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Picard CheckIlluminaDirectory Failing

stoweystowey United StatesMember, Broadie admin

Hello,

I have a MiSeq run that I wish to run ExtractIlluminaBarcodes and IlluminaBasecallsToSam on, however, they can't find the files needed. When I run CheckIlluminaDiretcory I get this result (pasted below). Does anyone what I may be doing wrong?

Thanks!

~Sarah

10:41am [email protected] /cil/shed/sandboxes/stowey/20170714_NewDGE/TestData $ java -Xmx16G -jar /seq/software/picard-public/current/picard.jar CheckIlluminaDirectory BASECALLS_DIR= /btl/data/MiSeq0/runs/DGE_Dev/141120_M03102_0040_000000000-ABNVV/Data/Intensities/BaseCalls/ READ_STRUCTURE=17T8B46T L=1
10:43:44.783 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/seq/software/picard-public/2.14.0/picard.jar!/com/intel/gkl/native/libgkl_compression.so
[Thu Oct 26 10:43:44 EDT 2017] CheckIlluminaDirectory BASECALLS_DIR=/btl/data/MiSeq0/runs/DGE_Dev/141120_M03102_0040_000000000-ABNVV/Data/Intensities/BaseCalls READ_STRUCTURE=17T8B46T LANES=[1] FAKE_FILES=false LINK_LOCS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
[Thu Oct 26 10:43:44 EDT 2017] Executing as [email protected]ut.broadinstitute.org on Linux 2.6.32-642.3.1.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_121-b13; Deflater: Intel; Inflater: Intel; Picard version: 2.14.0-SNAPSHOT
INFO 2017-10-26 10:43:44 CheckIlluminaDirectory Checking lanes(1 in basecalls directory (/btl/data/MiSeq0/runs/DGE_Dev/141120_M03102_0040_000000000-ABNVV/Data/Intensities/BaseCalls)

INFO 2017-10-26 10:43:44 CheckIlluminaDirectory Expected cycles: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71
INFO 2017-10-26 10:43:44 CheckIlluminaDirectory Checking lane 1
INFO 2017-10-26 10:43:44 CheckIlluminaDirectory Expected tiles: 1101, 1102, 1103, 1104, 1105, 1106, 1107, 1108, 1109, 1110, 1111, 1112, 1113, 1114, 2101, 2102, 2103, 2104, 2105, 2106, 2107, 2108, 2109, 2110, 2111, 2112, 2113, 2114
INFO 2017-10-26 10:43:44 CheckIlluminaDirectory Could not find a format with available files for the following data types: Position, BaseCalls, PF, QualityScores
INFO 2017-10-26 10:43:44 CheckIlluminaDirectory Lane 1 FAILED Total Errors: 4
INFO 2017-10-26 10:43:44 CheckIlluminaDirectory FAILED! There were 4 in the following lanes: 1
[Thu Oct 26 10:43:44 EDT 2017] picard.illumina.CheckIlluminaDirectory done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2027945984
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
1.736u 5.608s 0:14.28 51.3% 0+0k 6072+840io 3pf+0w
10:43am [email protected] /cil/shed/sandboxes/stowey/20170714_NewDGE/TestData $

Answers

  • Tiffany_at_BroadTiffany_at_Broad Cambridge, MAMember, Administrator, Broadie, Moderator admin

    Hi @stowey , I moved this question to the GATK specific forum. Thanks for posting!

  • SheilaSheila Broad InstituteMember, Broadie admin

    @stowey
    Hi Sarah,

    I am not a Picard expert, but I have some things that hopefully will help you.

    This thread has some information that may help.

    Try running with LINK_LOCS=true.

    I hope those two things help at least with a couple of the issues. I will check have to check with the team if they don't.

    -Sheila

    P.S. If you google "CheckIlluminaDirectory Could not find a format with available files for the following data types:" there were some helpful threads as well.

  • stoweystowey United StatesMember, Broadie admin

    Hi Sheila and Geraldine,

    I wanted to follow up and let you know what the issue was. It turns out, IlluminaBasecallsToSam automatically picks up the zipped barcode files. From the documentation:

    "The barcodes directory with _barcode.txt files"

    However, the code that generates these files ExtractIlluminaBarcodes and output them in either zipped or unzipped format.

    If both zipped and unzipped formats exist, IlluminaBasecallsToSam picks up only one of them. In my case, it was picking up the wrong one.

    It may be helpful for the tool to check for this if its automatically picking one. Or perhaps there could be a parameter to the tool to say only pick up the zipped or unzipped versions.

    Thanks!

  • shleeshlee CambridgeMember, Broadie ✭✭✭✭✭

    Hi @stowey,

    How do you know which of the zipped or unzipped is correct? Shouldn't they be the same file?

  • stoweystowey United StatesMember, Broadie admin

    So the originally zipped files were created by an original pipeline which was not aware of the UMI. I created new ones with the UMI appropriately tagged.

  • SheilaSheila Broad InstituteMember, Broadie admin

    @stowey
    Hi,

    Interesting, so you are saying the tool outputs both zipped and unzipped files at random? I will see what we can do about the documentation.

    -Sheila

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