Rsubread error when aligning (- FATAL: INFLATE-ERROR=-5)
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Entering edit mode
@thomas-carroll-7019
Last seen 15 months ago
United States/New York/The Rockefeller …

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          

software error rsubread alignment • 977 views
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3
Entering edit mode
Wei Shi ★ 3.3k
@wei-shi-2183
Last seen 22 hours ago
Australia/Melbourne/Olivia Newton-John …

Sorry for the slow response. We downloaded the encode data used in your mapping and found that there is a bug in processing gzipped fastq input in align() function, which was introduced in the last release. It should be fixed soon.
 

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