[DNAmethylome]

CONTRA error messages

Do you have the "scripts" directory in your contra folder? Seems like the python script cannot read that directory.

Jason

Hi Dr. Li,

I have some problems running CONTRA, I have posted a thread here:

http://seqanswers.com/forums/showthread.php?t=62000

Could you please help me on that?

Thanks a lot!

-J

[xxqtony]

I tried to run CONTRA v2.0.6 and eventually got it run, but it seems to hang over there for half an hour for a pair of 1.3M sample and 0.8M control bam files. Here is the output I got on the screen. Anyone has clue why?

./contra.py --target target_test.bed -s bamfiles/Sample.32.NA18924.3cp.bam -c bamfiles/Control.75.NA19351.bam -f /share/references/hg19/hg19.fa -o out.run
target : target_test.bed
test : bamfiles/Sample.32.NA18924.3cp.bam
control : bamfiles/Control.75.NA19351.bam
fasta : /share/references/hg19/hg19.fa
outfolder : out.run
numBin : [20]
minreaddepth : 10
minNBases : 10
sam : False
pval : 0.05
sampleName : No-SampleName
nomultimapped : False
plot : False
bedInput : False
minExon : 2000
largeDeletion : False
removeDups : False
Creating Output Folder : Done.
Converting TEST Sample...
Converting CONTROL Sample...
DEBUG 123 genomeCoverageBed -ibam bamfiles/Sample.32.NA18924.3cp.bam -bga -g out.run/buf/sample.Genome
DEBUG 123 genomeCoverageBed -ibam bamfiles/Control.75.NA19351.bam -bga -g out.run/buf/sample.Genome
Getting targeted regions DOC...
chr22
Targeted regions pre-processing: Done
Getting targeted regions DOC...
chr22
Targeted regions pre-processing: Done
Test file read depth = 230090
Control file read depth = 155939
Pre-processing Completed.
Getting the Log Ratio ...
Binning ...

[DNAmethylome]

Hi,

What is your python version?

I tried to run CONTRA v2.0.6 and eventually got it run, but it seems to hang over there for half an hour for a pair of 1.3M sample and 0.8M control bam files. Here is the output I got on the screen. Anyone has clue why?

./contra.py --target target_test.bed -s bamfiles/Sample.32.NA18924.3cp.bam -c bamfiles/Control.75.NA19351.bam -f /share/references/hg19/hg19.fa -o out.run
target : target_test.bed
test : bamfiles/Sample.32.NA18924.3cp.bam
control : bamfiles/Control.75.NA19351.bam
fasta : /share/references/hg19/hg19.fa
outfolder : out.run
numBin : [20]
minreaddepth : 10
minNBases : 10
sam : False
pval : 0.05
sampleName : No-SampleName
nomultimapped : False
plot : False
bedInput : False
minExon : 2000
largeDeletion : False
removeDups : False
Creating Output Folder : Done.
Converting TEST Sample...
Converting CONTROL Sample...
DEBUG 123 genomeCoverageBed -ibam bamfiles/Sample.32.NA18924.3cp.bam -bga -g out.run/buf/sample.Genome
DEBUG 123 genomeCoverageBed -ibam bamfiles/Control.75.NA19351.bam -bga -g out.run/buf/sample.Genome
Getting targeted regions DOC...
chr22
Targeted regions pre-processing: Done
Getting targeted regions DOC...
chr22
Targeted regions pre-processing: Done
Test file read depth = 230090
Control file read depth = 155939
Pre-processing Completed.
Getting the Log Ratio ...
Binning ...

[xxqtony]

I also got errors when I use the provided testing files (at sourceforge dot net contra-cnv testing files folder). I used the command in README file, screen output copied below:

~/programs/CONTRA.v2.0.6/contra.py -t 0247401_D_BED_20090724_hg19_MERGED.bed -s P0667T_GATKrealigned_duplicates_marked.bam -c P0667N_GATKrealigned_duplicates_marked.bam -f /share/references/hg19/human_g1k_v37.fasta -o P0667Test
target : 0247401_D_BED_20090724_hg19_MERGED.bed
test : P0667T_GATKrealigned_duplicates_marked.bam
control : P0667N_GATKrealigned_duplicates_marked.bam
fasta : /share/references/hg19/human_g1k_v37.fasta
outfolder : P0667Test
numBin : [20]
minreaddepth : 10
minNBases : 10
sam : False
pval : 0.05
sampleName : No-SampleName
nomultimapped : False
plot : False
bedInput : False
minExon : 2000
largeDeletion : False
removeDups : False
Creating Output Folder : Done.
begining to sort 0247401_D_BED_20090724_hg19_MERGED.bed into?
[bam_header_read] EOF marker is absent. The input is probably truncated.
Converting TEST Sample...
DEBUG 123 genomeCoverageBed -ibam P0667T_GATKrealigned_duplicates_marked.bam -bga -g P0667Test/buf/sample.Genome
Converting CONTROL Sample...
DEBUG 123 genomeCoverageBed -ibam P0667N_GATKrealigned_duplicates_marked.bam -bga -g P0667Test/buf/sample.Genome
Getting targeted regions DOC...
chr1
chr10
chr11
chr12
chr13
chr14
chr15
chr16
WARNING: P0667Test/buf/testData/chr/chr16.txt NOT FOUND (should be generated by splitByChromosome3). Likely due to no reads found in a targeted chromosome (chr16), in turn likely due to currupted bam files
chr17
WARNING: P0667Test/buf/testData/chr/chr17.txt NOT FOUND (should be generated by splitByChromosome3). Likely due to no reads found in a targeted chromosome (chr17), in turn likely due to currupted bam files
chr18
WARNING: P0667Test/buf/testData/chr/chr18.txt NOT FOUND (should be generated by splitByChromosome3). Likely due to no reads found in a targeted chromosome (chr18), in turn likely due to currupted bam files
chr19
WARNING: P0667Test/buf/testData/chr/chr19.txt NOT FOUND (should be generated by splitByChromosome3). Likely due to no reads found in a targeted chromosome (chr19), in turn likely due to currupted bam files
chr2
chr20
WARNING: P0667Test/buf/testData/chr/chr20.txt NOT FOUND (should be generated by splitByChromosome3). Likely due to no reads found in a targeted chromosome (chr20), in turn likely due to currupted bam files
chr21
WARNING: P0667Test/buf/testData/chr/chr21.txt NOT FOUND (should be generated by splitByChromosome3). Likely due to no reads found in a targeted chromosome (chr21), in turn likely due to currupted bam files
chr22
WARNING: P0667Test/buf/testData/chr/chr22.txt NOT FOUND (should be generated by splitByChromosome3). Likely due to no reads found in a targeted chromosome (chr22), in turn likely due to currupted bam files
chr3
chr4
chr5
chr6
chr7
chr8
chr9
chrX
WARNING: P0667Test/buf/testData/chr/chrX.txt NOT FOUND (should be generated by splitByChromosome3). Likely due to no reads found in a targeted chromosome (chrX), in turn likely due to currupted bam files
Targeted regions pre-processing: Done
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
Test file read depth = 227284587
Control file read depth = 304798449
Pre-processing Completed.
Getting the Log Ratio ...
Initial: 5292
Check_Init.id: 3021
_Exon: 0
Check_Init.exon: 0
Error. Comparing different Gene



BTW, I'm using python 2.7.6 and R 3.2.1

[aditisk]

I am trying to run Contra with the test data provided. I am using the Nimblegen V2 baseline file that is provided and I am running into this error:

Process Process-2:
Traceback (most recent call last):
File "/home/software/rhel6/python/2.7.3/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap
self.run()
File "/home/software/rhel6/python/2.7.3/lib/python2.7/multiprocessing/process.py", line 114, in run
self._target(*self._args, **self._kwargs)
File "/home/software/rhel6/med/contra/2.0.6/contra.py", line 345, in convertBamSimple
convertGeneCoordinate(targetList, folder)
File "/usr/cac/rhel6/med/contra/2.0.6/scripts/convert_gene_coordinate.py", line 77, in convertGeneCoordinate
cov = covFile[t].split()
IndexError: list index out of range
Traceback (most recent call last):
File "/home/software/rhel6/med/contra/2.0.6/contra.py", line 613, in <module>
main()
File "/home/software/rhel6/med/contra/2.0.6/contra.py", line 585, in main
n1 = int(file.readlines(open(folder+"temp.txt"))[0].strip("\n"))
IOError: [Errno 2] No such file or directory: '/scratch/chadbren_flux/aditisk/Bam/Contra_Out/Sample_Baseline/buf/ctrData/temp.txt'

Does anyone have an idea as to what might be the problem ?

Thanks,
Aditi