hi,
I have come across a problem when aligning some encode data.
My command is here and the output below. The other files i have aligned all seem to work and this file aligned using BWA,
Any suggestions as to what may be wrong?
align(index,"/Users/tcarroll/wgEncodeSydhTfbsCh12InputIggrabRawData.fastq.gz",nthreads=4,type=1,complexIndels=FALSE,phredOffset=64)
all seems is okay until..
|| Map reads... ||
|| 37% completed, 5.1 mins elapsed, total=37680k reads, rate=46.7k/s ||
|| 43% completed, 5.7 mins elapsed, total=38721k reads, rate=49.9k/s ||
FATAL: INFLATE-ERROR=-5 POS=779172028
|| Finish the 6,512,627 reads... ||
FATAL: INFLATE-ERROR=-5 POS=779172028
|| ||
|| Completed successfully. ||
|| ||
\\============================================================================//
//================================= Summary ==================================\\
|| ||
|| Processed : 20,493,639 reads ||
|| Mapped : 851,708 reads (4.2%) ||
|| Indels : 1,103 ||
|| ||
|| Running time : 6.1 minutes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11 (El Capitan)
locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] QuasR_1.10.0 Rbowtie_1.10.0 Rsubread_1.20.2 ShortRead_1.28.0
[5] GenomicAlignments_1.6.1 SummarizedExperiment_1.0.1 Biobase_2.30.0 Rsamtools_1.22.0
[9] GenomicRanges_1.22.1 GenomeInfoDb_1.6.1 Biostrings_2.38.2 XVector_0.10.0
[13] IRanges_2.4.4 S4Vectors_0.8.3 BiocGenerics_0.16.1 BiocParallel_1.4.0
loaded via a namespace (and not attached):
[1] AnnotationDbi_1.32.0 zlibbioc_1.16.0 BSgenome_1.38.0 lattice_0.20-33 hwriter_1.3.2
[6] tools_3.2.2 grid_3.2.2 DBI_0.3.1 latticeExtra_0.6-26 lambda.r_1.1.7
[11] futile.logger_1.4.1 GenomicFiles_1.6.0 rtracklayer_1.30.1 RColorBrewer_1.1-2 futile.options_1.0.0
[16] bitops_1.0-6 biomaRt_2.26.1 RCurl_1.95-4.7 RSQLite_1.0.0 BiocInstaller_1.20.1
[21] GenomicFeatures_1.22.5 XML_3.98-1.3
>
