question about Solid data analysis using bowtie?

[Jetse]

Did anyone of you solve this problem?
I have exactly the same problem now.

Mapping left_kept_reads to genome GRCh37_gatk_colorspace with Bowtie
Mapping left_kept_reads_seg1 to genome GRCh37_gatk_colorspace with Bowtie (1/2)
Mapping left_kept_reads_seg2 to genome GRCh37_gatk_colorspace with Bowtie (2/2)
Mapping right_kept_reads to genome GRCh37_gatk_colorspace with Bowtie
[FAILED]
Error running bowtie:
Too few quality values for read: 28 I
are you sure this is a FASTQ-int file?
terminate called after throwing an instance of 'int'

All 4 files are exactly 200000 lines (so 100000 reads). Mapping the left reads works, but when mapping the right reads it fails...

[EDIT]
For anyone who has this error too, check whether you have added the --quals option, also check the command on order of files (first all csfasta files than the qual files). This solved my error...

[Chirag]

Hey guys,
How did you solve this problem ? Could you please help me with this ?
I am also getting this error, when using tophat mapping on colorspace file.

This is my command: [Works fine until half-way]

tophat --output-dir /results --color -p 8 --no-coverage-search /bowtie_alignment_reference/mm9_c F3.csfasta F3.QV.qual


I get this error:
Mapping left_kept_reads_seg1 to genome mm9_c with Bowtie (1/3)
Mapping left_kept_reads_seg2 to genome mm9_c with Bowtie (2/3)
Mapping left_kept_reads_seg3 to genome mm9_c with Bowtie (3/3)

[2012-10-20 22:11:02] Mapping right_kept_reads to genome mm9_c with Bowtie
[FAILED]
Error running bowtie:
Too few quality values for read: 39 I
are you sure this is a FASTQ-int file?
terminate called after throwing an instance of 'int'


regards
Chirag

[adamdeluca]

Truncated Qual file

I have had this error when SAET failed and a truncated qual file was produced.

[wangleibio]

ok,i have deleted it, thanks!

[nilshomer]

Please only post to one forum. Cross-posting is like spam, unacceptable.

[wangleibio]

hello ,everyone
I am trying to run bowtie with the solid sequence data flower9_1_F3.csfasta and flower9_1_F3_QV.qual
I built the bowtie-build -C index successfully and moved the generated index files to the Bowtie indexes subdirectory. I run the command:
bowtie -n 3 --best --strata -a -e 150 -p 4 ../cDNA_reference/TAIR9_cdna -C -f flower9_1_F3.csfasta -Q flower9_1_F3_QV.qual --un fllower9-unmap > flower9-map &
and the output i got is an error showing on console

[wanglei@mu01 data]$ [wanglei@mu01 data]$ Too few quality values for read: 425_2031_2008_F3
are you sure this is a FASTQ-int file?
terminate called after throwing an instance of 'int'
Too few quality values for read: 425_2042_1847_F3
are you sure this is a FASTQ-int file?
terminate called after throwing an instance of 'int'
Too few quality values for read: 1277_2042_2013_F3
are you sure this is a FASTQ-int file?
Could you please help me to sort out this issue?
thanks
wanglei