error in Exomedepth tools

usegalaxy.org support
1

Hello everyone, I am new in usegalaxy, and I want to execute exomeDepth tool. I have files correct for this (BED file, two file.bam, one for control and the other for de treatment) in theoric. when I execute and finish the tool, I read this messenger

“Warning message:
In scan(file = file, what = what, sep = sep, quote = quote, dec = dec, :
number of items read is not a multiple of the number of columns
Error in countBamInGRanges.exomeDepth(bam.file = bam, index = index, granges = target, :
Some sequences in the target data frame cannot be found in the index of the BAM file
Calls: suppressMessages … withCallingHandlers → getBamCounts → countBamInGRanges.exomeDepth
Execution halted”

I want know if someone could help me with this??

Thanks

MLF

2

Welcome, @mlf!

Can you check your inputs based on the assumptions found in the ExomeDepth information (below the Execute button)? There is a specific warning related to gender and some details regarding aggregate reference, minimum number of exons, etc.

1 Like
3

Hello @David,

Thank you for your reply. My inputs are one file of exon.bed, and two files, one control condition, and one file for the treatment. I don’t stand why I have errors. Do you use these tools? or could you show me some files? Or maybe you know of a tutorial for this tool?

Thank you for your time

4

Hi, @mlf

I don’t have any file that I could share, but I can show you what I use to find example files to test tools:

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  • look for test folder/files; this particular case of ExomeDepth was really obvious, because there are only one folder and it’s the test-data, but sometimes you have to search better;

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image756×520 23.3 KB

That’s it, you got the tool’s example files to test and maybe compare to the ones you have.
Hope that helps.

1 Like
5

Hi @David,

Thank you for your reply. I want to say that I cloned that repository for the tools exomeDepth, but there is an error maybe in the input files or the database build for the genome of reference? I to use “Human Feb. 2009 GRCh37/hg19”

"Warning message:
In scan(file = file, what = what, sep = sep, quote = quote, dec = dec, :
number of items read is not a multiple of the number of columns
Warning messages:
1: In .Seqinfo.mergexy(x, y) :
Each of the 2 combined objects has sequence levels not in the other:

  • in ‘x’: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22
  • in ‘y’: chrM, chr1, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY, chr1_gl000191_random, chr1_gl000192_random, chr4_ctg9_hap1, chr4_gl000193_random, chr4_gl000194_random, chr6_apd_hap1, chr6_cox_hap2, chr6_dbb_hap3, chr6_mann_hap4, chr6_mcf_hap5, chr6_qbl_hap6, chr6_ssto_hap7, chr7_gl000195_random, chr8_gl000196_random, chr8_gl000197_random, chr9_gl000198_random, chr9_gl000199_random, chr9_gl000200_random, chr9_gl000201_random, chr11_gl000202_random, chr17_ctg5_hap1, chr17_gl000203_random, chr17_gl000204_random, chr17_gl000205_random, chr17_gl000206_random, chr18_gl000207_random, chr19_gl000208_random, chr19_gl000209_random, chr21_gl000210_random, chrUn_gl000211, chrUn_gl000212, chrUn_gl000213, chrUn_gl000214, chrUn_gl000215, chr [… truncated]
    2: In .Seqinfo.mergexy(x, y) :
    Each of the 2 combined objects has sequence levels not in the other:
  • in ‘x’: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22
  • in ‘y’: chr1, chr1_gl000191_random, chr1_gl000192_random, chr3, chr4, chr4_gl000193_random, chr4_gl000194_random, chr5, chr6, chr7, chr7_gl000195_random, chr8, chr8_gl000196_random, chr8_gl000197_random, chr9, chr9_gl000198_random, chr9_gl000199_random, chr9_gl000200_random, chr9_gl000201_random, chr10, chr11, chr11_gl000202_random, chr12, chr13, chr14, chr15, chr16, chr17, chr17_gl000203_random, chr17_gl000204_random, chr17_gl000205_random, chr17_gl000206_random, chr18, chr18_gl000207_random, chr19, chr19_gl000208_random, chr19_gl000209_random, chr20, chr21, chr21_gl000210_random, chr22, chrM, chrUn_gl000211, chrUn_gl000212, chrUn_gl000213, chrUn_gl000214, chrUn_gl000215, chrUn_gl000216, chrUn_gl000217, chrUn_gl000218, chrUn_gl000219, chrUn_gl000220, chrUn_gl000221, chrUn_gl000222, chrUn_gl000223, chrUn_gl000224, chrUn_gl000 [… truncated]
    Error in [.data.frame(all.exons@CNV.calls, , c(7, 5, 6, 3)) :
    undefined columns selected
    Calls: cbind → [ → [.data.frame
    Execution halted"

I would appreciate you if could you help me.

thank you for everything

6

A similar issue was solved here and was related to versioning, but I can’t test to confirm if that’s your case.