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 stowey@stout /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 stowey@stout.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 stowey@stout /cil/shed/sandboxes/stowey/20170714_NewDGE/TestData $
