Re: [mg-rast] Your MG-RAST submission (3892)
Hi Ulrich, The latest job you submitted (3905) still has two header lines which do not begin on new lines: 411932 >v69.48 411933 GGGGGCAGGGGGGGTCAGGAGCTACTGACTGG ... 411950 AGGCTTTCCAAGGACCAAAAATTGAGCCGTCATTAACTTTGTATTGGGAA 411951 A>v69.49 411952 AAGGTGGTCAAATTAAGTTAGAATTTAAA ... and 412899 >v62.24 412900 TAGAGTGTAGTGGGTTTTGATTACAGCTCCTG ... 412909 GATATTAACTTTTATACTGGAGATATGAAAAACATAATTTAATTACTCTG 412910 GGG>v62.25 412911 CATCACAGTAATA ... There are also a large number of sequences which have non-IUPAC characters, eg.
vj57.: bad char '4' 4cTCCGTACTTCGATTCTCCTCCCCTCTTACCCTCTGGCGCTAGTGGTCACCCCTTTTCCCTCCGCGCGGTACT
vijay15.: bad char '36' 36CCACGACAATTGGACCCTAAGCTCATGTTTTCATGTTTTTCTTTCTATTTGGGTGCATTTGGGACCATTATGCTACTG
where the digits are not accepted, and 354538 >v47.1 354539 NNTTAAGTTATGCAGCTGTGTAXXXXXXXXXXXXXXXXXXXXXXXXXXXX 354540 XXXXXXXXXXXXXCCCCCTTCCTGAATTCTGATCCTCCTCGTCTGGGGTT where the 'X's are not accepted. MG-RAST can only process sequence data containing IUPAC-standard compliant nucleotide and nucleotide ambiguity characters. See <http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html#500> for a list of valid IUPAC nucleotide characters. Changing the 'X's to 'N's should fix this. A small number of non-IUPAC characters in the sequence data will be converted to 'N's without causing the job to fail. You can delete a job by going to the job 'details' page, one of the options in the green menu bar is 'delete this job'. Regards, Mark D'Souza -- for the MG-RAST team [email protected] http://metagenomics.nmpdr.org/ ----- "Ulrich Melcher" <[email protected]> wrote:
From: "Ulrich Melcher" <[email protected]> To: [email protected] Sent: Monday, June 29, 2009 8:55:55 AM GMT -06:00 US/Canada Central Subject: Re: Your MG-RAST submission (3892)
I corrected the errors you mentioned below, but still had a failed file. I tried the file in formatdb and was alerted to additional errors. I
corrected those also. The formatdb acceptable file was, however, still not acceptable to MG-
RAST.
The main reason for this message, though, is wanting instruction as to how to remove the failed submissions from your server and my list
of submissions.
Peace, Ulrich Melcher
On 26/06/2009, at 17.24, [email protected] wrote:
Hi,
The job you submitted to MG-RAST has failed as the sequence file doe not conform to the fasta standard, it has multiple sequence ID
(header) lines which do not begin on a new line, e.g.
p01_05TGP00060_AGTG.8
tCGGTGCAGATCTTGGTGGTAGTAGcAAATATTCAAATGAGAACTTTGAAGGCcGAAGAGGAGAAAGGTT
CCATG
TGAACGGCACTTGCACATGGGTAAGCCGATCCTAAGGgACGGGGTAACCCCGGCAGATAGCGCGATCACG
CGCATCCCCC
GAAAGGGAATCGGGTTAAGATTTCCCGAGCCGGGATGTGGCGGTTGACGGCGACGTTAGGAAGTCCGGAG
ACGCCGGCGG
GGGCCTCGGGAAGAGTTATCTTTTCTGCTTAACGGCCTGCCAACCCTGGAATCGGTTCAGCCGGAGGTAG
GGTCCAGTGG
TCGGAAGAGCACCGCACGTCGCGCGGTGTCCGGTGCGCCCCCGGCGGCCCATGAAAATCCGGAGGACCGA
GTACCGTCCA
CGCCCGGTCGTACTCATAACCGCATCAGGTCTCCAAGGTGAACAGCCTCTGGCCAATGGAACAATGTAGG
CAAGGGAAGT CGGCAaaCGGATCCGTAACTTCGGgAAAAggtA >p01_05TGP00060_AGTG.9
GTTACAGCAGTTATCCTCTCCGCACTTGGCTACCCAGCGTTTACCGTAGGCACGATAACTGGTACACCAG
AGGTGCGTCC
TTCCCGGTCCTCTCGTACTAGGGAAAGGTCCTCTCAATGCTCTAACGCCCACATCAGGTACGGAGgATCC
GAAGGCACT
p01_05TGP00060_AGTG.10
TCAGGCGGCACCAGTCTAGAGGCGGTTCATACAACACTGGTGTAAaCcAAGGCAGAAACCATGgTCCAGC
CcATGGTCAC
CACCAAAGTCAGGGAGGAAgCAGGGgTGATGACCCCcACCATGCCGGAGCAATCAAGATGACAACaCACA
GCcTCCGCCT
TGGCGACGGGGAAAtCGTGAAAaCAaCGAGAAACCTCCGCcTAAGTGCCACACGCCAAGCCCTCGCaGAG
GACtACTAGG A >p01_05TGP00060_AGTG.11
cAATAGgATCagaaTCCTATAaTGTTATCCCATGCtAATGTATCCAGAGCGTAGgCTTgCTTTGAGCACT
CTAATTTCTt
CAAAGtAACAgCGCcGGAGgCACGaCCcGGCCAgTTAAGGCCAGGAGCGcATCGCCGGcAGAAGGGACGA
GCCGACCGGT GCACACcGGAGGCGgACCgATCgACCCAg >p01_05TGP00060_AGTG.12
GGACTACCCGCTGAGTTTAAGCATATAAATAAGCGGAGGAGAAGAAACTTACAAGGATTCCCCTAGTAAC
GGCGAGCGAA
CcGGGAGCAGCCCAGCTTGAGAATCGGGCGGCCGTGCCGTTCGAATTGTAGTCTGGAGAGGCGTCCTCAG
CGACGGACCG
GGCCcAAGTCCCCTGGAAaGGGgCgCCTGGGAGGGTGAGAGCCCCGTCcTGCCCGGaCCCTGTCGCCCCA
cGAGGCGCcG TCAAcGaGTCGGGTTgTTGGGAtGCAGCCcAAG >p01_05TGP00060_AGTG.13
GGCACTCGCCCAGATGGCCGGGTGTGGGTCGCGCGCTTCAGCGCCATCCATTTTCGGGGCTAGTTGATTC
GGCAGGTGAG
TTGTTACACACTCCTTAGCGGATTTCGACTTCCATGACCACCGTCCTGCTGTCTTAATCGACCAACACCC
TTTGTGGGTT
CTAGGTTAGCGCGCAGTTGGGCACCGTAACCCGGCTTCCGGTTCATCCCGCATCGCCAGTTCTGCTTACC
AAAAATGGCC CA...
In addition, there are special characters included in the sequence
data, e.g.
v65.32 TCATCGGGATTTCTGCACCCTTCTCATTAGCC AGAACTTGGTCACCTGTTACCGTTTCTGGCTACTAGAAAGCTTGGAATTT TAGTATTCTGCACCTAGGATGTACTTTGGTCAAGGTAAGAAAGAAAAATA CGATTTGTGTATTTGTGCCATCTGTGGTATTTTCCACACATGTATATAGA TCCTTTTAAAAGAAACATATACTTTAACTAAATATGCAAGAGTGCAGCAA ATAGTCTGCAATTATAAAATGAAATAAGTCTGTTATGACCCAGCCTTCAT AATAACTAAAATTATAGCCATGTTACTCATAGAACTGACAAGTGTCTTTC CATTCACATATAATTGTTTCATGTCCGAATTATGTGCCGTGACACATATC AAGTAATACACATGTTCTACATTTAGACATTTGTATATTTAATCCATATT CCCAAAATGACTCCATCAGATATTAACTATAATTATCCCATTTTACAGAT GAGGGACTTGGGGATAGTTATGCATTTTATCGCAAGACACAATGGGAAGT AGCTGAGTCTGAATTTAAACCCAGCTGGTCAGGTTCCAGAGCTTGTGCTC TTAATCACCTGCTATGAGCCCTTTCATTAAATATACAATTGCATAAATGA GAAATTCAATTTGGTCAGGCATAGTGGCTCACACCTGTAATCCCAACACT TTGGGAGGCCGAGGTGGGCAGATCACTTGAGCCCAGGAGTTTGAGACCGC CTGCACAT ^@>^@v^@6^@0^@.^@C^@o^@n^@t^@i^@g^@1^@
^@T^@G^@G^@C^@A^@G^@T^@C^@A^@G^@A^@G^@G^@C^@G^@A^@T^@G^@A^@A^@G^@G^@A^
@C^@G^@T^@G^@C^@T^@A^@A^@T^@C^@T^@G^@
^@C^@G^@A^@T^@A^@A^@G^@C^@G^@T^@C^@G^@G^@T^@G^@A^@G^@G^@T^@G^@A^@T^@A^
@T^@G^@A^@A^@C^@C^@G^@T^@T^@A^@T^@A^@A^@C^@C^@G^@G^@C^@G^@A^@T^@T^@T^@
C^@C^@G^@A^@
^@A^@T^@G^@G^@G^@G^@A^@A^@A^@C^@C^@C^@A^@G^@T^@G^@T^@G^@A^@T^@T^@C^@G^
@T^@C^@A^@C^@A^@C^@T^@A^@T^@C^@A^@T^@T^@A^@A^@C^@T^@G^@A^@A^@T^@C^@C^@
A^@T^@A^@G^@
^@G^@T^@T^@A^@A^@T^@G^@A^@G^@G^@C^@G^@A^@A^@C^@C^@G^@G^@G^@G^@G^@A^@A^
@C^@T^@G^@A^@A^@A^@C^@A^@T^@C^@T^@A^@A^@G^@T^@A^@C^@C^@C^@C^@G^@A^@G^@
G^@A^@A^@A^@
^@A^@G^@A^@A^@A^@T^@C^@A^@A^@C^@C^@G^@A^@G^@A^@T^@T^@C^@C^@C^@C^@C^@A^
@G^@T^@A^@G^@C^@G^@G^@C^@G^@A^@G^@C^@G^@A^@A^@C^@G^@G^@G^@G^@A^@G^@G^@
A^@G^@C^@C^@ ^@C^@A^@T^@A^@G^@C^@C^@T^@G^@
^@A^@A^@T^@C^@A^@G^@T^@G^@T^@G^@T^@G^@T^@G^@T^@T^@A^@G^@T^@G^@G^@A^@A^
@G^@C^@G^@T^@C^@T^@
Please edit your sequence file to plain ASCII text in fasta format
and resubmit it to the MG-RAST server.
Regards, Mark D'Souza -- for the MG-RAST team
participants (1)
-
dsouza＠mcs.anl.gov