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ribotricer-results's Issues

samples for real application

They located at
/staging/as/wenzhenl/re-ribo-analysis/SRP090415_human/mapped_hg38_reverse
SRX2189157
read lengths: 27,28,29,30
offsets: 12,12,12,12

SRX2189159
read lengths: 27,28,29,30
offsets: 12,12,12,12

installation ORF-RATER

Just want to document the way to install ORF-RATER to make it really work

conda install pysam=0.14 plastid pytables scikit-learn pybedtools ucsc-gtftogenepred ucsc-genepredtobed python-igraph

The pysam version need to be specified, the latest version 0.15 and the version required by plastid in its requirements 0.8.4 doesn't work, the error output is

File "libchtslib.pxd", line 2590, in init plastid.genomics.map_factories
ValueError: pysam.libchtslib.HTSFile has the wrong size, try recompiling. Expected 88, got 80

RiboTaper issues 

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
------------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 Dec 17 18:59:49 2018"
[1] "--- track_analysis Done! --- Mon Dec 17 22:08:37 2018"
Running calculations exons_ccds...
[1] "--- analyzing exonsccds exonic tracks --- Mon Dec 17 22:08:40 2018"
[1] "--- track_analysis Done! --- Tue Dec 18 00:18:21 2018"
Running calculations nonccds...
[1] "--- analyzing nonccds exonic tracks --- Tue Dec 18 00:18:22 2018"
[1] "--- track_analysis Done! --- Tue Dec 18 01:25:33 2018"
Annotate exons...
[1] "--- annotating exons --- Tue Dec 18 01:25:34 2018"
[1] "--- annotating exons, Done! --- Tue Dec 18 02:14:48 2018"
Making quality plots...
[1] "--- create QC plots --- Tue Dec 18 02:14:48 2018"
[1] FALSE
 [1]  1  2  3  4  5  6  7  8  9 10 11 12 13 14
null device
          1
[1] "--- QC plots Done! --- Tue Dec 18 02:18:00 2018"
CCDS ORF finding...
[1] "--- CCDS ORF finding --- Tue Dec 18 02:18:01 2018"
Error in { : task 2 failed - "argument of length 0"
Calls: %dopar% -> <Anonymous>
Execution halted

Taking unique - best alignments...
Calculating P-sites...
------------processing 28 nt reads with offset of + 12
------------processing 29 nt reads with offset of + 13
------------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 --- Tue Dec 18 00:48:55 2018"
[1] "--- track_analysis Done! --- Tue Dec 18 03:02:09 2018"
Running calculations exons_ccds...
[1] "--- analyzing exonsccds exonic tracks --- Tue Dec 18 03:02:10 2018"
[1] "--- track_analysis Done! --- Tue Dec 18 05:09:24 2018"
Running calculations nonccds...
[1] "--- analyzing nonccds exonic tracks --- Tue Dec 18 05:09:25 2018"
[1] "--- track_analysis Done! --- Tue Dec 18 06:02:27 2018"
Annotate exons...
[1] "--- annotating exons --- Tue Dec 18 06:02:27 2018"
[1] "--- annotating exons, Done! --- Tue Dec 18 06:42:09 2018"
Making quality plots...
[1] "--- create QC plots --- Tue Dec 18 06:42:10 2018"
[1] FALSE
 [1]  1  2  3  4  5  6  7  8  9 10 11 12 13 14
null device
          1
[1] "--- QC plots Done! --- Tue Dec 18 06:46:45 2018"
CCDS ORF finding...
[1] "--- CCDS ORF finding --- Tue Dec 18 06:46:45 2018"
Error in { : task 4 failed - "argument of length 0"
Calls: %dopar% -> <Anonymous>
Execution halted

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
------------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 Dec 17 14:57:26 2018"
[1] "--- track_analysis Done! --- Mon Dec 17 22:54:23 2018"
Running calculations exons_ccds...
[1] "--- analyzing exonsccds exonic tracks --- Mon Dec 17 22:54:24 2018"
[1] "--- track_analysis Done! --- Tue Dec 18 11:40:32 2018"
Running calculations nonccds...
[1] "--- analyzing nonccds exonic tracks --- Tue Dec 18 11:40:34 2018"
[1] "--- track_analysis Done! --- Tue Dec 18 13:34:48 2018"
Annotate exons...
[1] "--- annotating exons --- Tue Dec 18 13:34:48 2018"
[1] "--- annotating exons, Done! --- Tue Dec 18 14:29:20 2018"
Making quality plots...
[1] "--- create QC plots --- Tue Dec 18 14:29:22 2018"
[1] FALSE
 [1]  1  2  3  4  5  6  7  8  9 10 11 12 13 14
null device
          1
[1] "--- QC plots Done! --- Tue Dec 18 14:31:03 2018"
CCDS ORF finding...
[1] "--- CCDS ORF finding --- Tue Dec 18 14:31:04 2018"
Error in { :
  task 4 failed - "arguments imply differing number of rows: 670, 642"
Calls: %dopar% -> <Anonymous>
Execution halted

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