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model 25 completed out of 25 Error in parse(text = x) : <text>:2:0: unexpected end of input #10

Closed GoogleCodeExporter closed 8 years ago

GoogleCodeExporter commented 8 years ago 
1) What operating system are you using?
Linux server
2) What error message was displayed?
model  24  completed out of  25         ....[1] "The estimated proportion of 
enrichment for   
scer2_1315_polii_FC62TE4_7_CTT_files/test2_chrIX_win250bp_offset125bp.txt  has 
exceeded 0.5, suggesting difficulty in estimating enrichment.  Switching to 
more conservative model"

model  25  completed out of  25         Error in parse(text = x) : <text>:2:0: 
unexpected end of input
1: exp_count~ 
  ^

3) What was the exact command you used that resulted in the error?
zinba(
  align='Out_dir/',
  numProc=4,                    
  seq='test2.bed',
  basecountfile='test2.basecount',
  filetype="bed",
  outfile="scer2_1315_polii_FC62TE4_7_CTT",
  twoBit="/Database/Ucsc/scer2/map36/sacCer2.2bit",
  extension=100,
  printFullOut=1,
  refinepeaks=1,        
broad=T
)

4) Please copy and paste any additional screen output that resulted from
running the command

This is my entire command.

library(zinba)
generateAlignability(
   mapdir='/Database/Ucsc/scer2/map36/',
   outdir='Out_dir', 
   athresh=1,  
   extension=100,  
   twoBitFile='/Database/Ucsc/scer2/map36/sacCer2.2bit'
)   

basealigncount(
   inputfile='test2.bed', 
   outputfile='test2.basecount', 
   extension=100, 
   filetype='bed',
   twoBitFile='/Database/Ucsc/scer2/map36/sacCer2.2bit' )

zinba(
  align='Out_dir/',
  numProc=4,                    
  seq='test2.bed',
  basecountfile='test2.basecount',
  filetype="bed",
  outfile="scer2_1315_polii_FC62TE4_7_CTT",
  twoBit="/Database/Ucsc/scer2/map36/sacCer2.2bit",
  extension=100,
  printFullOut=1,
  refinepeaks=1,        
broad=T
)

and Many people who research in yeast.
I think they also need scer2 mappability files that made by your team.

---------------- ALIGN ADJUST COMPLETED SUCCESSFULLY ----------------
> basealigncount(
+    inputfile='test2.bed', 
+    outputfile='test2.basecount', 
+    extension=100, 
+    filetype='bed',
+    twoBitFile='/Database/Ucsc/scer2/map36/sacCer2.2bit' )

Importing reads from file test2.bed ....
        Reads are formatted as bed ....
        Extending reads by 100 bp....
        Getting chromosome lengths from .2bit file: /Database/Ucsc/scer2/map36/sacCer2.2bit
                For 2micron length is 6318
                For chrI length is 230208
                For chrII length is 813178
                For chrIII length is 316617
                For chrIV length is 1531919
                For chrIX length is 439885
                For chrV length is 576869
                For chrVI length is 270148
                For chrVII length is 1090947
                For chrVIII length is 562643
                For chrX length is 745742
                For chrXI length is 666454
                For chrXII length is 1078175
                For chrXIII length is 924429
                For chrXIV length is 784333
                For chrXV length is 1091289
                For chrXVI length is 948062
                For chrM length is 85779
                For chrM length is 85779

Loading bed formatted reads
        Skipped 0 reads
        Loaded 500000 reads
        Sorting reads ...COMPLETE

Calculating counts at each base
Processing 500000 reads
        Processing 2micron..........
                Initializing length to 6318
                18892 reads mapped to 2micron
                Printed results to test2.basecount
        Processing chrI..........
                Initializing length to 230208
                38414 reads mapped to chrI
                Printed results to test2.basecount
        Processing chrII..........
                Initializing length to 813178
                146335 reads mapped to chrII
                Printed results to test2.basecount
        Processing chrIII..........
                Initializing length to 316617
                51602 reads mapped to chrIII
                Printed results to test2.basecount
        Processing chrIV..........
                Initializing length to 1531919
                229042 reads mapped to chrIV
                Printed results to test2.basecount
        Processing chrIX..........
                Initializing length to 439885
                15715 reads mapped to chrIX
                Printed results to test2.basecount
-------- BASE ALIGN COUNTS COMPLETE SUCCESSFULLY --------
> zinba(
+   align='Out_dir/',
+   numProc=4,                    
+   seq='test2.bed',
+   basecountfile='test2.basecount',
+   filetype="bed",
+   outfile="scer2_1315_polii_FC62TE4_7_CTT",
+   twoBit="/Database/Ucsc/scer2/map36/sacCer2.2bit",
+   extension=100,
+   printFullOut=1,
+   refinepeaks=1,        
+ broad=T
+ )
[1] "parameters in effect:"
$filelist
NULL

$formula
NULL

$formulaE
NULL

$formulaZ
NULL

$outfile
[1] "scer2_1315_polii_FC62TE4_7_CTT"

$seq
[1] "test2.bed"

$align
[1] "Out_dir/"

$input
[1] "none"

$twoBit
[1] "/Database/Ucsc/scer2/map36/sacCer2.2bit"

$winSize
[1] 250

$offset
[1] 125

$cnvWinSize
[1] 1e+05

$cnvOffset
[1] 2500

$basecountfile
[1] "test2.basecount"

$threshold
[1] 0.05

$peakconfidence
[1] 0.95

$tol
[1] 1e-05

$numProc
[1] 4

$buildwin
[1] 1

$winGap
[1] 5000

$pWinSize
[1] 200

$pquant
[1] 1

$refinepeaks
[1] 1

$printFullOut
[1] 1

$method
[1] "mixture"

$initmethod
[1] "count"

$diff
[1] 0

$filetype
[1] "bed"

$extension
[1] 100

$cleanup
[1] FALSE

$selectmodel
[1] TRUE

$selectchr
[1] "chr22"

$selecttype
[1] "dirty"

$selectcovs
[1] "gcPerc"     "align_perc"

$FDR
[1] TRUE

Loading required package: multicore
Loading required package: doMC
Loading required package: foreach
Loading required package: iterators
Loading required package: codetools
foreach: simple, scalable parallel programming from Revolution Analytics
Use Revolution R for scalability, fault tolerance and more.
http://www.revolutionanalytics.com

Overwriting previously existing directory scer2_1315_polii_FC62TE4_7_CTT_files/

--------BEGIN BUILDING WINDOW DATA-------- 2012-01-12 15:20:46 

Importing reads from file test2.bed 
        Filetype is bed 
        Extension is 100 
        Getting chromosome lengths from .2bit file: /Database/Ucsc/scer2/map36/sacCer2.2bit
                For 2micron length is 6318
                For chrI length is 230208
                For chrII length is 813178
                For chrIII length is 316617
                For chrIV length is 1531919
                For chrIX length is 439885
                For chrV length is 576869
                For chrVI length is 270148
                For chrVII length is 1090947
                For chrVIII length is 562643
                For chrX length is 745742
                For chrXI length is 666454
                For chrXII length is 1078175
                For chrXIII length is 924429
                For chrXIV length is 784333
                For chrXV length is 1091289
                For chrXVI length is 948062
                For chrM length is 85779
                For chrM length is 85779
        Importing bed formatted reads
        Skipped 0 reads
        Imported 500000 reads
        Sorting reads ...COMPLETE

Building window data

Processing 2micron
        Initializing to length 6318
        Mapping reads to chromosome......
        Getting alignability info from:
                Out_dir/2micron.wig
        Getting sequence from .2bit file:
                /Database/Ucsc/scer2/map36/sacCer2.2bit
        Getting counts for 100000bp windows..........
                Refining boundaries....
                        Global variance is 0.201313
                        Refining 0 boundaries
        Getting counts for zinba windows..........
                Offset 0bp......
        Printed out data to scer2_1315_polii_FC62TE4_7_CTT_files/test2_2micron_win250bp_offset0bp.txt
                Offset 125bp......
        Printed out data to scer2_1315_polii_FC62TE4_7_CTT_files/test2_2micron_win250bp_offset125bp.txt

Processing chrI
        Initializing to length 230208
        Mapping reads to chromosome......
        Getting alignability info from:
                Out_dir/chrI.wig
        Getting sequence from .2bit file:
                /Database/Ucsc/scer2/map36/sacCer2.2bit
        Getting counts for 100000bp windows..........
                Refining boundaries....
                        Global variance is 0.000276553
                        Refining 0 boundaries
        Getting counts for zinba windows..........
                Offset 0bp......
        Printed out data to scer2_1315_polii_FC62TE4_7_CTT_files/test2_chrI_win250bp_offset0bp.txt
                Offset 125bp......
        Printed out data to scer2_1315_polii_FC62TE4_7_CTT_files/test2_chrI_win250bp_offset125bp.txt

Processing chrII
        Initializing to length 813178
        Mapping reads to chromosome......
        Getting alignability info from:
                Out_dir/chrII.wig
        Getting sequence from .2bit file:
                /Database/Ucsc/scer2/map36/sacCer2.2bit
        Getting counts for 100000bp windows..........
                Refining boundaries....
                        Global variance is 0.00134974
                        Refining 2 boundaries
        Getting counts for zinba windows..........
                Offset 0bp......
        Printed out data to scer2_1315_polii_FC62TE4_7_CTT_files/test2_chrII_win250bp_offset0bp.txt
                Offset 125bp......
        Printed out data to scer2_1315_polii_FC62TE4_7_CTT_files/test2_chrII_win250bp_offset125bp.txt

Processing chrIII
        Initializing to length 316617
        Mapping reads to chromosome......
        Getting alignability info from:
                Out_dir/chrIII.wig
        Getting sequence from .2bit file:
                /Database/Ucsc/scer2/map36/sacCer2.2bit
        Getting counts for 100000bp windows..........
                Refining boundaries....
                        Global variance is 0.000388305
                        Refining 1 boundaries
        Getting counts for zinba windows..........
                Offset 0bp......
        Printed out data to scer2_1315_polii_FC62TE4_7_CTT_files/test2_chrIII_win250bp_offset0bp.txt
                Offset 125bp......
        Printed out data to scer2_1315_polii_FC62TE4_7_CTT_files/test2_chrIII_win250bp_offset125bp.txt

Processing chrIV
        Initializing to length 1531919
        Mapping reads to chromosome......
        Getting alignability info from:
                Out_dir/chrIV.wig
        Getting sequence from .2bit file:
                /Database/Ucsc/scer2/map36/sacCer2.2bit
        Getting counts for 100000bp windows..........
                Refining boundaries....
                        Global variance is 0.00061571
                        Refining 2 boundaries
        Getting counts for zinba windows..........
                Offset 0bp......
        Printed out data to scer2_1315_polii_FC62TE4_7_CTT_files/test2_chrIV_win250bp_offset0bp.txt
                Offset 125bp......
        Printed out data to scer2_1315_polii_FC62TE4_7_CTT_files/test2_chrIV_win250bp_offset125bp.txt

Processing chrIX
        Initializing to length 439885
        Mapping reads to chromosome......
        Getting alignability info from:
                Out_dir/chrIX.wig
        Getting sequence from .2bit file:
                /Database/Ucsc/scer2/map36/sacCer2.2bit
        Getting counts for 100000bp windows..........
                Refining boundaries....
                        Global variance is 0.000683106
                        Refining 1 boundaries
        Getting counts for zinba windows..........
                Offset 0bp......
        Printed out data to scer2_1315_polii_FC62TE4_7_CTT_files/test2_chrIX_win250bp_offset0bp.txt
                Offset 125bp......
        Printed out data to scer2_1315_polii_FC62TE4_7_CTT_files/test2_chrIX_win250bp_offset125bp.txt

--------BUILD WINDOWS COMPLETE-------

--------STARTING MODEL SELECTION-------- 2012-01-12 15:20:50 

Specified chromosome not found or specified, using 
scer2_1315_polii_FC62TE4_7_CTT_files/test2_chrIX_win250bp_offset125bp.txt 
$`1`
exp_count ~ 1
<environment: 0x103e91f20>

$`2`
exp_count ~ align_perc + 1
<environment: 0x103e91f20>

$`3`
exp_count ~ gcPerc + 1
<environment: 0x103e91f20>

$`4`
exp_count ~ align_perc + gcPerc + 1
<environment: 0x103e91f20>

$`5`
exp_count ~ align_perc + gcPerc + align_perc:gcPerc + 1
<environment: 0x103e91f20>

...........[1] "The estimated proportion of enrichment for   
scer2_1315_polii_FC62TE4_7_CTT_files/test2_chrIX_win250bp_offset125bp.txt  has 
exceeded 0.5, suggesting difficulty in estimating enrichment.  Switching to 
more conservative model"
[1] "The estimated proportion of enrichment for   
scer2_1315_polii_FC62TE4_7_CTT_files/test2_chrIX_win250bp_offset125bp.txt  has 
exceeded 0.5, suggesting difficulty in estimating enrichment.  Switching to 
more conservative model"
.
model  1  completed out of  25  [1] "The estimated proportion of enrichment for 
  scer2_1315_polii_FC62TE4_7_CTT_files/test2_chrIX_win250bp_offset125bp.txt  
has exceeded 0.5, suggesting difficulty in estimating enrichment.  Switching to 
more conservative model"
[1] "The estimated proportion of enrichment for   
scer2_1315_polii_FC62TE4_7_CTT_files/test2_chrIX_win250bp_offset125bp.txt  has 
exceeded 0.5, suggesting difficulty in estimating enrichment.  Switching to 
more conservative model"

model  2  completed out of  25 
model  4  completed out of  25 
model  3  completed out of  25  ...........[1] "The estimated proportion of 
enrichment for   
scer2_1315_polii_FC62TE4_7_CTT_files/test2_chrIX_win250bp_offset125bp.txt  has 
exceeded 0.5, suggesting difficulty in estimating enrichment.  Switching to 
more conservative model"

model  5  completed out of  25  ..[1] "The estimated proportion of enrichment 
for   scer2_1315_polii_FC62TE4_7_CTT_files/test2_chrIX_win250bp_offset125bp.txt 
 has exceeded 0.5, suggesting difficulty in estimating enrichment.  Switching 
to more conservative model"
[1] "The estimated proportion of enrichment for   
scer2_1315_polii_FC62TE4_7_CTT_files/test2_chrIX_win250bp_offset125bp.txt  has 
exceeded 0.5, suggesting difficulty in estimating enrichment.  Switching to 
more conservative model"
.[1] "The estimated proportion of enrichment for   
scer2_1315_polii_FC62TE4_7_CTT_files/test2_chrIX_win250bp_offset125bp.txt  has 
exceeded 0.5, suggesting difficulty in estimating enrichment.  Switching to 
more conservative model"

model  8  completed out of  25 
model  6  completed out of  25 
model  7  completed out of  25  ..........[1] "The estimated proportion of 
enrichment for   
scer2_1315_polii_FC62TE4_7_CTT_files/test2_chrIX_win250bp_offset125bp.txt  has 
exceeded 0.5, suggesting difficulty in estimating enrichment.  Switching to 
more conservative model"
..[1] "The estimated proportion of enrichment for   
scer2_1315_polii_FC62TE4_7_CTT_files/test2_chrIX_win250bp_offset125bp.txt  has 
exceeded 0.5, suggesting difficulty in estimating enrichment.  Switching to 
more conservative model"
[1] "The estimated proportion of enrichment for   
scer2_1315_polii_FC62TE4_7_CTT_files/test2_chrIX_win250bp_offset125bp.txt  has 
exceeded 0.5, suggesting difficulty in estimating enrichment.  Switching to 
more conservative model"
.
model  9  completed out of  25 
model  11  completed out of  25 
model  10  completed out of  25         .[1] "The estimated proportion of 
enrichment for   
scer2_1315_polii_FC62TE4_7_CTT_files/test2_chrIX_win250bp_offset125bp.txt  has 
exceeded 0.5, suggesting difficulty in estimating enrichment.  Switching to 
more conservative model"

model  12  completed out of  25         .........[1] "The estimated proportion 
of enrichment for   
scer2_1315_polii_FC62TE4_7_CTT_files/test2_chrIX_win250bp_offset125bp.txt  has 
exceeded 0.5, suggesting difficulty in estimating enrichment.  Switching to 
more conservative model"
..[1] "The estimated proportion of enrichment for   
scer2_1315_polii_FC62TE4_7_CTT_files/test2_chrIX_win250bp_offset125bp.txt  has 
exceeded 0.5, suggesting difficulty in estimating enrichment.  Switching to 
more conservative model"
[1] "The estimated proportion of enrichment for   
scer2_1315_polii_FC62TE4_7_CTT_files/test2_chrIX_win250bp_offset125bp.txt  has 
exceeded 0.5, suggesting difficulty in estimating enrichment.  Switching to 
more conservative model"
.
model  13  completed out of  25 
model  15  completed out of  25 
model  14  completed out of  25         .[1] "The estimated proportion of 
enrichment for   
scer2_1315_polii_FC62TE4_7_CTT_files/test2_chrIX_win250bp_offset125bp.txt  has 
exceeded 0.5, suggesting difficulty in estimating enrichment.  Switching to 
more conservative model"

model  16  completed out of  25         .............[1] "The estimated 
proportion of enrichment for   
scer2_1315_polii_FC62TE4_7_CTT_files/test2_chrIX_win250bp_offset125bp.txt  has 
exceeded 0.5, suggesting difficulty in estimating enrichment.  Switching to 
more conservative model"
[1] "The estimated proportion of enrichment for   
scer2_1315_polii_FC62TE4_7_CTT_files/test2_chrIX_win250bp_offset125bp.txt  has 
exceeded 0.5, suggesting difficulty in estimating enrichment.  Switching to 
more conservative model"
.[1] "The estimated proportion of enrichment for   
scer2_1315_polii_FC62TE4_7_CTT_files/test2_chrIX_win250bp_offset125bp.txt  has 
exceeded 0.5, suggesting difficulty in estimating enrichment.  Switching to 
more conservative model"

model  17  completed out of  25 
model  18  completed out of  25 
model  19  completed out of  25         ..[1] "The estimated proportion of 
enrichment for   
scer2_1315_polii_FC62TE4_7_CTT_files/test2_chrIX_win250bp_offset125bp.txt  has 
exceeded 0.5, suggesting difficulty in estimating enrichment.  Switching to 
more conservative model"

model  20  completed out of  25         ............[1] "The estimated 
proportion of enrichment for   
scer2_1315_polii_FC62TE4_7_CTT_files/test2_chrIX_win250bp_offset125bp.txt  has 
exceeded 0.5, suggesting difficulty in estimating enrichment.  Switching to 
more conservative model"
.[1] "The estimated proportion of enrichment for   
scer2_1315_polii_FC62TE4_7_CTT_files/test2_chrIX_win250bp_offset125bp.txt  has 
exceeded 0.5, suggesting difficulty in estimating enrichment.  Switching to 
more conservative model"

model  21  completed out of  25         .
model  22  completed out of  25         [1] "The estimated proportion of 
enrichment for   
scer2_1315_polii_FC62TE4_7_CTT_files/test2_chrIX_win250bp_offset125bp.txt  has 
exceeded 0.5, suggesting difficulty in estimating enrichment.  Switching to 
more conservative model"
.
model  23  completed out of  25         .[1] "The estimated proportion of 
enrichment for   
scer2_1315_polii_FC62TE4_7_CTT_files/test2_chrIX_win250bp_offset125bp.txt  has 
exceeded 0.5, suggesting difficulty in estimating enrichment.  Switching to 
more conservative model"

model  24  completed out of  25         ....[1] "The estimated proportion of 
enrichment for   
scer2_1315_polii_FC62TE4_7_CTT_files/test2_chrIX_win250bp_offset125bp.txt  has 
exceeded 0.5, suggesting difficulty in estimating enrichment.  Switching to 
more conservative model"

model  25  completed out of  25         Error in parse(text = x) : <text>:2:0: 
unexpected end of input
1: exp_count~ 
  ^

Original issue reported on code.google.com by junna...@gmail.com on 12 Jan 2012 at 10:28

GoogleCodeExporter commented 8 years ago 
[deleted comment]
GoogleCodeExporter commented 8 years ago 
We are current working on an update that will help better diagnose the issue 
that you are having.  The update should finish testing by this saturday, and I 
will notify you when it is posted.

Original comment by homer...@gmail.com on 31 Jan 2012 at 5:36

GoogleCodeExporter commented 8 years ago 
we are currently incorporating these issues into a new zinba version, check 
back soon for a comprehensive update

Original comment by homer...@gmail.com on 20 Nov 2012 at 8:54