RC454 error message: ERROR getQualAtPos, BAC1.R1.frag1-10006/1 208 >= 0

[Hung-Ying Lin]

Hi all,

I tried to use RC454 in my research. The runMosaik.pl looks normal, but in rc454.pl part I always got this error message. 

Can anyone give me some ideas about that?

Thanks a lot,

Hung-Ying

$perl rc454.pl R1.arf.1.qlx BACseq.R1.nobless.arf.fq.fasta BACseq.R1.nobless.arf.fq.1.qual R1.short.all.fasta R1.arf.1.filter

Reading Qual file...

Reading Read file...

Cleaning Incomplete Extension data...

building slices size 5

Use of uninitialized value $cleanqual in pattern match (m//) at rc454.pl line 509, <INPUT> line 1925052.

Use of uninitialized value $cleanqual in pattern match (m//) at rc454.pl line 513, <INPUT> line 1925052.

Use of uninitialized value $clnqual in pattern match (m//) at rc454.pl line 1581, <INPUT> line 1925052.

Use of uninitialized value $clnqual in pattern match (m//) at rc454.pl line 1585, <INPUT> line 1925052.

Use of uninitialized value $clnqual in concatenation (.) or string at rc454.pl line 1590, <INPUT> line 1925052.

Use of uninitialized value $cleanqual in pattern match (m//) at rc454.pl line 509, <INPUT> line 1925052.

Use of uninitialized value $cleanqual in pattern match (m//) at rc454.pl line 513, <INPUT> line 1925052.

Use of uninitialized value $clnqual in pattern match (m//) at rc454.pl line 1581, <INPUT> line 1925052.

Use of uninitialized value $clnqual in pattern match (m//) at rc454.pl line 1585, <INPUT> line 1925052.

Use of uninitialized value $clnqual in concatenation (.) or string at rc454.pl line 1590, <INPUT> line 1925052.

Use of uninitialized value $qualstr in split at rc454.pl line 1402, <INPUT> line 1925052.

ERROR getQualAtPos, BAC1.R1.frag1-10006/1 208 >= 0

Died at rc454.pl line 1409, <INPUT> line 1925052.

[Fielfluff]

Hi Hung Ying,

I had a similar problem to you but my warnings were a little different (the variables $cleanqual etc.).

I was able to fix mine up and this may solve your case too because I got the same error as you did: ERROR getQualAtPos, BAC1.R1.frag1-10006/1 208 >= 0.

If you open up your:

1) R1.arf.1.qlx
2) BACseq.R1.nobless.arf.fq.fasta
3) BACseq.R1.nobless.arf.fq.1.qual

Can you check if your .qual and your .fasta file the ">" string is the same as qlx string?

For example, in my case I changed in the .fasta and .qual file:

>SRR494199.1 F0DRRT203GDUUS length=559

to

>F0DRRT203GDUUS


to match with the .qlx file unique read ID:

>Read F0DRRT203GDUUS 27 583 585 + JQ403051_HIV1Sub9213Day0 1 504