no peaks found by using QuEST

[nultontj]

I'm using QuEST to analyze our lab's chIP-seq data and comparing it with the analysis done by our informatician who is using a different approach.  However, when I run the analysis, this is what I get...

Found the following contigs:

gi|125716887|ref|NC_009009.1| Streptococcus sanguinis SK36 chromosome, complete genome: 2388435 bps

Your genome looks fine and does not appear to contain any
duplicated chromosome entries.

Estimated size of the genome is 2388.4 Kb ( 0.00 Gbps ).

Converting ChIP reads file into the QuEST format.
If the counter below stays at zero, the program can't
match the ChIP alignments to the reference genome that you provided.
In this case check that the sequences you have provided match the formats
accepted by QuEST (see README.txt) and that names of contigs in the alignment
files are *exactly* the same as in your genome or genome table.

align_file:         not_pur_959.sam
output_file:        /home/nultontj/july_chIP_959/QuEST_analysis/data/ChIP_uncollapsed.QuEST
genome_table:       /home/nultontj/july_chIP_959/QuEST_analysis/parameters/genome_table
alignment_type:     bowtie
report_file:        /home/nultontj/july_chIP_959/QuEST_analysis/data/ChIP_read_num_uncollapsed.txt
error_report_file:  /home/nultontj/july_chIP_959/QuEST_analysis/module_outputs/align_2_QuEST_ChIP.report.txt

Bad contig size 0 in gi|125716887|ref|NC_009009.1| Streptococcus sanguinis SK36 chromosome, complete genome 2388435. Skipping.
aligments: 81.81 M, matched : 0.00 M, not in gt: 0.000 M, offending: 81.810 M

Lines read: 81813685
Alignments matched: 0
Offending lines: 81813685

Checking for duplicate hits...
[ This screens for contiguity of bowtie alignment order ]
Seems like there are no alignments to check. Are you sure your bowtie file is ok?


Collapsing ChIP data...

Specified parameters:
executable      /home/nultontj/july_chIP_959/QuEST_2.4/collapse_reads
align_file      /home/nultontj/july_chIP_959/QuEST_analysis/data/ChIP_uncollapsed.QuEST
output_path     /home/nultontj/july_chIP_959/QuEST_analysis/bin_align/ChIP
genome_table    /home/nultontj/july_chIP_959/QuEST_analysis/parameters/genome_table
QuEST_collapsed_file    /home/nultontj/july_chIP_959/QuEST_analysis/data/ChIP.QuEST
collapse_reads  true
collapse_window 100
count_threshold 2
stack_p_value_threshold 0.001
percent_positions_hit_threshold 30
report_file     /home/nultontj/july_chIP_959/QuEST_analysis/data/ChIP_read_num.txt
new_stack_size  1
read 0.00 M reads

sorting hits

-------------------------
contig: gi|125716887|ref|NC_009009.1|

+ reads: 0
- reads: 0

+ reads after collapsing: 0
- reads after collapsing: 0

stacks collapsed: 0
reads in collapsed stacks: 0
done!

After collapsing, there are 0 ChIP read alignments
No ChIP reads were found in your data. Please check your alignment files.

I've mapped the contigs with bowtie2, not specifying the -z option.  This has resulted in the .sam

files  WT (background and control) and FLAGged gene 959. 

The mapped files do contain identical chromosome name as the .fa file used instead of the genome table.

What is in grey is what I think may be causing the problem, either that or somehow the bowtie files aren't right.

I would really appreciate any help you may be able to give me.

Regards,
Tara