Thank you very much Matt. That worked.
Kind regards,
Stathis
From: Matt Sooknah [mailto:msook...@broadinstitute.org]
Sent: 04 December 2014 06:57
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,
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<mailto: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<mailto:msook...@broadinstitute.org>]
Sent: 04 December 2014 03:53
To: Kanterakis, Efstathios
Cc:
samtools-help@lists.sourceforge.net<mailto: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<mailto: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<mailto: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
