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gnilihzeux / RiboTaper

A copy RiboTaper v1.3.1a and some debugs by myself
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CCDS ORF finding error #2

Open Timothy-sun opened 3 years ago

Timothy-sun commented 3 years ago

Parameters used:

/ifs/home/sunhang/Riboseq/20210308/ribo.bam /ifs/home/sunhang/Riboseq/20210308/rna.bam /ifs/home/sunhang/Riboseq/20210308/annotation 26,28,29 9,12,12 16 --------------- Taking unique - best alignments... Calculating P-sites... ------------processing 26 nt reads with offset of + 9 ------------processing 28 nt reads with offset of + 12 ------------processing 29 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 --- Mon Mar 8 13:43:29 2021" [1] "--- track_analysis Done! --- Mon Mar 8 13:58:54 2021" Running calculations exons_ccds... [1] "--- analyzing exonsccds exonic tracks --- Mon Mar 8 13:58:54 2021" [1] "--- track_analysis Done! --- Mon Mar 8 14:29:42 2021" Running calculations nonccds... [1] "--- analyzing nonccds exonic tracks --- Mon Mar 8 14:29:45 2021" [1] "--- track_analysis Done! --- Mon Mar 8 14:39:01 2021" Annotate exons... [1] "--- annotating exons --- Mon Mar 8 14:39:01 2021" [1] "--- annotating exons, Done! --- Mon Mar 8 14:41:14 2021" Making quality plots... [1] "--- create QC plots --- Mon Mar 8 14:41:15 2021" [1] FALSE [1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 null device 1 [1] "--- QC plots Done! --- Mon Mar 8 14:41:58 2021" CCDS ORF finding... [1] "--- CCDS ORF finding --- Mon Mar 8 14:41:58 2021" Error in { : task 4 failed - "arguments imply differing number of rows: 669, 649" Calls: %dopar% ->
ding1109 commented 1 month ago

Parameters used:

/ifs/home/sunhang/Riboseq/20210308/ribo.bam /ifs/home/sunhang/Riboseq/20210308/rna.bam /ifs/home/sunhang/Riboseq/20210308/annotation 26,28,29 9,12,12 16 Taking unique - best alignments... Calculating P-sites... ------------processing 26 nt reads with offset of + 9 ------------processing 28 nt reads with offset of + 12 ------------processing 29 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 --- Mon Mar 8 13:43:29 2021" [1] "--- track_analysis Done! --- Mon Mar 8 13:58:54 2021" Running calculations exons_ccds... [1] "--- analyzing exonsccds exonic tracks --- Mon Mar 8 13:58:54 2021" [1] "--- track_analysis Done! --- Mon Mar 8 14:29:42 2021" Running calculations nonccds... [1] "--- analyzing nonccds exonic tracks --- Mon Mar 8 14:29:45 2021" [1] "--- track_analysis Done! --- Mon Mar 8 14:39:01 2021" Annotate exons... [1] "--- annotating exons --- Mon Mar 8 14:39:01 2021" [1] "--- annotating exons, Done! --- Mon Mar 8 14:41:14 2021" Making quality plots... [1] "--- create QC plots --- Mon Mar 8 14:41:15 2021" [1] FALSE [1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 null device 1 [1] "--- QC plots Done! --- Mon Mar 8 14:41:58 2021" CCDS ORF finding... [1] "--- CCDS ORF finding --- Mon Mar 8 14:41:58 2021" Error in { : task 4 failed - "arguments imply differing number of rows: 669, 649" Calls: %dopar% ->

I encountered the same issue as described： Making quality plots... [1] "--- create QC plots --- Mon Jul 15 20:17:09 2024" [1] FALSE [1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 null device 1 [1] "--- QC plots Done! --- Mon Jul 15 20:18:18 2024" CCDS ORF finding... [1] "--- CCDS ORF finding --- Mon Jul 15 20:18:18 2024" Error in { : task 1 failed - "arguments imply differing number of rows: 2551, 1893" Calls: %dopar% -> Execution halted

Could you please let me know if you have resolved this issue and, if so, how you managed to fix it?

Thank you very much for your assistance.