boboppie / RiboTaper

A copy of RiboTaper v1.2
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create QC plots error #3

Open gnilihzeux opened 4 years ago

gnilihzeux commented 4 years ago

Dear author, It's amazing that RiboTaper has his github site. I had been using RiboTaper for Ribo-seq analysis. But I had suffer a error and had no idea how to solve it.

Error information

Parameters used:

<Ribo_bamfile> /geneseed/Projects/ribo_test_20200415/HepG2/03-star/HepG2/HepG2.Aligned.sortedByCoord.out.bam
<RNA_bamfile> /geneseed/Projects/ribo_test_20200415/HepG2_rna/06-STAR_align/HepG2/HepG2.f66.bam
<annotation_dir> /geneseed/Database/ref_genome/hg19/RiboTaper_anno
<comma-sep_read_lenghts_ribo> 28,29,30,31,32
<comma-sep_cutoffs> 12,12,12,12,12
<n_cores> 16

---------------

Taking unique - best alignments...
Calculating P-sites...
------------processing 28 nt reads with offset of + 12
------------processing 29 nt reads with offset of + 12
------------processing 30 nt reads with offset of + 12
------------processing 31 nt reads with offset of + 12
------------processing 32 nt reads with offset of + 12
------------Done!
------------processing RNA-seq with offset of + 25
------------P_sites and RNA_sites calculated !!!
Creating tracks...
-----Calculating coverage tracks for each exon-----
-----Merging tracks together-----
-----Calculating coverage tracks for each exon-----
-----Merging tracks together-----
-----Calculating coverage tracks for each exon-----
-----Merging tracks together-----
Running calculations ccds...
[1] "--- analyzing ccds exonic tracks --- Sat May  9 16:03:21 2020"
[1] "--- track_analysis Done! --- Sat May  9 16:15:22 2020"
Running calculations exons_ccds...
[1] "--- analyzing exonsccds exonic tracks --- Sat May  9 16:15:23 2020"
[1] "--- track_analysis Done! --- Sat May  9 16:43:29 2020"
Running calculations nonccds...
[1] "--- analyzing nonccds exonic tracks --- Sat May  9 16:43:30 2020"
[1] "--- track_analysis Done! --- Sat May  9 16:48:50 2020"
Annotate exons...
[1] "--- annotating exons --- Sat May  9 16:48:51 2020"
[1] "--- annotating exons, Done! --- Sat May  9 16:51:07 2020"
Making quality plots...
[1] "--- create QC plots --- Sat May  9 16:51:08 2020"
Error in (function (..., deparse.level = 1, make.row.names = TRUE, stringsAsFactors = default.stringsAsFactors(),  :
  Wrong number of variable columns
Calls: do.call -> <Anonymous>
Exit
z626093820 commented 2 years ago

do you slove it?,I have the same error? thank you