Picard CheckIlluminaDirectory: BaseCalls file format not found

[user 31888]

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  [B][COLOR="Red"]Could not find a format with available files for the following data types: BaseCalls[/COLOR][/B]
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?

[GenoMax]

Looking at picard command line overview the entire BaseCalls directory is required (https://broadinstitute.github.io/pic...-overview.html).

[user 31888]

You are right GenoMax !

The program needs to look in the 'BaseCalls' directory.
Plus, the tree architecture needs to be conserved since it will call some files from 'InterOp' dir as well.