Hi Stathis,
Ah, I see the problem - run CheckIlluminaDirectory with LINK_LOCS=true. This
is a recent option added to deal with the HiSeqX run conventions. It will
create per-tile locs files that are symlinks to s.locs. Then
CollectHiSeqXPfFailMetrics
should work.
-Matt
On Thu, Dec 4, 2014 at 11:13 AM, Kanterakis, Efstathios <
ekantera...@illumina.com> wrote:
> Thanks Matt.
>
> Here it goes:
>
> Java -jar picard.jar CheckIlluminaDirectory
> BASECALLS_DIR=/path/to/BaseCalls/ L=1 RS=151T151T T=1101
>
> [Thu Dec 04 16:07:29 GMT 2014] picard.illumina.CheckIlluminaDirectory
> BASECALLS_DIR=/path/to/Data/Intensities/BaseCalls READ_STRUCTURE=151T151T
> LANES=[1] TILE_NUMBERS=[1101] 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
>
> [Thu Dec 04 16:07:29 GMT 2014] Java HotSpot(TM) 64-Bit Server VM
> 1.6.0_45-b06; Picard version:
> 1.125(3ee9690e33b8a6c5330c7b525394542d12410d83_1416431570) IntelDeflater
>
> INFO 2014-12-04 16:07:29 CheckIlluminaDirectory Checking lanes(1
> in basecalls directory (/path/to/Data/Intensities/BaseCalls)
>
>
>
> INFO 2014-12-04 16:07:29 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, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172,
> 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187,
> 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202,
> 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217,
> 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232,
> 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247,
> 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262,
> 263, 264, 265, 266, 267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277,
> 278, 279, 280, 281, 282, 283, 284, 285, 286, 287, 288, 289, 290, 291, 292,
> 293, 294, 295, 296, 297, 298, 299, 300, 301, 302
>
> INFO 2014-12-04 16:07:29 CheckIlluminaDirectory Checking lane 1
>
> INFO 2014-12-04 16:07:29 CheckIlluminaDirectory Expected tiles:
> 1101
>
> INFO 2014-12-04 16:07:34 CheckIlluminaDirectory Could not find a
> format with available files for the following data types: Position
>
> INFO 2014-12-04 16:07:34 CheckIlluminaDirectory Lane 1 FAILED
> Total Errors: 1
>
> INFO 2014-12-04 16:07:34 CheckIlluminaDirectory FAILED! There were
> 1 in the following lanes: 1
>
> [Thu Dec 04 16:07:34 GMT 2014] picard.illumina.CheckIlluminaDirectory
> done. Elapsed time: 0.10 minutes.
>
> Runtime.totalMemory()=252116992
>
>
>
> There is a s.locs file under /Data/Intensities. Perhaps this is a new
> Illumina convention.
>
> Under /Data/Intensities/BaseCalls/L001 there are tile folders and one
> .filter file per tile
>
>
>
> -Stathis
>
>
>
>
>
> *From:* Matt Sooknah [mailto:msook...@broadinstitute.org]
> *Sent:* 04 December 2014 03:53
> *To:* Kanterakis, Efstathios
> *Cc:* samtools-help@lists.sourceforge.net
> *Subject:* Re: [Samtools-help] CollectHiSeqXPfFailMetrics Error: Could
> not find a format with available files for the following data types:
> Position
>
>
>
> Hi Stathis,
>
>
>
> Could you try running CheckIlluminaDirectory on one of the basecalling
> dirs and send us the output? It looks like it can't find any .locs or
> analogous files.
>
>
>
> -Matt
>
>
>
> On Wed, Dec 3, 2014 at 10:58 AM, Kanterakis, Efstathios <
> ekantera...@illumina.com> wrote:
>
> Hello,
>
> I’m running the following command from picard-tools-1.125 (jre1.7.0):
>
> java -Xmx2g -jar picard.jar CollectHiSeqXPfFailMetrics
> BASECALLS_DIR=Data/Intensities/BaseCalls LANE=1 OUTPUT=out.txt
> VALIDATION_STRINGENCY=LENIENT
>
>
>
> and get:
>
> Exception in thread "main" picard.PicardException: Could not find a format
> with available files for the following data types: Position
>
> at
> picard.illumina.parser.IlluminaDataProviderFactory.<init>(IlluminaDataProviderFactory.java:172)
>
> at
> picard.illumina.parser.IlluminaDataProviderFactory.<init>(IlluminaDataProviderFactory.java:127)
>
> at
> picard.illumina.quality.CollectHiSeqXPfFailMetrics.doWork(CollectHiSeqXPfFailMetrics.java:127)
>
> at
> picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:187)
>
> at
> picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:89)
>
> at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:99)
>
>
>
> I’ve tried it on a number of HiSeqX runs (2x36, 2x151, 2x151 indexed) and
> they all failed.
>
>
>
> Any ideas?
>
>
>
> Thank you,
>
> Stathis
>
>
>
>
>
> ------------------------------------------------------------------------------
> Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
> from Actuate! Instantly Supercharge Your Business Reports and Dashboards
> with Interactivity, Sharing, Native Excel Exports, App Integration & more
> Get technology previously reserved for billion-dollar corporations, FREE
>
> http://pubads.g.doubleclick.net/gampad/clk?id=164703151&iu=/4140/ostg.clktrk
> _______________________________________________
> Samtools-help mailing list
> Samtools-help@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/samtools-help
>
>
>
------------------------------------------------------------------------------
Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
from Actuate! Instantly Supercharge Your Business Reports and Dashboards
with Interactivity, Sharing, Native Excel Exports, App Integration & more
Get technology previously reserved for billion-dollar corporations, FREE
http://pubads.g.doubleclick.net/gampad/clk?id=164703151&iu=/4140/ostg.clktrk
_______________________________________________
Samtools-help mailing list
Samtools-help@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/samtools-help
