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6.4 years ago
mh.noroozi
•
0
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.
One possible reason
@ERR688528.1874 FCC1MNHACXX:3:1101:8825:2830#AAGGATGC/2
is not the same length of correspondingR1
read. Doessmalt
need reads from R1/R2 to be identical length?It is a bug that is fixed in 0.7.6 version. From the SMALT release history: