CONTRA updates

[jtjli]

Hi guys,

Contra has a new update (v2.0.4) -- see contra-cnv.sf.net. Here are my answers to some commonly asked questions:

1) error: /buf/chrxx.txt
This is due to the bam files NOT containing reads on a chromosome that is defined in the BED file. E.g. 10,000 regions on Chr12 are defined in the target bed file, but the bam file has no read mapped to Chr12.
In most cases, this is due to a truncated, corrupted bam file. So I have not "fixed" the script logic. Rather I am just catching this error and outputing an error message in the latest version.

2) WARNING chrxx not found. & EMPTY VCF FILE
In fasta/bam files where chromosome names have been defined with "chr" prefix, some times the script would fail. This has been fixed -- thx Eric Ho for pointing this out. This *should* fix the empty vcf file issue for some of you... let me know if it doesn't.

3) baseline.py error...
i haven't been able to catch the same error as reported by some of you. but perhaps point 1 about is relevant.. so check the bam files for presence of all chromosomes.

4) false positive/negative rates..
at exon level, the FPR is high. I have a script to detect gene-level gains and losses, and works well one some of our in house data. If you are interested, let me know.


Best wishes,
Jason

[jmatés]

Hi!

Hard work trying to run CONTRA...! I try with python 2.6 / 2.7, and the updated and recommended versions of BEDTools... without success...

When running CONTRA with the test files I get this warning...

python contra.py --target 0247401_D_BED_20090724_hg19_MERGED.bed --test P0667T_GATKrealigned_duplicates_marked.bam --control P0667N_GATKrealigned_duplicates_marked.bam --fasta hg19.fasta --outFolder ~/CONTRA.v2.0.4/ContraTest/sampleName/

Significance Test ...  
[1] "/home/administrador/CONTRA.v2.0.4/ContraTest/sampleName/buf/bin20.txt"
[1] "End of cn_analysis.R"
[1] 11616
Generating Output Files ... 
DEBUG 266b
fastaFromBed -fi hg19.fasta -bed /home/administrador/CONTRA.v2.0.4/ContraTest/sampleName/buf/CNATable.10rd.10bases.20bins.BED -fo /home/administrador/CONTRA.v2.0.4/ContraTest/sampleName/buf/CNATable.10rd.10bases.20bins.fastaOut.txt -name
[B][COLOR="Red"]Error[/COLOR]: The requested bed file (/home/administrador/CONTRA.v2.0.4/ContraTest/sampleName/buf/CNATable.10rd.10bases.20bins.BED) could not be opened. Exiting![/B]
Creating VCF file ... 
/home/administrador/CONTRA.v2.0.4/ContraTest/sampleName/table/CNATable.10rd.10bases.20bins.vcf created. 
Done...

I'm a noobie programming apprentice ... and I don't yet understand what the lines of code referents to "DEBUG 266b" means... any hint?

In other hand, trying it with a pair of my own files...

python2.6 contra.py --target prova_CONTRA_awk.nochr.bed --test 0001.clean.bam --control 0009.clean.bam --fasta hg19.fasta --outFolder ~/CONTRA.v2.0.4/ContraTest/sampleName/

Significance Test ...  
[1] "/home/administrador/CONTRA.v2.0.4/ContraTest/sampleName/buf/bin20.txt"
Error en if (boundary.f.sd < 0) { : 
  valor ausente donde TRUE/FALSE es necesario
Ejecución interrumpida
Generating Output Files ... 
Process Process-3:
Traceback (most recent call last):
  File "/usr/lib/python2.6/multiprocessing/process.py", line 232, in _bootstrap
    self.run()
  File "/usr/lib/python2.6/multiprocessing/process.py", line 88, in run
    self._target(*self._args, **self._kwargs)
  File "contra.py", line 406, in analysisPerBin
    if "CNATable" in tName:
UnboundLocalError: local variable 'tName' referenced before assignment
Done...

In another thread I've read that it could be due to not having installed Rscript, but it's not my situation... and I have BEDTools and R in my path...

A little lost... anyone can shed some light, please?

Thanks!

[sheenams]

I'm getting this same error with both versions. Anyone have a fix yet?

[id0]

I am running CONTRA 2.0.4 and I also got "Error: The requested bed file (...) could not be opened. Exiting!".

If you look at the previous command fastaFromBed, there seems to be a problem with the -bed argument. The contra/buf/CNATable.10rd.10bases.20bins.BED file is actually empty. From what I gather, it seems to be due to the fact that there are no significant results.

[mikesh]

I had the same problem. Fixed by rolling back to previous version of BEDtools, the one from the CONTRA package.

[sheenams]

Rolling back to bedtools from the package (I'm using 2.0.3) got rid of the bed error for me.

[wolfpack14]

I have good news for anyone who has the following error running test code on CONTRA-2.0.4:

user@ubuntu:~/Downloads$ python ./CONTRA.v2.0.4/contra.py -t 0247401_D_BED_20090724_hg19_MERGED.bed -s P0667T_GATKrealigned_duplicates_marked.bam -c P0667N_GATKrealigned_duplicates_marked.bam -f /mnt/hgfs/VMShare/human_g1k_v37.fasta -o P0667Test --plot
target : 0247401_D_BED_20090724_hg19_MERGED.bed
test : P0667T_GATKrealigned_duplicates_marked.bam
control : P0667N_GATKrealigned_duplicates_marked.bam
fasta : /mnt/hgfs/VMShare/human_g1k_v37.fasta
outfolder : P0667Test
numBin : [20]
minreaddepth : 10
minNBases : 10
sam : False
pval : 0.05
sampleName : No-SampleName
nomultimapped : False
plot : True
bedInput : False
minExon : 2000
largeDeletion : False
Creating Output Folder : Done.
Converting CONTROL Sample...
Converting TEST Sample...
splitByChromosome
Getting targeted regions DOC...
chr1
chr10
ERROR: P0667Test/buf/testData/chr/chr10.txt NOT FOUND (should be generated by splitByChromosome3). Likely due to no reads found in a targeted chromosome (chr10), in turn likely due to corrupted bam files
splitByChromosome
Getting targeted regions DOC...
chr1
chr10
chr11
chr12
chr13
chr14
chr15
chr16
chr17
chr18
chr19
chr2
chr20
chr21
chr22
chr3
chr4
chr5
chr6
chr7
chr8
chr9
chrX
Targeted regions pre-processing: Done
Traceback (most recent call last):
File "./CONTRA.v2.0.4/contra.py", line 573, in <module>
main()
File "./CONTRA.v2.0.4/contra.py", line 543, in main
t1 = int(file.readlines(open(folder+"temp.txt"))[0].strip("\n"))
IOError: [Errno 2] No such file or directory: 'P0667Test/buf/testData/temp.txt'

For some reason, CONTRA has an error running concurrently on some machines (I was using Ubuntu 13.10 on VMWare Player). I have developed a workaround that seems to solve the problem.

First, open contra.py and goto line 528. You'll notice the code looks like the following:

# start the processes
pTest.start()
cTest.start()

# wait for all the processes to finish before continuing
pTest.join()
cTest.join()

To resolve the concurrent processing problem, I forced the code to run sequentially. To do this, change the code to the following:

# start the processes
cTest.start()
cTest.join()

# wait for all the processes to finish before continuing
pTest.start()
pTest.join()

Run the code as normal and it should complete. If anyone was curious, I am using the following dependencies:

R-3.0.2
BEDTools-2.17.0
SAMTools-0.1.19
Python-2.7.5

[wolfpack14]

I know this was posted a long time ago, but I resolved your issue. The problem is with this line:

Error en if (boundary.f.sd < 0) { :
valor ausente donde TRUE/FALSE es necesario

Your data is small so CONTRA is forcing it into 1 bin (Check your output to confirm this). There is a bug in the script "cn_analysis.v3.R" where it calls what you defined your bin size as (20 by default) and not by how many bins CONTRA actually created.

The solution is to force your output into 1 bin since CONTRA is automatically doing this. You can do this by using the --numBin=1 option.

In other hand, trying it with a pair of my own files...

python2.6 contra.py --target prova_CONTRA_awk.nochr.bed --test 0001.clean.bam --control 0009.clean.bam --fasta hg19.fasta --outFolder ~/CONTRA.v2.0.4/ContraTest/sampleName/

Significance Test ...  
[1] "/home/administrador/CONTRA.v2.0.4/ContraTest/sampleName/buf/bin20.txt"
Error en if (boundary.f.sd < 0) { : 
  valor ausente donde TRUE/FALSE es necesario
Ejecución interrumpida
Generating Output Files ... 
Process Process-3:
Traceback (most recent call last):
  File "/usr/lib/python2.6/multiprocessing/process.py", line 232, in _bootstrap
    self.run()
  File "/usr/lib/python2.6/multiprocessing/process.py", line 88, in run
    self._target(*self._args, **self._kwargs)
  File "contra.py", line 406, in analysisPerBin
    if "CNATable" in tName:
UnboundLocalError: local variable 'tName' referenced before assignment
Done...

In another thread I've read that it could be due to not having installed Rscript, but it's not my situation... and I have BEDTools and R in my path...

A little lost... anyone can shed some light, please?

Thanks!