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BoevaLab / SV-Bay

Detection of structural variants in cancer mate-pair and paired-end data
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Error running main_probabilities.py #4

Open alvaralmstedt opened 7 years ago

alvaralmstedt commented 7 years ago

Hi! I'm having an issue running main_probabilities.py in my dataset of 60x wgs tumour. It is crashing with the following error:

[xalmal@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 looked in the log file and it seems to be complaining that the .gem file and .fa files for chromosome 1 are of different lengths. I used the hg19 fasta and gems from the zip files linked to from the documentation here, so I feel that it should work. I will also paste the main_probabilities.log here:

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.

PS. How did you generate these .gem files so that I can try to generate new ones for myself?

Thank you!

/Alvar

zhanghappy123 commented 7 years ago

Hi,alvaralmstedt: I indeed get some errors while running SV-Bay first step (main_clustering.py)on my own data, can you give me your all test data? I wonder know why own data have some problem. thanks

alvaralmstedt commented 7 years ago

Hi zhanghappy123! Unfortunately I cannot give out my data as it is from patients. What is the error you are getting? I had some issues with the clustering step as well but i managed to fix it by installing the versions of of all the prerequisites that 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
BioXRay commented 5 years ago

Hi zhanghappy123! Unfortunately I cannot give out my data as it is from patients. What is the error you are getting? I had some issues with the clustering step as well but i managed to fix it by installing the versions of of all the prerequisites that 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

Hi! We got the error running the src/main_clustering.py in my Mate-Pairs data. As following error: Traceback (most recent call last): File "/home/cdx/genome_tools/SV-Bay/src/main_clustering.py", line 89, in Process(data_file, config) File "/home/cdx/genome_tools/SV-Bay/src/main_clustering.py", line 80, in Process cf.PerformClustering() File "/home/cdx/genome_tools/SV-Bay/src/chrfragments.py", line 175, in PerformClustering utils.clust(self.fr_abn, self.chr, 'fr', self.biggest_normal, self.smallest_normal, self.config, self.flag_direction) File "/home/cdx/genome_tools/SV-Bay/src/utils.py", line 65, in clust clusters = cluster.Clustering(fragments, M, S, chrm, chrm, 0, config,direction) File "/home/cdx/genome_tools/SV-Bay/src/cluster.py", line 414, in Clustering new_clusters = KMeansSplit(cluster_for_kmeans, D) File "/home/cdx/genome_tools/SV-Bay/src/cluster.py", line 342, in KMeansSplit (res_my, idx_my) = kmeans2(array(zip(x)), k) File "/usr/lib/python2.7/dist-packages/scipy/cluster/vq.py", line 783, in kmeans2 return _kmeans2(data, clusters, iter, nc, _valid_miss_meth[missing]) File "/usr/lib/python2.7/dist-packages/scipy/cluster/vq.py", line 797, in _kmeans2 new_code, has_members = _vq.update_cluster_means(data, label, nc) File "scipy/cluster/_vq.pyx", line 340, in scipy.cluster._vq.update_cluster_means (scipy/cluster/_vq.c:4654) TypeError: type other than float or double not supported Could you give some suggestion? That the scipy verison is 0.17.0. We hope you reply as soon as possible. Thank you!

guanghaoli commented 5 months ago

Hi! I'm having an issue running main_probabilities.py in my dataset of 60x wgs tumour. It is crashing with the following error:

[xalmal@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 looked in the log file and it seems to be complaining that the .gem file and .fa files for chromosome 1 are of different lengths. I used the hg19 fasta and gems from the zip files linked to from the documentation here, so I feel that it should work. I will also paste the main_probabilities.log here:

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.

PS. How did you generate these .gem files so that I can try to generate new ones for myself?

Thank you!

/Alvar

Hi Alvar, Have you solve this problem? I also have this problem.

Guanghao