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Picard 2.9.4 is now available. Download and read release notes here.
GATK 3.7 is here! Be sure to read the Version Highlights and optionally the full Release Notes.

Picard CheckIlluminaDirectory: BaseCalls file format not found

Hi,

I recently used the MiSeq for a 2 x 76 paired-end sequencing run.

I moved the 'L001' directory from BaseSpace to our cluster (with Picard 2.1.0; java 1.8.0_77)
The 'L001' directory contains the sub-directories named 'C1.1', 'C2.1',..., 'C158.1', each containing the '.bcl' and '.stats' files.

I then run the following command:
java -jar picard.jar CheckIlluminaDirectory \
B=L001/ \
RS=76T6B76T \
L=1 \
DATA_TYPES=BaseCalls

It returns:
picard.illumina.CheckIlluminaDirectory BASECALLS_DIR=/home/user/L001 DATA_TYPES=[BaseCalls] READ_STRUCTURE=76T6B76T 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

INFO     CheckIlluminaDirectory  Checking lanes(1 in basecalls directory (/home/user/L001)

INFO    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, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158

INFO    CheckIlluminaDirectory  Checking lane 1

INFO    CheckIlluminaDirectory  Expected tiles: 1101, 1102, 1103, 1104, 1105, 1106, 1107, 1108, 1109, 1110, 1111, 1112, 1113, 1114, 1115, 1116, 1117, 1118, 1119, 2101, 2102, 2103, 2104, 2105, 2106, 2107, 2108, 2109, 2110, 2111, 2112, 2113, 2114, 2115, 2116, 2117, 2118, 2119

INFO    CheckIlluminaDirectory  Could not find a format with available files for the following data types: BaseCalls
INFO    CheckIlluminaDirectory  Lane 1 FAILED  Total Errors: 1
INFO    CheckIlluminaDirectory  FAILED! There were 1 in the following lanes: 1

picard.illumina.CheckIlluminaDirectory done. Elapsed time: 0.00 minutes.

Runtime.totalMemory()=995098624

To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp

Is this program intended to be ran directly on BaseSpace in order to respect the directory tree with all the sequencing metrics files?

Issue · Github
by Sheila

Issue Number
798
State
closed
Last Updated
Assignee
Array
Milestone
Array
Closed By
chandrans

Best Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie
    Accepted Answer

    Ah, that makes sense! Thanks for letting us know what you found.

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Hi @user31888, the program isn't designed to run on BaseSpace as such (we run it on local machines) but I wouldn't be surprised if there was something about the way the information is structured that gets broken when you copy it. I'll ask on our end (only a handful of our people have direct experience with this part of the toolkit) but you may also want to ask Illumina support whether copying those files preserves the integrity of the data.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie
    Accepted Answer

    Ah, that makes sense! Thanks for letting us know what you found.

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