Question: SV-bay .gem file issue
0
gravatar for alvar.almstedt
13 months ago by
alvar.almstedt0 wrote:

Hello!

I am trying to run the program SV-bay (https://github.com/InstitutCurie/SV-Bay, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4896370/) in order to find translocations in our 60x tumour + 30x normal WGS datasets. However, Im having issues getting the second step main_probabilities.py) to run. In the log file, it is complaining about the gem files and the fasta files being of different lengths:

main_probabilities.py    line:197  INFO     [2016-11-11 11:12:22,971]   Chromosomes to process:['chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr20', 'chr21', 'chr22', 'chrX', 'chrY']
bayesianinput.py         line:48   INFO     [2016-11-11 11:12:22,971]   Loading data...

bayesianinput.py         line:106  INFO     [2016-11-11 11:12:22,971]   Loading normal fragments...
bayesianinput.py         line:137  INFO     [2016-11-11 11:32:03,126]   Loading links...
bayesianinput.py         line:158  INFO     [2016-11-11 11:32:21,881]   Constructing sublinks...
bayesianinput.py         line:223  WARNING  [2016-11-11 11:32:32,877]   Lambda file not found, calculating lambda
bayesianinput.py         line:252  INFO     [2016-11-11 11:32:32,877]   Started calculating lambda_gen
bayesianinput.py         line:67   WARNING  [2016-11-11 11:32:39,167]   Lengths of .fa and .gem sequences do not match for chrom chr1 (249250626 and 248956422)
bayesianinput.py         line:69   WARNING  [2016-11-11 11:32:39,167]   Some flanking regions will be truncated to match the minimal length                 and some links (intersecting with chrom tail) will be dropped.
bayesianinput.py         line:70   WARNING  [2016-11-11 11:32:39,167]   Please fix your .gem file.

Which is interesting because I am using the hg19 fasta and gem files provided on the GitHub page (see link above). The actual python error that the program is printing out looks as follows:

[x@bespin sv-bay-data]$ /apps/CLC_ExternalApps/SV-Bay/miniconda2/bin/python2.7 -B /apps/CLC_ExternalApps/SV-Bay/SV-Bay/src/main_probabilities.py -c /apps/CLC_ExternalApps/SV-Bay/SV-Bay/config/config.yaml
Traceback (most recent call last):
  File "/apps/CLC_ExternalApps/SV-Bay/SV-Bay/src/main_probabilities.py", line 199, in <module>
    input_data = BayesianInputData(config, stats, chromosomes)
  File "/apps/CLC_ExternalApps/SV-Bay/SV-Bay/src/bayesianinput.py", line 57, in __init__
    self.__LoadLambda(config, stats)
  File "/apps/CLC_ExternalApps/SV-Bay/SV-Bay/src/bayesianinput.py", line 224, in __LoadLambda
    (lambda_norm,lambda_abnorm) = self.__CalculateLambda(config, stats)
  File "/apps/CLC_ExternalApps/SV-Bay/SV-Bay/src/bayesianinput.py", line 363, in __CalculateLambda
    if gem_val_abnormal[i/step]!=-1:
IndexError: list index out of range

I have successfully run through all the steps when doing the analysis on only a single chromosome (chr17). If anyone has a clue about what the problem is or how I can recreate the gem mappability files, I would be deeply grateful.

/A

software error • 413 views
ADD COMMENTlink modified 12 months ago by 12456090460 • written 13 months ago by alvar.almstedt0
0
gravatar for 1245609046
12 months ago by
12456090460
12456090460 wrote:

Hi I'm having issues getting the first step main_clustering.py) to run. In the log file,it is complaining follow: Traceback (most recent call last): File "~/SV-Bay/src/main_clustering.py", line 89, in <module> Process(data_file, config) File "~/SV-Bay/src/main_clustering.py", line 67, in Process cf.CollectStats() File "~/SV-Bay/src/chrfragments.py", line 58, in CollectStats self.chr = self.rf[0].first_read_chr IndexError: list index out of range can you tell me how to solve it ?

ADD COMMENTlink written 12 months ago by 12456090460
0
gravatar for 1245609046
12 months ago by
12456090460
12456090460 wrote:

Hi I'm having issues getting the first step main_clustering.py) to run. In the log file,it is complaining follow: Traceback (most recent call last): File "/SV-Bay/src/main_clustering.py", line 89, in Process(data_file, config)

File "/SV-Bay/src/main_clustering.py", line 67, in Process cf.CollectStats()

File "~/SV-Bay/src/chrfragments.py", line 58, in CollectStats self.chr = self.rf[0].first_read_chr

IndexError: list index out of range

anyone tell me how to solve it ? thanks

ADD COMMENTlink written 12 months ago by 12456090460

I had issues with the clustering step too. The thing that solved it was to use the exact versions of of the prerequisites there were out when the last commit of SV-bay was done: numpy==1.8.2 scipy==0.13.3 matplotlib==1.3.1 pyaml==16.9.0 pysam==0.9.1.4 joblib==0.10.2

I installed a separate python via miniconda and put these exact versions into it.

ADD REPLYlink written 12 months ago by alvar.almstedt0

can you give me your test data ? I wonder to know the reason and different of my data.

ADD REPLYlink written 12 months ago by 12456090460

Sorry, I cannot give you my test data because it is from patients.

ADD REPLYlink written 12 months ago by alvar.almstedt0
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