BETA-plus error: ValueError: max() arg is an empty sequence

[mij...@broadinstitute.org]

I have been trying to get BETA-plus to work on Galaxy-Cistrome website but repeated to get errors.

I think that my differential expression files might have some problems since I successfully ran BETA-minus.

Here's the error message I found after running it.

Would anyone help me solving these problems?

Thank you for your help.

cut: write error: Broken pipe
cut: write error: Broken pipe
[16:15:17] Argument List:
[16:15:17] Name = NA
[16:15:17] Peak File = /data4/CistromeAP/galaxy_database/files/001/556/dataset_1556922.dat
[16:15:17] Top Peaks Number = 10000
[16:15:17] Distance = 100000 bp
[16:15:17] Genome = hg19
[16:15:17] Expression File = /data4/CistromeAP/galaxy_database/files/001/557/dataset_1557290.dat
[16:15:17] Genome Sequence fasta formated data = /data4/CistromeAP/static_libraries/assembly/hg19/rawgenome/hg19.fasta
[16:15:17] Expression Type = RNA-Seq, Cuffdiff result
[16:15:17] Number of differential expressed genes = 0.5
[16:15:17] Differential expressed gene FDR Threshold = 1.0
[16:15:17] Up/Down Prediction Cutoff = 1.000000
[16:15:17] Function prediction based on regulatory potential
[16:15:17] Check /data4/CistromeAP/galaxy_database/files/001/556/dataset_1556922.dat successfully!
[16:15:17] XLOC_000001 XLOC_000001 DDX11L1 chr1:11873-29370 ht29_gfp_dox ht29_p14_dox NOTEST 0.00707054 0.000945008 -2.90342 0.0242064 0.980688 1 no
is not the header of the expression file
[16:15:17] Checking the differential expression infomation...
[16:15:17] Take the first line with Differential Information as an example: XLOC_000001 XLOC_000001 DDX11L1 chr1:11873-29370 ht29_gfp_dox ht29_p14_dox NOTEST 0.00707054 0.000945008 -2.90342 0.0242064 0.980688 1 no

[16:15:17] Differential Expression file format successful passed
[16:15:17] You do not like filter peak by CFCT boundary, it will be filtered only by the distance
[16:15:17] Read file </data4/CistromeAP/galaxy_database/files/001/556/dataset_1556922.dat> OK! All <5386> peaks.
[16:15:24] Process <50801> genes
[16:15:28] Finished! Preliminary results saved into temporary file: <NA.txt>
[8440, 7692]
[16:15:28] Genes were seprated to two parts: up regulated and down regulated.
[16:15:28] Prepare file for the Up/Down Test
Traceback (most recent call last):
  File "/usr/local/bin/BETA", line 4, in <module>
    __import__('pkg_resources').run_script('BETA-Package==1.0.7', 'BETA')
  File "/data4/CistromeAP/galaxy-dist/lib/pkg_resources.py", line 489, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/data4/CistromeAP/galaxy-dist/lib/pkg_resources.py", line 1207, in run_script
    execfile(script_filename, namespace, namespace)
  File "/usr/local/lib/python2.7/dist-packages/BETA_Package-1.0.7-py2.7.egg/EGG-INFO/scripts/BETA", line 193, in <module>
    main()
  File "/usr/local/lib/python2.7/dist-packages/BETA_Package-1.0.7-py2.7.egg/EGG-INFO/scripts/BETA", line 186, in main
    plusrun(argparser)
  File "/usr/local/lib/python2.7/dist-packages/BETA_Package-1.0.7-py2.7.egg/BETA/runbeta.py", line 107, in plusrun
    e.ChGS()
  File "/usr/local/lib/python2.7/dist-packages/BETA_Package-1.0.7-py2.7.egg/BETA/expr_combine.py", line 203, in ChGS
    scorerun(self.name + '.txt', 'notdiff.txt', 'up_list.txt', 'down_list.txt', 'upregulate', 'downregulate', self.name, self.gname2)
  File "/usr/local/lib/python2.7/dist-packages/BETA_Package-1.0.7-py2.7.egg/BETA/Up_Down_score.py", line 315, in scorerun
    rscript = write_R_code(bgscore, genesets_score, label, name)
  File "/usr/local/lib/python2.7/dist-packages/BETA_Package-1.0.7-py2.7.egg/BETA/Up_Down_score.py", line 157, in write_R_code
    tempmax = max(genesets_score[l])
ValueError: max() arg is an empty sequence (I guess that it would be the problem...)

[beta-user]

Did you solve the problem?