Error with generate_QuEST_parameters.pl

[harukao]

Hi.
I run QuEST 2.4 on Fedora 12.

I had an error while onfiguring QuEST to run with your data:
./generate_QuEST_parameters.pl -sam_align_ChIP /boo/IP.sam -
sam_align_RX_noIP /boo/noIP.sam -rp /foo/ -ap ~/foo/quest/

It said:
>>
Error during the execution of command:
/foo/QuEST_2.4/collapse_reads align_file=/foo/quest//data/
ChIP_uncollapsed.QuEST output_path=/foo/quest//bin_align/ChIP
genome_table=/foo/quest//parameters/genome_table QuEST_collapsed_file=/
foo/quest//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=/foo/quest//data/
ChIP_read_num.txt new_stack_size=1
<<


Ignoring this message, I tried to run QuEST:
./run_QuEST_with_param_file.pl -ap ~/foo/quest/

Then it said:
>>
Failed to open /home/harukao/clock/quest/parameters/QuEST.batch.pars.
Aborting.
<<


I'm not sure why I get no 'QuEST.batch.pars'.
Is it something to do with the reference genome? (mm9.fa)

Please help.

Thanks.

Haruka, Japan.

[Anton]

Hi Haruka,

can you see if it creates ~/foo/quest directory (trying to rule out
write permissions conflct).

QuEST.batch.pars is a file generated by the
generate_QuEST_parameters.pl script and contains paths and other
information that QuEST uses to perform data analysis.

Anton.

[harukao]

Hi Anton,

Thank you for your reply.

It created '~/foo/quest directory'.

After I posted this discussion, I modified the command like this:
./generate_QuEST_parameters.pl -sam_align_ChIP /boo/IP.sam -
sam_align_RX_noIP /boo/noIP.sam -rp /foo/mm9 -ap ~/foo/quest/

This time, I tried '-rp /foo/mm9' which contains mouse genome fasta
file divided by each of chromosomes
instead of /foo ( which contains a fasta file including whole mouse
genome information).

I don't know why, but this time it worked!

So, the problem was solved.

Thanks.

[Jing Lu]

Hi Anto,

I also got the same problem. But before it, I had "collapse_reads:
collapse_reads.cpp: 163: int main(int, char**): Assertion
'cur_contig_size >=0' failed."

and "collapse_reads" is "true".

What does that mean?

Thank you,
Jing

On Jan 21, 7:24 pm, Anton <valo...@gmail.com> wrote:
> Hi Haruka,
>
> can you see if it creates ~/foo/quest directory (trying to rule out
> write permissions conflct).
>
> QuEST.batch.pars is a file generated by the
> generate_QuEST_parameters.pl script and contains paths and other
> information that QuEST uses to perform data analysis.
>
> Anton.
>
> On Jan 20, 5:52 pm, harukao <yui.furut...@gmail.com> wrote:
>
>
>
>
>
>
>
> > Hi.
> > I run QuEST 2.4 on Fedora 12.
>
> > I had an error while onfiguring QuEST to run with your data:
> >         ./generate_QuEST_parameters.pl -sam_align_ChIP /boo/IP.sam -
> > sam_align_RX_noIP /boo/noIP.sam -rp /foo/ -ap ~/foo/quest/
>
> > It said:
>
> > Error during the execution of command:
> > /foo/QuEST_2.4/collapse_readsalign_file=/foo/quest//data/
> > ChIP_uncollapsed.QuEST output_path=/foo/quest//bin_align/ChIP
> > genome_table=/foo/quest//parameters/genome_table QuEST_collapsed_file=/

> > foo/quest//data/ChIP.QuESTcollapse_reads=true collapse_window=100

[Anton]

Hey Jing, that's the step which eliminates "stacks" resulting from
mapping and PCR artifacts.
Can you cut-and-paste the genome table contents?
Thanks, Anton.

[Jing Lu]

I used both -rp and -gt. They all had the same error. Thank you.

For -rp, I made it like -rp /hg19_illumina.
For -gt, I paste it below.

chr1 249250621
chr2 492449994
chr3 690472424
chr4 881626700
chr5 1062541960
chr6 1233657027
chr7 1392795690
chr8 1539159712
chr9 1680373143
chrM 1680389714
chrX 1835660274
chrY 1895033840
chr10 2030568587
chr11 2165575103
chr12 2299426998
chr13 2414596876
chr14 2521946416
chr15 2624477808
chr16 2714832561
chr17 2796027771
chr18 2874105019
chr19 2933234002
chr20 2996259522
chr21 3044389417
chr22 3095693983
illumina_pe_pcr_primer_1 3095694081
illumina_pe_pcr_primer_2 3095694179
illumina_genomic_pcr_primer_1 3095694277
illumina_genomic_pcr_primer_2 3095694375
spikein_phiX174 3095699761

[Anton]

Sorry for the delay.
It seems like your genome table contains a cumulative size up. For
instance, human chr2 is 243M, but your genome table shows 492M which
seems to be a sum of chr1 and chr2 sizes. Below I've pasted genome
table for hg19 that I use. Best, Anton.

chr18 78077248
chr5 180915260
chrX 155270560
chr11 135006516
chr15 102531392
chr12 133851895
chr21 48129895
chr7 159138663
chr3 198022430
chr22 51304566
chr20 63025520
chr16 90354753
chr14 107349540
chr9 141213431
chr8 146364022
chr17 81195210
chr2 243199373
chr4 191154276
chr19 59128983
chrM 16571
chr6 171115067
chr1 249250621
chr10 135534747
chr13 115169878
chrY 59373566

[huben...@163.com]

Bad contig size -2095031117 in 13 2199936179. Skipping.

Bad contig size -1987681577 in 14 2307285719. Skipping.

Bad contig size -1885150185 in 15 2409817111. Skipping.

Bad contig size -1794795432 in 16 2500171864. Skipping.

Bad contig size -1713600222 in 17 2581367074. Skipping.

Bad contig size -1635522974 in 18 2659444322. Skipping.

Bad contig size -1576393991 in 19 2718573305. Skipping.

Bad contig size -1513368471 in 20 2781598825. Skipping.

Bad contig size -1465238576 in 21 2829728720. Skipping.

Bad contig size -1413934010 in 22 2881033286. Skipping.

Bad contig size -1258663450 in X 3036303846. Skipping.

Bad contig size -1199289884 in Y 3095677412. Skipping.

collapse_reads: collapse_reads.cpp:163: int main(int, char**): Assertion `cur_contig_size >= 0' failed.

I  can`t SOLVE  it .Could  you help me?

在 2011年1月21日星期五UTC+8上午9时52分49秒，harukao写道：

[Anton]

Hi Huben,

can you paste your genome table you are using? You can find it in the QuEST analysis directory.

Best, Anton

[huben...@163.com]

chr1 249250621

chr2 243199373

chr3 198022430

chr4 191154276

chr5 180915260

chr6 171115067

chr7 159138663

chr8 146364022

chr9 141213431

chr10 135534747

chr11 135006516

chr12 133851895

chr13 115169878

chr14 107349540

chr15 102531392

chr16 90354753

chr17 81195210

chr18 78077248

chr19 59128983

chr20 63025520

chr21 48129895

chr22 51304566

chrX 155270560

chrY 59373566

在 2013年10月23日星期三UTC+8上午3时38分59秒，Anton写道：

[Anton]

Hubin, it looks like it's unable to properly process your genome table.

Not sure what's the cause, but perhaps you can grab the one that I am using and try again.

https://dl.dropboxusercontent.com/u/14340754/genome_table

Sorry for your difficulties. 

Best, Anton

[hubenxia123]

Yes,I have used yours.but the result is the same

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[Anton]

Then something may be off with your compiler or OS.

What OS are you using?

You can also try building the genome table using QuEST by providing full reference genome.

Anton

[hubenxia123]

I  used  linux--redhat.

 

Thanks.

[Anton]

Are you using the latest QuEST version 2.4?

You can grab it here:

http://www-hsc.usc.edu/~valouev/QuEST/QuEST.html

download source