Trinity can not recognize the reads

[Simonli]

Well, this is basically a followup from here (http://seqanswers.com/forums/showthread.php?t=34703): I first use *.fasta to feed trinity, it shows my reads could not be deciphered as being /1 or /2 of a PE fragment.
and my fasta files was like:

>HISEQ:190:C2L5LACXX:7:1101:2055:1989 1:N:0:ATCATG
AACAATTTCATCCTCGAATCCTACCACACGGGCGCTGGCACCGCCTACGCCGTCCTCGCTGAGAACACCACCGAAGCCAACCCTCGCACCTTCTACGTGA
>HISEQ:190:C2L5LACXX:7:1101:3448:1999 1:N:0:ATCACG
GTCGTATGCAAAGGATTCAACCCCACGCATTGTAAAATTGCAAGACGCCAGTTAGTCCTAAAGAGTTTCTTCAATAGGACCGTTACCAGCCAGCTAAGAT
>HISEQ:190:C2L5LACXX:7:1101:3524:1986 1:N:0:ATCACG
CTTGTCCTTCTTCTCTTTCCTCTCTTTGGTTTTATCTGACACAAGATCCTTCTCAATCTTATCGAGACTCGGCCTCTGCTTGAGTTTCTCAGAGTCATTA
>HISEQ:190:C2L5LACXX:7:1101:4204:1996 1:N:0:ATCACG
GTGTTAAAAGGGCTAGAGATCGAAATGTTAGACAAAGCGAAATGGAGCAAAGACTGGCAGATCCCAACCAATCCCAATCACGCCGAGAACAAACTTGGTC
>HISEQ:190:C2L5LACXX:7:1101:4587:2000 1:N:0:ATCACG

Then I wrote a script (hope this would help somebody has the same problem) to add /1 or /2 to the fasta files:

f = open("merged1.fasta")
output = open("1.fasta",'w')
i = 1
for line in f:
if (i % 2) > 0:
str = line.split()
output.write(str[0]+' ')
output.write(str[1][2:]+"/1\n")
else:
output.write(line)
i = i+1

Then the fasta files turn to:

>HISEQ:190:C2L5LACXX:7:1101:2055:1989 N:0:ATCATG/1
AACAATTTCATCCTCGAATCCTACCACACGGGCGCTGGCACCGCCTACGCCGTCCTCGCTGAGAACACCACCGAAGCCAACCCTCGCACCTTCTACGTGA
>HISEQ:190:C2L5LACXX:7:1101:3448:1999 N:0:ATCACG/1
GTCGTATGCAAAGGATTCAACCCCACGCATTGTAAAATTGCAAGACGCCAGTTAGTCCTAAAGAGTTTCTTCAATAGGACCGTTACCAGCCAGCTAAGAT
>HISEQ:190:C2L5LACXX:7:1101:3524:1986 N:0:ATCACG/1
CTTGTCCTTCTTCTCTTTCCTCTCTTTGGTTTTATCTGACACAAGATCCTTCTCAATCTTATCGAGACTCGGCCTCTGCTTGAGTTTCTCAGAGTCATTA
>HISEQ:190:C2L5LACXX:7:1101:4204:1996 N:0:ATCACG/1
GTGTTAAAAGGGCTAGAGATCGAAATGTTAGACAAAGCGAAATGGAGCAAAGACTGGCAGATCCCAACCAATCCCAATCACGCCGAGAACAAACTTGGTC
>HISEQ:190:C2L5LACXX:7:1101:4587:2000 N:0:ATCACG/1

Then I feed these reads to run Trinity again(I use seperate 4 stages), the first stage(inchworm) was good, however in the 2nd stage,

The error report showing:

Use of uninitialized value $pm_temp in division (/) at /local_scratch/.../Trinity.pl line 887
Use of uninitialized value $pm_temp in division (/) at /local_scratch/.../Trinity.pl line 890

So it seems manually rename the reads doesn`t work...

Anybody any ideas can figure that out?

Simon

[Simonli]

correction, the second trial changed the python script a little bit and the output heading is like this:

>HISEQ:190:C2L5LACXX:7:1101:2055:1989/1
AACAATTTCATCCTCGAATCCTACCACACGGGCGCTGGCACCGCCTACGCCGTCCTCGCTGAGAACACCACCGAAGCCAACCCTCGCACCTTCTACGTGA

I`ll see if it works.