isSecondaryAlignment error

[girdhar3]

Hi
I am trying to get tss map for a set of genes

here is my code

ngs.plot.r -G hg19 -R tss -C bamfile -O bamfile.tss -T H3K4me3 -L 3000 -E /genelist -F protein_coding

genelist format
ENSG00000270986
ENSG00000077782
ENSG00000272048
ENSG00000015532
ENSG00000100902
ENSG00000165548

bam file is sorted

@hd VN:1.5 SO:coordinate
@sq SN:chr1 LN:249250621
@sq SN:chr2 LN:243199373
@sq SN:chr3 LN:198022430
@sq SN:chr4 LN:191154276
@sq SN:chr5 LN:180915260
@sq SN:chr6 LN:171115067
@sq SN:chr7 LN:159138663
@sq SN:chr8 LN:146364022
@sq SN:chr9 LN:141213431

@pg ID:bwa PN:bwa

ERROR

Loading R libraries.....Done
Analyze bam files and calculate coverageWarning message:
'isNotPrimaryRead' is deprecated.
Use 'isSecondaryAlignment' instead.
See help("Deprecated")
...........................................Error in { : task 1 failed - "object 'isize' not found"
Calls: covMatrix -> %dopar% ->
Execution halted

Do you know why?

[jdblischak]

The warning message about the argument isNotPrimaryRead appears to have been fixed in the most recent commit: c8f1265 What version are you using? Can you try downloading the latest version and re-run your command?

That's just a warning though, so I am doubtful if that will solve the error about not finding the object isize. My guess is that if you are subsetting with Ensembl gene IDs but your reads are mapped to the UCSC chromsomes, that the chromosome names are incompatible. What happens when you run your command omitting the -E option?

Also, did you run -E /genelist as you wrote or -E genelist?