[Bioc-sig-seq] ShortRead qa() no longer working

[Martin Morgan]

  On 8/25/2010 5:00 PM, Dario Strbenac wrote:
> Hello again,
>
> Both of those checks worked out, and I still get the error :
>
>> fl = list.files(path, "fastq.gz", full=TRUE)
>> fl
> [1] "C:/Users/dario/Documents/Garvan/rawData/seq/Ramaciotti/25-03-2010/s_1_1/s_1_sequence.fastq.gz"
>>
>>
>> .Call(ShortRead:::.read_solexa_fastq, fl, TRUE)
> $sread
>    A DNAStringSet instance of length 27278762
>             width seq
>         [1]    36 TTCAATGATTCCATTTGATTCCATNNGNNNNNNNNT
>         [2]    36 TGGAATCGTCATCGAATGAATTGANNGNNNNNNNNG
>         [3]    36 TATAAAAACTAGACGGAGTCATTCNNANNNNNNNNT
>         [4]    36 GCAAAGCTCTTTTCCGTTTGACTCNNGNNNNNNNNA
>         [5]    36 TGTTGATTCCATTCGATTCCATTCNNTNANNNNNNC
>         [6]    36 GGAGTTCGAGACTGGCCTGGCCAANATNGNNNNNNC
>         [7]    36 GAACAGTTTCATCACATGTAGTAAGCANAGNNNNNG
>         [8]    36 TGACTCCTTTCATTTCCATTCGATNATNANNNNNNT
>         [9]    36 TAAGGAGGATTTTAGGTATGGGTTTTTCATANNTGC
>         ...   ... ...
> [27278754]    36 GAACCTGAGAGGCGGAGGTTGCGGTGNGCAAAGAGT
> [27278755]    36 TGGAATCTAATGGAATAATTGAACAGNAATGAATGG
> [27278756]    36 GGAATCAATATCAAACGGAAAAAAACNGAATTATCG
> [27278757]    36 TGGAAATGAATGGAATCATCATCGAANGGAATCGAA
> [27278758]    36 NATCACTCCCGGCTAACTTTTCATATNTTTTGTAGA
> [27278759]    36 NCATGCTGAGAAAGTTCTTCATGACGNATGCATTTA
> [27278760]    36 NAATGGACTCAAATGGAATTATCCTCNAATGGAATC
> [27278761]    36 NAGAAAAGGAAATATCTTCGTATAAANACTAGACAG
> [27278762]    36 NTATCGAATGGAATCGAAGAGAATCANCGAATGGCC
>
> $id
>    A BStringSet instance of length 27278762
>             width seq
>         [1]    22 GAPC:1:1:1142:2476#0/1
>         [2]    23 GAPC:1:1:1142:10510#0/1
>         [3]    23 GAPC:1:1:1143:16066#0/1
>         [4]    23 GAPC:1:1:1144:20655#0/1
>         [5]    23 GAPC:1:1:1144:15460#0/1
>         [6]    22 GAPC:1:1:1145:9727#0/1
>         [7]    22 GAPC:1:1:1145:4010#0/1
>         [8]    23 GAPC:1:1:1145:21159#0/1
>         [9]    22 GAPC:1:1:1147:6527#0/1
>         ...   ... ...
> [27278754]    25 GAPC:1:120:19834:3792#0/1
> [27278755]    26 GAPC:1:120:19836:10159#0/1
> [27278756]    26 GAPC:1:120:19838:12475#0/1
> [27278757]    25 GAPC:1:120:19840:4819#0/1
> [27278758]    26 GAPC:1:120:19844:11082#0/1
> [27278759]    25 GAPC:1:120:19848:9908#0/1
> [27278760]    25 GAPC:1:120:19854:3323#0/1
> [27278761]    26 GAPC:1:120:19856:17724#0/1
> [27278762]    25 GAPC:1:120:19864:9093#0/1
>
> $quality
>    A BStringSet instance of length 27278762
>             width seq
>         [1]    36 babbbbbbbbbbbbbbb`bbBBBBBBBBBBBBBBBB
>         [2]    36 bbbbbbbbbbbbbbb\bb^^BBBBBBBBBBBBBBBB
>         [3]    36 a_aa\ab]]aabbbbbbb_bBBBBBBBBBBBBBBBB
>         [4]    36 bYbb\bbbbbbbb^`^XZ]^BBBBBBBBBBBBBBBB
>         [5]    36 ___[_YU^Y^^^^aaT^W^^BBBBBBBBBBBBBBBB
>         [6]    36 OOONNOOOON\bb_bbbbbBBBBBBBBBBBBBBBBB
>         [7]    36 BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
>         [8]    36 ^bY_bb_bb]^b_bbbb\b^BBBBBBBBBBBBBBBB
>         [9]    36 OOOOLOGNNO]]SZ]`TW^`]XU]]a`aa`BBBBBB
>         ...   ... ...
> [27278754]    36 ]Z]]]Q___[UWWWZ]^`O^BBBBBBBBBBBBBBBB
> [27278755]    36 b`bb`bbbca````_bbba`[a_a`[B^[^^^Z^^`
> [27278756]    36 `bbbbb`_bZ\X\Z\a_aBBBBBBBBBBBBBBBBBB
> [27278757]    36 bbbbb__a___aa_aabbab_bbbbBBBBBBBBBBB
> [27278758]    36 BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
> [27278759]    36 BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
> [27278760]    36 BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
> [27278761]    36 BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
> [27278762]    36 BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
>
>>
>> QAfastq<- qa(path, "fastq.gz", "fastq")
> Error in stop(msg, " ", errors, domain = NA) :
>    no function to return from, jumping to top level
> Error in slot(object, ".srlist") :
>    cannot get a slot (".srlist") from an object of type "NULL"
> In addition: Warning message:
> UnspecifiedWarning
>    elements: 1
>    UnspecifiedError: qa(readFastq(dirPath, pattern, ...), pattern, verbose = verbose)
>   error in evaluating the argument 'dirPath' in selecting a method for function 'qa'

hmm. I'm assuming that

   example(readFastq)
   qa(analysisPath(sp), "s_1_sequence.txt", "fastq")

works, too. The error is I think occurring in ShortRead:::.qa_fastq_lane

 > ShortRead:::.qa_fastq_lane
function (dirPath, pattern, ..., type = "fastq", verbose = FALSE)
{
     if (verbose)
         message("qa 'fastq' pattern:", pattern)
     qa(readFastq(dirPath, pattern, ...), pattern, verbose = verbose)
}
<environment: namespace:ShortRead>

This should be verified with traceback() after the error occurs.

You can try adding verbose=TRUE to your function call

   debug(ShortRead:::.qa_fastq_lane)

and then the instructions for ?browser to step through, or to invoke the 
components of the function call as appropriate, e.g., readFastq(dirPath, 
pattern), the return type of which should always have 
class(readFastq(dirPath, pattern)) == "ShortReadQ".

It might also help to narrow down whether it is the file (e.g., size) or 
the file location; can you read the file from another directory 
location, or read a file in the same location that contains a smaller 
number of reads?

I'm sorry not to be able to provide more direct assistance; I can't get 
a reproducible example on my end.

Martin