gravatar for corinne_hutfilz

2 hours ago by

The script I had working 2 years ago for DiffBind no longer works. Dba.count seems to reject files it accepted before.

   sets_counted_g=dba.count(sets_g)
Computing summits...
Sample: H:/(filepath truncated)/file_sorted.bam125  
Re-centering peaks...
Indexing H:/(filepath truncated)/file_sorted.bam
[E::hts_idx_push] NO_COOR reads not in a single block at the end 2 -1
Error in FUN(X[[i]], ...) : failed to build index
  file: H:/CH_DATA/ATAC/2020_Second_postprocessing/bam/PoolCH-7_sorted.bam
In addition: Warning message:
Parallel execution unavailable: executing serially.

I thought I'd sorted this file by position, but I went ahead and re-sorted it using

samtools sort file_sorted.bam -o file_sorted_byposition.bam

The result still fails to count:

sets_counted_g=dba.count(sets_g)
Computing summits...
Sample: H:/(filepath truncated)/file_sorted_byposition.bam125 
Re-centering peaks...
Error in colnames(result)[4:ncol(result)] <- colnames(classes) : 
  replacement has length zero
In addition: Warning message:
Parallel execution unavailable: executing serially

Tagged this with both samtools and Diffbind because it looks like a samtools problem, but the script worked as-is 2 years ago for DiffBind. So maybe DiffBind is involved. Picard ValidateSamFile returned no errors on the file.



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