file for which the index was
  constructed, and none of the matching segments exceeded the threshold of the Smith-Waterman alignment score (set with -m).