IlluminaBasecallsToFastq

[flcaza]

Hi all,

I have a small problem :

java -jar ~/Downloads/picard/picard.jar IlluminaBasecallsToFastq BASECALLS_DIR=./raw/19854859/Data/Intensities/BaseCalls/ LANE=1 OUTPUT_PREFIX=1111 RUN_BARCODE=19854859 MACHINE_NAME=M00911 READ_STRUCTURE=151T6M151T FIRST_TILE=1111 TILE_LIMIT=1 FLOWCELL_BARCODE=AR4JF
[Tue Feb 28 04:10:29 EST 2017] picard.illumina.IlluminaBasecallsToFastq BASECALLS_DIR=./raw/19854859/Data/Intensities/BaseCalls LANE=1 OUTPUT_PREFIX=1111 RUN_BARCODE=19854859 MACHINE_NAME=M00911 FLOWCELL_BARCODE=AR4JF READ_STRUCTURE=151T6M151T FIRST_TILE=1111 TILE_LIMIT=1 ADAPTERS_TO_CHECK=[INDEXED, DUAL_INDEXED, NEXTERA_V2, FLUIDIGM] NUM_PROCESSORS=0 APPLY_EAMSS_FILTER=true FORCE_GC=true MAX_READS_IN_RAM_PER_TILE=1200000 MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false READ_NAME_FORMAT=CASAVA_1_8 COMPRESS_OUTPUTS=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
[Tue Feb 28 04:10:29 EST 2017] Executing as root@debian on Linux 3.16.0-4-amd64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_121-b13; Picard version: 2.9.0-9-gb9978f5-SNAPSHOT
[Tue Feb 28 04:10:29 EST 2017] picard.illumina.IlluminaBasecallsToFastq done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=32440320
To get help, see http://broadinstitute.github.io/pica...ml#GettingHelp
Exception in thread "main" picard.PicardException: Could not find a format with available files for the following data types: BaseCalls, PF, Position, QualityScores
at picard.illumina.parser.IlluminaDataProviderFactory.<init>(IlluminaDataProviderFactory.java:173)
at picard.illumina.IlluminaBasecallsConverter.<init>(IlluminaBasecallsConverter.java:250)
at picard.illumina.IlluminaBasecallsToFastq.initialize(IlluminaBasecallsToFastq.java:276)
at picard.illumina.IlluminaBasecallsToFastq.doWork(IlluminaBasecallsToFastq.java:219)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:205)
at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:94)
at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:104)


What is wrong here ? I can see this but how i can get skip this 3 data types ? or how can i can get a list with all data types and put let`s say null on that 3 ?

root@debian:# java -version
java version "1.8.0_121"
Java(TM) SE Runtime Environment (build 1.8.0_121-b13)
Java HotSpot(TM) 64-Bit Server VM (build 25.121-b13, mixed mode)
root@debian:#

Picard version: 2.9.0-9-gb9978f5-SNAPSHOT

Thank you in advance !

[GenoMax]

Take a look at this thread to see if the solution in there can be applied in your case: http://seqanswers.com/forums/showthread.php?t=19538

[flcaza]

Hi GenoMax,

Actually nop It was first read when i search for my error but no one answer to that thread.

He have same error like me

Exception in thread "main" net.sf.picard.PicardException: Could not find a format with available files for the following data types: Position, Barcodes, BaseCalls, QualityScores, PF

and last post from user "drea11" I is again from 7 month ago where no one answer it to exactly the same problem

Do you have a link/book/whatever for "dummy" where to read about all of this ?

Thank you !

[GenoMax]

Is your read specification correct? READ_STRUCTURE=151T6M151T

[flcaza]

well yes ....

It is from here

http://biorxiv.org/content/biorxiv/early/2016/09/09/074237.2.full.pdf

but maybe of course it is soo easy to copy and now i wonder is the answer is not here:

4.4 Molecular procedures
The oligo pool was synthesized by Twist Bioscience. The lyophilized pool consisted of 72,000 oligos
of 200nt, which included the 152nt payload flanked by landing sites for sequencing primers:
GTTCAGAGTTCTACAGTCCGACGATC[N152]TGGAATTCTCGGGTGCCAAGG
The pool was resuspended in 20uL TE for a final concentration of 150 ng/ul. PCR was performed
using Q5 Hot Start High-Fidelity 2X Master Mix (NEB # M0494) and Illumina small RNA
primers RP1 and RPl1 (100ng oligos, 2.5ul of each primer (10µM), 25ul Q5 Master Mix in a 50ul
reaction).
PCR Primer (RP1):
5’ AATGATACGGCGACCACCGAGATCTACACGTTCAGAGTTCTACAGTCCGA
21
peer-reviewed) is the author/funder. It is made available under a CC-BY-NC 4.0 International license.
bioRxiv preprint first posted online Sep. 9, 2016; doi: http://dx.doi.org/10.1101/074237. The copyright holder for this preprint (which was not
PCR Primer, Index 1 (RPI1):
5’ CAAGCAGAAGACGGCATACGAGATCGTGATGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
Thermocycling conditions were as follows: 30s at 98C; 10 cycles of: 10s at 98C, 30s at 60C, 30s
at 72C, followed by a 5 min. extension at 72C. The library was then purified in a 1:1 Agencourt
AMPure XP (Beckman Coulter # A63880) bead cleanup and eluted in 20ul water. This library
was considered the master pool. Running the library on a BioAnalyzer showed an average size of
263nt, close to the expected 265nt expected by the oligo length (152nt before annealing sites) and
the two PCR adapters of length 50nt and 63nt.
Supplementary Figure 9: BioAnalyzer results for the oligo pool. The average fragment
size was 263nt, concordant with an oligo length of 200nt and the two PCR adapters.
We sequenced the oligo pool using on a single flow cell of the Miseq v3 kit (Illumina # MS-102-
3001) at the New York Genome Center using a a 150 pair-end read protocol. Raw .bcl files were
downloaded from BaseSpace and analyzed using the commands below

I try to understand this and at this moment is impossible for me with my knowledge, but i will research more ...

Thank you !

[GenoMax]

If this is a published dataset why are you not getting the fastq files directly from EBI-ENA if you have the accession number?

[flcaza]

Well i do not know how to do it, i see on advanced search are a looot of rows, and i do not know how to match it from .pdf file.

Second I see this is European Nucleotide Archive and i do not know it is an US Nucleotide Archive or exist. I am new in this domain but i like it and i want to learn more.

And if you think i want the voucher well i think it is already expired; what i want is to know how to do it, and learn something new and interesting.

Thank you !

[flcaza]

hmm i search on EBI-ENA for bioRxiv who are create this document and i do not fine anything related to "storage"; there are some ddsX mutant, some experiments but nothing related to storage.

... I will search more