Hi,

I am running Rsubread to align some RNA-seq data (paired end). I've tried some fastq files and it worked perfectly, however in some fastq it shoots me an error after a while (it starts the alignment but it stops always at the same position, i.e. 35%)  

The code is just this:

# Index
indexdirectory= "hg19index/hg19index"

#Alignment
align(index=indexdirectory,
      readfile1="uniquefastq/unique_C42_sh8_ETOH_1_R1.fastq.gz",
      readfile2="uniquefastq/unique_C42_sh8_ETOH_1_R2.fastq.gz",
      type="rna",
      input_format="gzFASTQ",
      output_file="C42_sh8_ETOH_1.bam",
      nthreads=12,
      phredOffset=33,output_format="BAM",unique=TRUE,indels=5,detectSV=F)

And the error is: 

35% completed, 28 mins elapsed, rate=10.0k fragments per second

*** caught segfault ***
address 0x7fa02e4202d0, cause 'invalid permissions'

Traceback:
1: .C("R_align_wrapper", as.integer(n), as.character(cmd), PACKAGE = "Rsubread")
2: align(index=indexdirectory, readfile1="uniquefastq/unique_C42_sh8_ETOH_1_R1.fastq.gz", readfile2="uniquefastq/unique_C42_sh8_ETOH_1_R2.fastq.gz", type="rna", input_format="gzFASTQ", output_file="C42_sh8_ETOH_1.bam", nthreads=12, phredOffset=33,output_format="BAM",unique=TRUE,indels=5,detectSV=F)
3: eval(expr, envir, enclos)
4: eval(ei, envir)
5: withVisible(eval(ei, envir))
6: source("RNAseq.R")

Possible actions:

....

How could I solve it? I guess that the problem might be in the fastq file.

Another question related to this, does the setting of phredOffset number have any influence on the output?

Thank you!