Extracting file list from remote gzipped tar file without downloading tar (getting "embedded nuls" error)

I'm trying to get a file list (and then extract specific files) from a large (300-600 MB) remotely-hosted tar.gz file -- without downloading the entire file. However, I don't quite understand whether my file should be treated as binary or not, or how to get rid of embedded nuls without manipulating the file. I've seen questions that address remote gzipped binary files or untarring local gzipped files but not untarring remotely-hosted gzipped tar files.

I've tried using gzfile:

example.url <- "https://neon-microbial-raw-seq-files.s3.data.neonscience.org/2017/BMI_B69RN_ITS_R1_fastq.tar.gz"
  con <- gzfile(example.url)
  test.list <- utils::untar(
    tarfile = con,
    list = T)

which returns:

Error in readBin(con, "raw", n = 512L) : 
  can only read from a binary connection

If I run open(con, "rb"), I get an error saying the file doesn't exist. Opening the connection as binary without gzfile() instead gives an error about embedded nulls:

 bcon <- url("https://neon-microbial-raw-seq-files.s3.data.neonscience.org/2017/BMI_B69RN_ITS_R1_fastq.tar.gz") 
  open(bcon, "rb")
  test.list <- utils::untar(
    tarfile = bcon,
    list = T)

which returns:

Error in rawToChar(block[seq_len(ns)]) : 
  embedded nul in string: '\037\x8b\b\0\x9e\x9c\xbbZ\0\003\xec[is䶙\x9e\xcf\xfe\025\xfe\xc8\003\xea\xe6\t\x9eM\022\004\001T\xaa\034'\xb1\xb9\x95\xfd65\xb5\xf1Ʈ\xb5=\x8e=\xaeڟ\xbf\xef\001\xb2[Rk\xd4s9\x9br \x89\r\002 \xc0\026\037>\xef\x89\xc3\xf1p\x9c\xbex\xfd\xe3\u07ff\xf8\xee\xc7\xffy\xf1iJ\xc2\xe5\xa9\xcf$K'

Lastly, using gzcon returns a different error involving embedded nulls:

 test.list <- utils::untar(
    tarfile = gzcon(url(example.url)),
    list = T)

which returns:

Error in rawToChar(block[seq_len(ns)]) : 
  embedded nul in string: '././@LongLink\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\00000000\00000000\00000000\000000000201\000000000000\0011556\0 L\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0ustar  \0root\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0root'

Any help is appreciated!

Solution

You can get the contents of the tar.gz by opening a binary read connection, wrapping it with gzcon and then using untar, as shown below.

However, this does download the whole archive, since untar needs to read the whole file to see what's in it. There is no master directory in a tar file for untar to read; each file always has its own 512-byte header block. You don't need to save it to your hard disk to read the directory, but it may be just as easy to do so.

example.url <- "https://neon-microbial-raw-seq-files.s3.data.neonscience.org/2017/BMI_B69RN_ITS_R1_fastq.tar.gz"
con <- file(example.url, open = "rb")
gzcon_con <- gzcon(con)
untar(gzcon_con, list = TRUE)
#>  [1] "hpc/home/minardsmitha/NEON/16S_ITS_Aug-Sept_2017/Sept_5_Run_B69RN/RAW_FASTQ/ITS/RAW_Upload_to_BOX/BMI_Plate1WellA10_ITS_R1.fastq"
#>  [2] "hpc/home/minardsmitha/NEON/16S_ITS_Aug-Sept_2017/Sept_5_Run_B69RN/RAW_FASTQ/ITS/RAW_Upload_to_BOX/BMI_Plate1WellA11_ITS_R1.fastq"
#>  [3] "hpc/home/minardsmitha/NEON/16S_ITS_Aug-Sept_2017/Sept_5_Run_B69RN/RAW_FASTQ/ITS/RAW_Upload_to_BOX/BMI_Plate1WellA12_ITS_R1.fastq"
#>  [4] "hpc/home/minardsmitha/NEON/16S_ITS_Aug-Sept_2017/Sept_5_Run_B69RN/RAW_FASTQ/ITS/RAW_Upload_to_BOX/BMI_Plate1WellA1_ITS_R1.fastq" 
#>  [5] "hpc/home/minardsmitha/NEON/16S_ITS_Aug-Sept_2017/Sept_5_Run_B69RN/RAW_FASTQ/ITS/RAW_Upload_to_BOX/BMI_Plate1WellA2_ITS_R1.fastq" 
#>  [6] "hpc/home/minardsmitha/NEON/16S_ITS_Aug-Sept_2017/Sept_5_Run_B69RN/RAW_FASTQ/ITS/RAW_Upload_to_BOX/BMI_Plate1WellA3_ITS_R1.fastq" 
#>  [7] "hpc/home/minardsmitha/NEON/16S_ITS_Aug-Sept_2017/Sept_5_Run_B69RN/RAW_FASTQ/ITS/RAW_Upload_to_BOX/BMI_Plate1WellA4_ITS_R1.fastq" 
#>  [8] "hpc/home/minardsmitha/NEON/16S_ITS_Aug-Sept_2017/Sept_5_Run_B69RN/RAW_FASTQ/ITS/RAW_Upload_to_BOX/BMI_Plate1WellA5_ITS_R1.fastq" 
#>  [9] "hpc/home/minardsmitha/NEON/16S_ITS_Aug-Sept_2017/Sept_5_Run_B69RN/RAW_FASTQ/ITS/RAW_Upload_to_BOX/BMI_Plate1WellA6_ITS_R1.fastq" 
#> [10] "hpc/home/minardsmitha/NEON/16S_ITS_Aug-Sept_2017/Sept_5_Run_B69RN/RAW_FASTQ/ITS/RAW_Upload_to_BOX/BMI_Plate1WellA7_ITS_R1.fastq" 
#> [11] "hpc/home/minardsmitha/NEON/16S_ITS_Aug-Sept_2017/Sept_5_Run_B69RN/RAW_FASTQ/ITS/RAW_Upload_to_BOX/BMI_Plate1WellA8_ITS_R1.fastq" 
#> [12] "hpc/home/minardsmitha/NEON/16S_ITS_Aug-Sept_2017/Sept_5_Run_B69RN/RAW_FASTQ/ITS/RAW_Upload_to_BOX/BMI_Plate1WellB11_ITS_R1.fastq"
#> [13] "hpc/home/minardsmitha/NEON/16S_ITS_Aug-Sept_2017/Sept_5_Run_B69RN/RAW_FASTQ/ITS/RAW_Upload_to_BOX/BMI_Plate1WellB12_ITS_R1.fastq"
#> [14] "hpc/home/minardsmitha/NEON/16S_ITS_Aug-Sept_2017/Sept_5_Run_B69RN/RAW_FASTQ/ITS/RAW_Upload_to_BOX/BMI_Plate1WellB1_ITS_R1.fastq" 
#> [15] "hpc/home/minardsmitha/NEON/16S_ITS_Aug-Sept_2017/Sept_5_Run_B69RN/RAW_FASTQ/ITS/RAW_Upload_to_BOX/BMI_Plate1WellB2_ITS_R1.fastq" 
#> [16] "hpc/home/minardsmitha/NEON/16S_ITS_Aug-Sept_2017/Sept_5_Run_B69RN/RAW_FASTQ/ITS/RAW_Upload_to_BOX/BMI_Plate1WellB3_ITS_R1.fastq" 
#> [17] "hpc/home/minardsmitha/NEON/16S_ITS_Aug-Sept_2017/Sept_5_Run_B69RN/RAW_FASTQ/ITS/RAW_Upload_to_BOX/BMI_Plate1WellB4_ITS_R1.fastq" 
#> [18] "hpc/home/minardsmitha/NEON/16S_ITS_Aug-Sept_2017/Sept_5_Run_B69RN/RAW_FASTQ/ITS/RAW_Upload_to_BOX/BMI_Plate1WellB5_ITS_R1.fastq" 
#> [19] "hpc/home/minardsmitha/NEON/16S_ITS_Aug-Sept_2017/Sept_5_Run_B69RN/RAW_FASTQ/ITS/RAW_Upload_to_BOX/BMI_Plate1WellB6_ITS_R1.fastq" 
#> [20] "hpc/home/minardsmitha/NEON/16S_ITS_Aug-Sept_2017/Sept_5_Run_B69RN/RAW_FASTQ/ITS/RAW_Upload_to_BOX/BMI_Plate1WellB7_ITS_R1.fastq" 
#> [21] "hpc/home/minardsmitha/NEON/16S_ITS_Aug-Sept_2017/Sept_5_Run_B69RN/RAW_FASTQ/ITS/RAW_Upload_to_BOX/BMI_Plate1WellB8_ITS_R1.fastq" 
#> [22] "hpc/home/minardsmitha/NEON/16S_ITS_Aug-Sept_2017/Sept_5_Run_B69RN/RAW_FASTQ/ITS/RAW_Upload_to_BOX/BMI_Plate1WellB9_ITS_R1.fastq" 
#> [23] "hpc/home/minardsmitha/NEON/16S_ITS_Aug-Sept_2017/Sept_5_Run_B69RN/RAW_FASTQ/ITS/RAW_Upload_to_BOX/BMI_Plate1WellC10_ITS_R1.fastq"
#> [24] "hpc/home/minardsmitha/NEON/16S_ITS_Aug-Sept_2017/Sept_5_Run_B69RN/RAW_FASTQ/ITS/RAW_Upload_to_BOX/BMI_Plate1WellC11_ITS_R1.fastq"
#> [25] "hpc/home/minardsmitha/NEON/16S_ITS_Aug-Sept_2017/Sept_5_Run_B69RN/RAW_FASTQ/ITS/RAW_Upload_to_BOX/BMI_Plate1WellC12_ITS_R1.fastq"
#> [26] "hpc/home/minardsmitha/NEON/16S_ITS_Aug-Sept_2017/Sept_5_Run_B69RN/RAW_FASTQ/ITS/RAW_Upload_to_BOX/BMI_Plate1WellC1_ITS_R1.fastq" 
#> [27] "hpc/home/minardsmitha/NEON/16S_ITS_Aug-Sept_2017/Sept_5_Run_B69RN/RAW_FASTQ/ITS/RAW_Upload_to_BOX/BMI_Plate1WellC2_ITS_R1.fastq" 
#> [28] "hpc/home/minardsmitha/NEON/16S_ITS_Aug-Sept_2017/Sept_5_Run_B69RN/RAW_FASTQ/ITS/RAW_Upload_to_BOX/BMI_Plate1WellC3_ITS_R1.fastq" 
#> [29] "hpc/home/minardsmitha/NEON/16S_ITS_Aug-Sept_2017/Sept_5_Run_B69RN/RAW_FASTQ/ITS/RAW_Upload_to_BOX/BMI_Plate1WellC4_ITS_R1.fastq" 
#> [30] "hpc/home/minardsmitha/NEON/16S_ITS_Aug-Sept_2017/Sept_5_Run_B69RN/RAW_FASTQ/ITS/RAW_Upload_to_BOX/BMI_Plate1WellC5_ITS_R1.fastq" 
#> [31] "hpc/home/minardsmitha/NEON/16S_ITS_Aug-Sept_2017/Sept_5_Run_B69RN/RAW_FASTQ/ITS/RAW_Upload_to_BOX/BMI_Plate1WellC6_ITS_R1.fastq" 
#> [32] "hpc/home/minardsmitha/NEON/16S_ITS_Aug-Sept_2017/Sept_5_Run_B69RN/RAW_FASTQ/ITS/RAW_Upload_to_BOX/BMI_Plate1WellC7_ITS_R1.fastq" 
#> [33] "hpc/home/minardsmitha/NEON/16S_ITS_Aug-Sept_2017/Sept_5_Run_B69RN/RAW_FASTQ/ITS/RAW_Upload_to_BOX/BMI_Plate1WellC9_ITS_R1.fastq" 
#> [34] "hpc/home/minardsmitha/NEON/16S_ITS_Aug-Sept_2017/Sept_5_Run_B69RN/RAW_FASTQ/ITS/RAW_Upload_to_BOX/BMI_Plate1WellD10_ITS_R1.fastq"
#> [35] "hpc/home/minardsmitha/NEON/16S_ITS_Aug-Sept_2017/Sept_5_Run_B69RN/RAW_FASTQ/ITS/RAW_Upload_to_BOX/BMI_Plate1WellD11_ITS_R1.fastq"
#> [36] "hpc/home/minardsmitha/NEON/16S_ITS_Aug-Sept_2017/Sept_5_Run_B69RN/RAW_FASTQ/ITS/RAW_Upload_to_BOX/BMI_Plate1WellD12_ITS_R1.fastq"
#> [37] "hpc/home/minardsmitha/NEON/16S_ITS_Aug-Sept_2017/Sept_5_Run_B69RN/RAW_FASTQ/ITS/RAW_Upload_to_BOX/BMI_Plate1WellD1_ITS_R1.fastq" 
#> [38] "hpc/home/minardsmitha/NEON/16S_ITS_Aug-Sept_2017/Sept_5_Run_B69RN/RAW_FASTQ/ITS/RAW_Upload_to_BOX/BMI_Plate1WellD3_ITS_R1.fastq" 
#> [39] "hpc/home/minardsmitha/NEON/16S_ITS_Aug-Sept_2017/Sept_5_Run_B69RN/RAW_FASTQ/ITS/RAW_Upload_to_BOX/BMI_Plate1WellD4_ITS_R1.fastq" 
#> [40] "hpc/home/minardsmitha/NEON/16S_ITS_Aug-Sept_2017/Sept_5_Run_B69RN/RAW_FASTQ/ITS/RAW_Upload_to_BOX/BMI_Plate1WellD5_ITS_R1.fastq" 
#> [41] "hpc/home/minardsmitha/NEON/16S_ITS_Aug-Sept_2017/Sept_5_Run_B69RN/RAW_FASTQ/ITS/RAW_Upload_to_BOX/BMI_Plate1WellD6_ITS_R1.fastq" 
#> [42] "hpc/home/minardsmitha/NEON/16S_ITS_Aug-Sept_2017/Sept_5_Run_B69RN/RAW_FASTQ/ITS/RAW_Upload_to_BOX/BMI_Plate1WellD7_ITS_R1.fastq" 
#> [43] "hpc/home/minardsmitha/NEON/16S_ITS_Aug-Sept_2017/Sept_5_Run_B69RN/RAW_FASTQ/ITS/RAW_Upload_to_BOX/BMI_Plate1WellD8_ITS_R1.fastq" 
#> [44] "hpc/home/minardsmitha/NEON/16S_ITS_Aug-Sept_2017/Sept_5_Run_B69RN/RAW_FASTQ/ITS/RAW_Upload_to_BOX/BMI_Plate1WellD9_ITS_R1.fastq" 
#> [45] "hpc/home/minardsmitha/NEON/16S_ITS_Aug-Sept_2017/Sept_5_Run_B69RN/RAW_FASTQ/ITS/RAW_Upload_to_BOX/BMI_Plate1WellE10_ITS_R1.fastq"
#> [46] "hpc/home/minardsmitha/NEON/16S_ITS_Aug-Sept_2017/Sept_5_Run_B69RN/RAW_FASTQ/ITS/RAW_Upload_to_BOX/BMI_Plate1WellE11_ITS_R1.fastq"
#> [47] "hpc/home/minardsmitha/NEON/16S_ITS_Aug-Sept_2017/Sept_5_Run_B69RN/RAW_FASTQ/ITS/RAW_Upload_to_BOX/BMI_Plate1WellE12_ITS_R1.fastq"
#> [48] "hpc/home/minardsmitha/NEON/16S_ITS_Aug-Sept_2017/Sept_5_Run_B69RN/RAW_FASTQ/ITS/RAW_Upload_to_BOX/BMI_Plate1WellE1_ITS_R1.fastq" 
#> [49] "hpc/home/minardsmitha/NEON/16S_ITS_Aug-Sept_2017/Sept_5_Run_B69RN/RAW_FASTQ/ITS/RAW_Upload_to_BOX/BMI_Plate1WellE2_ITS_R1.fastq" 
#> [50] "hpc/home/minardsmitha/NEON/16S_ITS_Aug-Sept_2017/Sept_5_Run_B69RN/RAW_FASTQ/ITS/RAW_Upload_to_BOX/BMI_Plate1WellE4_ITS_R1.fastq" 
#> [51] "hpc/home/minardsmitha/NEON/16S_ITS_Aug-Sept_2017/Sept_5_Run_B69RN/RAW_FASTQ/ITS/RAW_Upload_to_BOX/BMI_Plate1WellE5_ITS_R1.fastq" 
#> [52] "hpc/home/minardsmitha/NEON/16S_ITS_Aug-Sept_2017/Sept_5_Run_B69RN/RAW_FASTQ/ITS/RAW_Upload_to_BOX/BMI_Plate1WellE6_ITS_R1.fastq" 
#> [53] "hpc/home/minardsmitha/NEON/16S_ITS_Aug-Sept_2017/Sept_5_Run_B69RN/RAW_FASTQ/ITS/RAW_Upload_to_BOX/BMI_Plate1WellE7_ITS_R1.fastq" 
#> [54] "hpc/home/minardsmitha/NEON/16S_ITS_Aug-Sept_2017/Sept_5_Run_B69RN/RAW_FASTQ/ITS/RAW_Upload_to_BOX/BMI_Plate1WellE8_ITS_R1.fastq" 
#> [55] "hpc/home/minardsmitha/NEON/16S_ITS_Aug-Sept_2017/Sept_5_Run_B69RN/RAW_FASTQ/ITS/RAW_Upload_to_BOX/BMI_Plate1WellE9_ITS_R1.fastq" 
#> [56] "hpc/home/minardsmitha/NEON/16S_ITS_Aug-Sept_2017/Sept_5_Run_B69RN/RAW_FASTQ/ITS/RAW_Upload_to_BOX/BMI_Plate1WellF10_ITS_R1.fastq"
#> [57] "hpc/home/minardsmitha/NEON/16S_ITS_Aug-Sept_2017/Sept_5_Run_B69RN/RAW_FASTQ/ITS/RAW_Upload_to_BOX/BMI_Plate1WellF11_ITS_R1.fastq"
#> [58] "hpc/home/minardsmitha/NEON/16S_ITS_Aug-Sept_2017/Sept_5_Run_B69RN/RAW_FASTQ/ITS/RAW_Upload_to_BOX/BMI_Plate1WellF12_ITS_R1.fastq"
#> [59] "hpc/home/minardsmitha/NEON/16S_ITS_Aug-Sept_2017/Sept_5_Run_B69RN/RAW_FASTQ/ITS/RAW_Upload_to_BOX/BMI_Plate1WellF1_ITS_R1.fastq" 
#> [60] "hpc/home/minardsmitha/NEON/16S_ITS_Aug-Sept_2017/Sept_5_Run_B69RN/RAW_FASTQ/ITS/RAW_Upload_to_BOX/BMI_Plate1WellF2_ITS_R1.fastq" 
#> [61] "hpc/home/minardsmitha/NEON/16S_ITS_Aug-Sept_2017/Sept_5_Run_B69RN/RAW_FASTQ/ITS/RAW_Upload_to_BOX/BMI_Plate1WellF3_ITS_R1.fastq" 
#> [62] "hpc/home/minardsmitha/NEON/16S_ITS_Aug-Sept_2017/Sept_5_Run_B69RN/RAW_FASTQ/ITS/RAW_Upload_to_BOX/BMI_Plate1WellF4_ITS_R1.fastq" 
#> [63] "hpc/home/minardsmitha/NEON/16S_ITS_Aug-Sept_2017/Sept_5_Run_B69RN/RAW_FASTQ/ITS/RAW_Upload_to_BOX/BMI_Plate1WellF5_ITS_R1.fastq" 
#> [64] "hpc/home/minardsmitha/NEON/16S_ITS_Aug-Sept_2017/Sept_5_Run_B69RN/RAW_FASTQ/ITS/RAW_Upload_to_BOX/BMI_Plate1WellF7_ITS_R1.fastq" 
#> [65] "hpc/home/minardsmitha/NEON/16S_ITS_Aug-Sept_2017/Sept_5_Run_B69RN/RAW_FASTQ/ITS/RAW_Upload_to_BOX/BMI_Plate1WellF8_ITS_R1.fastq" 
#> [66] "hpc/home/minardsmitha/NEON/16S_ITS_Aug-Sept_2017/Sept_5_Run_B69RN/RAW_FASTQ/ITS/RAW_Upload_to_BOX/BMI_Plate1WellF9_ITS_R1.fastq" 
#> [67] "hpc/home/minardsmitha/NEON/16S_ITS_Aug-Sept_2017/Sept_5_Run_B69RN/RAW_FASTQ/ITS/RAW_Upload_to_BOX/BMI_Plate1WellG10_ITS_R1.fastq"
#> [68] "hpc/home/minardsmitha/NEON/16S_ITS_Aug-Sept_2017/Sept_5_Run_B69RN/RAW_FASTQ/ITS/RAW_Upload_to_BOX/BMI_Plate1WellG11_ITS_R1.fastq"
#> [69] "hpc/home/minardsmitha/NEON/16S_ITS_Aug-Sept_2017/Sept_5_Run_B69RN/RAW_FASTQ/ITS/RAW_Upload_to_BOX/BMI_Plate1WellG12_ITS_R1.fastq"
#> [70] "hpc/home/minardsmitha/NEON/16S_ITS_Aug-Sept_2017/Sept_5_Run_B69RN/RAW_FASTQ/ITS/RAW_Upload_to_BOX/BMI_Plate1WellG1_ITS_R1.fastq" 
#> [71] "hpc/home/minardsmitha/NEON/16S_ITS_Aug-Sept_2017/Sept_5_Run_B69RN/RAW_FASTQ/ITS/RAW_Upload_to_BOX/BMI_Plate1WellG2_ITS_R1.fastq" 
#> [72] "hpc/home/minardsmitha/NEON/16S_ITS_Aug-Sept_2017/Sept_5_Run_B69RN/RAW_FASTQ/ITS/RAW_Upload_to_BOX/BMI_Plate1WellG3_ITS_R1.fastq" 
#> [73] "hpc/home/minardsmitha/NEON/16S_ITS_Aug-Sept_2017/Sept_5_Run_B69RN/RAW_FASTQ/ITS/RAW_Upload_to_BOX/BMI_Plate1WellG4_ITS_R1.fastq" 
#> [74] "hpc/home/minardsmitha/NEON/16S_ITS_Aug-Sept_2017/Sept_5_Run_B69RN/RAW_FASTQ/ITS/RAW_Upload_to_BOX/BMI_Plate1WellG5_ITS_R1.fastq" 
#> [75] "hpc/home/minardsmitha/NEON/16S_ITS_Aug-Sept_2017/Sept_5_Run_B69RN/RAW_FASTQ/ITS/RAW_Upload_to_BOX/BMI_Plate1WellG6_ITS_R1.fastq" 
#> [76] "hpc/home/minardsmitha/NEON/16S_ITS_Aug-Sept_2017/Sept_5_Run_B69RN/RAW_FASTQ/ITS/RAW_Upload_to_BOX/BMI_Plate1WellG7_ITS_R1.fastq" 
#> [77] "hpc/home/minardsmitha/NEON/16S_ITS_Aug-Sept_2017/Sept_5_Run_B69RN/RAW_FASTQ/ITS/RAW_Upload_to_BOX/BMI_Plate1WellG8_ITS_R1.fastq" 
#> [78] "hpc/home/minardsmitha/NEON/16S_ITS_Aug-Sept_2017/Sept_5_Run_B69RN/RAW_FASTQ/ITS/RAW_Upload_to_BOX/BMI_Plate1WellG9_ITS_R1.fastq" 
#> [79] "hpc/home/minardsmitha/NEON/16S_ITS_Aug-Sept_2017/Sept_5_Run_B69RN/RAW_FASTQ/ITS/RAW_Upload_to_BOX/BMI_Plate1WellH10_ITS_R1.fastq"
#> [80] "hpc/home/minardsmitha/NEON/16S_ITS_Aug-Sept_2017/Sept_5_Run_B69RN/RAW_FASTQ/ITS/RAW_Upload_to_BOX/BMI_Plate1WellH1_ITS_R1.fastq" 
#> [81] "hpc/home/minardsmitha/NEON/16S_ITS_Aug-Sept_2017/Sept_5_Run_B69RN/RAW_FASTQ/ITS/RAW_Upload_to_BOX/BMI_Plate1WellH3_ITS_R1.fastq" 
#> [82] "hpc/home/minardsmitha/NEON/16S_ITS_Aug-Sept_2017/Sept_5_Run_B69RN/RAW_FASTQ/ITS/RAW_Upload_to_BOX/BMI_Plate1WellH4_ITS_R1.fastq" 
#> [83] "hpc/home/minardsmitha/NEON/16S_ITS_Aug-Sept_2017/Sept_5_Run_B69RN/RAW_FASTQ/ITS/RAW_Upload_to_BOX/BMI_Plate1WellH5_ITS_R1.fastq" 
#> [84] "hpc/home/minardsmitha/NEON/16S_ITS_Aug-Sept_2017/Sept_5_Run_B69RN/RAW_FASTQ/ITS/RAW_Upload_to_BOX/BMI_Plate1WellH6_ITS_R1.fastq" 
#> [85] "hpc/home/minardsmitha/NEON/16S_ITS_Aug-Sept_2017/Sept_5_Run_B69RN/RAW_FASTQ/ITS/RAW_Upload_to_BOX/BMI_Plate1WellH7_ITS_R1.fastq" 
#> [86] "hpc/home/minardsmitha/NEON/16S_ITS_Aug-Sept_2017/Sept_5_Run_B69RN/RAW_FASTQ/ITS/RAW_Upload_to_BOX/BMI_Plate1WellH8_ITS_R1.fastq" 
#> [87] "hpc/home/minardsmitha/NEON/16S_ITS_Aug-Sept_2017/Sept_5_Run_B69RN/RAW_FASTQ/ITS/RAW_Upload_to_BOX/BMI_Plate1WellH9_ITS_R1.fastq"