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Member Posts: 27

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:
B=L001/ \
RS=76T6B76T \
L=1 \
DATA_TYPES=BaseCalls

It returns:

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  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

`

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

Tagged:

#### Issue · Github April 2016 by Sheila

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

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

Geraldine Van der Auwera, PhD