Hello,

Yesterday during a Bioc class I teach one of my students had an error that
we were unable to solve and that I cannot explain. Basically he was unable
to read in a Bowtie paired-end alignment into his R session in a Mac laptop.
Others with the same version of ShortRead installed were able to, including
another Mac user (with a slightly newer OS version). My best guess is that
he needs to update his OS, but it could be something else. Any tips are more
than welcome!

The original file could be read into R as expected without any problems by
everyone except this student. Next we tried a few combinations related to
the type of line endings. We also tried to update ShortRead using biocLite;
the newest version (1.6.2) was the same one for his R version 2.11.1 There
shouldn't be any need to update to R 2.12.0 for this case as we read the
same file in other laptops with R 2.11.1 without problems. We also checked
with list.files() that in the given directory and with the given pattern
there was only 1 file that met the criteria.

The error message points out to the first argument (dirPath), yet that given
path doesn't even have spaces or other weird characters.



Original file: encoded in ANSI with UNIX line endings and the last line is
empty. The first four lines look like this:

"
HWUSI-EAS636_0009:8:1:1385:8497#0/2    +    gi|49175990|ref|NC_000913.2|
3307673    NTGCNGTGCAGAGATANCGTCGCGGGAACCTGCANC
####################################    0    0:C>N,4:A>N,16:C>N,34:A>N
HWUSI-EAS636_0009:8:1:1385:8497#0/1    -    gi|49175990|ref|NC_000913.2|
3308006    AGAACCGACCATGCCGGTTTCGCCTACGGAGTACGG
CD5DBD=<:CA55?DDD5=?DADDCDD=ADDBADDD    0
HWUSI-EAS636_0009:8:1:1386:4848#0/1    +    gi|49175990|ref|NC_000913.2|
101607    GATGCGCGTCACCCTGAATGCGCCAGGTCGTCATAA
GGGGGGGGEGFEGFGGEEGCEFGFEFGCFGEEEGE:    0
HWUSI-EAS636_0009:8:1:1386:4848#0/2    -    gi|49175990|ref|NC_000913.2|
101964    GNTTGATACCCTGTTGATGNTGGAAGTGTATNCGGN
######??>?>==9=9=9=,=?????64223(355(    0    0:C>N,4:C>N,16:C>N,34:G>N
"
The last five lines are:
"
HWUSI-EAS636_0009:8:2:7696:5953#0/1    +    gi|49175990|ref|NC_000913.2|
3424343    CGGTACTGGTTCACTATCGGTCAGTCAGGAGTATTT
GGFFGGGGEGGGGFGGGGEGGGGAGGGGGGGGFGGF    1
HWUSI-EAS636_0009:8:2:7696:5953#0/2    -    gi|49175990|ref|NC_000913.2|
3424690    GGAAATCGCCGGTTATAACGGTTCATATCACCTTAC
EFFEFBGEDEGEGGGFGGFGGGGGGGGDGEEGGGGG    1
HWUSI-EAS636_0009:8:2:7697:13321#0/1    +    gi|49175990|ref|NC_000913.2|
3162047    CCTGCCTGAGTGATTGCCAGCAGCATATCGGAAGCA
GEEFGGFGGGFGGGGGGGGGGGGGFGGFGFBGFGGG    0
HWUSI-EAS636_0009:8:2:7697:13321#0/2    -    gi|49175990|ref|NC_000913.2|
3162401    TTGAAGCTATCACCCGCTTTATAATTCAGGCCCGGC
FGEGGGFFDFF?GGGGGEFGGGFGGFFGGFFGGGGG    0

"
If you need the original file I can upload it (around 3MB zipped).

Modified file 1: encoded in ANSI with Mac line endings and the last line is
empty.
Modified file 2: encoded in ANSI with Mac line endings without the last
empty line.
Modified file 3: encoded in UTF-8 with Unix line endings and the last line
is empty. This gave a different kind of error related to the encoding of the
file.
Modified file 4: encoded in ANSI with Unix line endings without the last
empty line.
Transformation of the line endings and encoding was done with Notepad++
version 5.7

Laptop OS: Mac OS X, Version 10.5.8


> sessionInfo()
R version 2.11.1 (2010-05-31)
i386-apple-darwin9.8.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] ShortRead_1.6.2     Rsamtools_1.0.8     lattice_0.18-8
 Biostrings_2.16.9   GenomicRanges_1.0.9
[6] IRanges_1.6.17

loaded via a namespace (and not attached):
[1] Biobase_2.8.0 grid_2.11.1   hwriter_1.2

> aln <-
readAligned(dirPath="/Users/luismanuelbolanos/Documents/PDCB/Sem1_Bioconductor/sesion9/",
pattern="R017_8_iterative_short.map", type="Bowtie")
Error: Input/Output
  'readAligned' failed to parse files
  dirPath:
'/Users/luismanuelbolanos/Documents/PDCB/Sem1_Bioconductor/sesion9/'
  pattern: 'R017_8_iterative_short.map'
  type: 'Bowtie'
  error: invalid first argument

We also tried with the original file moved to path:
"'/Users/luismanuelbolanos/Documents/"


Thank you and greetings,
Leonardo

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