New subject: probleme tool galaxy

8 Apr 2016


      Salut, je te laisse envoyer ta question sur la liste 
galaxy-user@listes.univ-lyon1.fr.
Je répondrais à ta question directement (tes séquences doivent être 
d'une longeur de 30 nt minimum) sur la liste histoire que tout le monde 
puisse bénéficier du retour d'expérience,
Par ailleurs est tu inscrite sur cette liste de diffusion ?
Merci pour ta contribution,
A+
Vincent

Le 08/04/16 14:37, Rita Rebollo a écrit :
...
Bonjour,
J'essaye d utiliser cd-hit-dup avec une trentaines de sequences en 
format fasta ou fastq et ça ne marche pas. Il me donne une erreur. J 
ai aussi essayé sur le galaxy.edu et ça ne marche pas non plus. 
Saurais tu dire pourquoi s il te plait?
Mon petit fichier:
@HWI-ST132:549:C0FYUACXX:5:1101:1213:1910_1:N:0:TGGTTT
TGGTCGATGGTTATTCTGGATAACG
+
?@@DDDFFHH<DFHHIHIIAHIIFG
@HWI-ST132:549:C0FYUACXX:5:1101:1106:1958_1:N:0:TGGTTT
AAAGATGAATCGGTAGATCGAAAT
+
;??DDBDFFFFFFBEHGBHFF;EH
@HWI-ST132:549:C0FYUACXX:5:1101:1944:1926_1:N:0:TGGTTT
ATAACAGTGAATTTTGGACAGTG
+
?@?D;AD=CAD<,A:,8A<CA3C
@HWI-ST132:549:C0FYUACXX:5:1101:1981:1949_1:N:0:TGGTTT
TATTGCACATTCACCGGCCTGA
+
@@@FDFFFHH4DFGHHIGGHIG
@HWI-ST132:549:C0FYUACXX:5:1101:1943:1970_1:N:0:TGGTTT
GAGGTTCCGCAAATCTGCATATAGGG
+
=@@DADBDHHDHHGIIIIIAHIIIII
@HWI-ST132:549:C0FYUACXX:5:1101:1752:1987_1:N:0:TGGTTT
AGATATGTTTGATATTCTTGGTTG
+
@@@FDDFFHGDHHIJGJJJGEIII
@HWI-ST132:549:C0FYUACXX:5:1101:1995:1987_1:N:0:TGGTTT
GGAACCTCGATGGACGTGGAGTGC
+
;<?DDDDDH<AF:?A?EHFBFEF>
@HWI-ST132:549:C0FYUACXX:5:1101:2027:1925_1:N:0:TGGTTT
TGTATGCATTGCTTTCACTTCACAGA
+
@@@FFFDFHFDBHIJIIIJFHHGGEI
@HWI-ST132:549:C0FYUACXX:5:1101:2449:1910_1:N:0:TGGTTT
TGAAATGACTTATTGCCCAATGAATTGC
+
CCCFFFFFHHHHHJJJJJJIJIIJJJJJ
@HWI-ST132:549:C0FYUACXX:5:1101:2306:1925_1:N:0:TGGTTT
CGGAGAACGCAGAAAGGTGAGCT
+
BCCFFFEFHHFHHJJJJFHJIJJ
@HWI-ST132:549:C0FYUACXX:5:1101:2470:1932_1:N:0:TGGTTT
TGGATAGCTGCACAACCCGTGGTACC
+
@@@FFFDDHHHHHHI@HHHHGIEH9E
@HWI-ST132:549:C0FYUACXX:5:1101:2332:1938_1:N:0:TGGTTT
CCCCCTTAAGGTGAAGTAGGACCTGTC
+
CCCFFFFFGHDACFGIHJIGIIJJJJJ
@HWI-ST132:549:C0FYUACXX:5:1101:2327:1996_1:N:0:TGGTTT
TTGCCTGTCTGTATCTCAATTGAAGT
+
@@@DDDBDDDHFBBEHGHBHEHCEFH
@HWI-ST132:549:C0FYUACXX:5:1101:2539:1874_1:N:0:TGGTTT
CTTCTGTAGTTTGTAATTCTTTTAAA
+
1=DDFFFFHFHHIIIIIIEHIIIIII
@HWI-ST132:549:C0FYUACXX:5:1101:2585:1888_1:N:0:TGGTTT
TCTTTGGTGATTTTAGCTGTAT
+
CCCFFFFDHHHHHJJJJJJJJJ
@HWI-ST132:549:C0FYUACXX:5:1101:2506:1903_1:N:0:TGGTTT
TTGGATCGGAGTCTAAACTTTCGGAGC
+
CBCFFFFFHGHHHJIIJIJJJHIHGHG
@HWI-ST132:549:C0FYUACXX:5:1101:2534:1932_1:N:0:TGGTTT
TGCATGGATTCCAGAGCAGACTCGGC
+
@C@FFFFFGGBHDBGIIIGGHII?FB
@HWI-ST132:549:C0FYUACXX:5:1101:2629:1937_1:N:0:TGGTTT
TGCTTGGACTACATATGGTTGAGGGTTGTA
+
CCCFFFFFHHHHHJJJJJHGGGIJJJJJJJ
@HWI-ST132:549:C0FYUACXX:5:1101:2808:1935_1:N:0:TGGTTT
TGGATGTTTTCGAGAAAAAGAGAGA
+
CCCFFFFFHHHHGJJIJJIJIJIJI
@HWI-ST132:549:C0FYUACXX:5:1101:3230:1884_1:N:0:TGGTTT
CGGGTTCAATTCCCGGTATGGGAACCA
+
@BCFDDFFHHHHHJJJFHIJJJJJJJI
@HWI-ST132:549:C0FYUACXX:5:1101:3201:1901_1:N:0:TGGTTT
TTCCCTTTGGCTTGAGAAATGCTGC
+
BBBFFFFFHHGHHJJJIJJJIIJFI
@HWI-ST132:549:C0FYUACXX:5:1101:3202:1980_1:N:0:TGGTTT
AGAGTATTGCCAGCAAACTAATCGGTC
+
??@DADFFHGDHGICHGGHGGIIIIII
@HWI-ST132:549:C0FYUACXX:5:1101:3183:1994_1:N:0:TGGTTT
TCACTGGGCTTTGTTTATCTCA
+
@@@FFDABFAHHGHGIJIIGHI
@HWI-ST132:549:C0FYUACXX:5:1101:3490:1888_1:N:0:TGGTTT
AGGTTGAACAGGCGTTCTGAAATGAA
+
==?ADDFFHHHHHJGIHJJIIIJJIJ
@HWI-ST132:549:C0FYUACXX:5:1101:3286:1900_1:N:0:TGGTTT
TAGTACATCGGAACACAAGAGTCAAAAAAA
+
B@BFFFFFHHHHHIJJJIJIIDHHIIJJJJ
@HWI-ST132:549:C0FYUACXX:5:1101:3389:1907_1:N:0:TGGTTT
TTATTTCGCTCGCTACTGATTGCAG
+
???DDD4A@D;@CEEC+22AA+ACE
@HWI-ST132:549:C0FYUACXX:5:1101:3323:1917_1:N:0:TGGTTT
TTTGGATTGGCTACCTCTGGGATTGGGA
+
111==2AB3CD<C;F@HDGEGBGEAD?C
@HWI-ST132:549:C0FYUACXX:5:1101:3398:1919_1:N:0:TGGTTT
TTCGTCGAAGATACAGAACTGTTATT
+
?@?DDDDFHGHGFEHIGGGIGHJJJJ
@HWI-ST132:549:C0FYUACXX:5:1101:3538:1907_1:N:0:TGGTTT
CGTTACTCTGCCCTTTCGCGACCCAGAA
+
@@@FFFFFHHHHHJJJJJJJIJJJIJGG
@HWI-ST132:549:C0FYUACXX:5:1101:3531:1929_1:N:0:TGGTTT
AAAAGAGTCGGACTCCTATTGTG
+
??@DDDFFHHFFHIHEGIHI@BH
@HWI-ST132:549:C0FYUACXX:5:1101:3648:1970_1:N:0:TGGTTT
TGGAAGACTAGTGATTTTGTTGTT
+
CCCFFFFFHHHHHEHJJJIJJJJJ
@HWI-ST132:549:C0FYUACXX:5:1101:3662:1998_1:N:0:TGGTTT
ATGGACTGAGAACCGGAATTTTT
+
CCCFFFFFHHHHHJJJIJIIJJJ
@HWI-ST132:549:C0FYUACXX:5:1101:3752:1916_1:N:0:TGGTTT
AGGACGAGATTCGCTAATGCAATGCC
+
CCCFFFFFHHHHHJJJJJJJJJIHIJ
@HWI-ST132:549:C0FYUACXX:5:1101:3864:1924_1:N:0:TGGTTT
TGCTTGGACTACATATGGTTGAGGGTTGTA
+
CCCFFFFFHHHHHJIJJJHIIJJJJIJJJJ
@HWI-ST132:549:C0FYUACXX:5:1101:3786:1958_1:N:0:TGGTTT
TGGAAAATAAAACCTTCTCGAAGGG
+
@C@FFFFFHHFHHJJJJJJJJJJII
@HWI-ST132:549:C0FYUACXX:5:1101:3793:1988_1:N:0:TGGTTT
GAATTCGTAGAAGGAAGATTTTTCGCGGT
+
=@@?DDDEHHHFBGGGGGHIIJIDGEFE?
@HWI-ST132:549:C0FYUACXX:5:1101:4123:1921_1:N:0:TGGTTT
GCATGGATTCCAGAGCAGACTCGGC
+
CCCFFFFFHHHHHIJJJJJJJJCGG
@HWI-ST132:549:C0FYUACXX:5:1101:4030:1974_1:N:0:TGGTTT
GAAGATATTAATTCGCGAGTCTTA
+
CCCFFFFFHHHHHJJJJJJGHIII
@HWI-ST132:549:C0FYUACXX:5:1101:4468:1880_1:N:0:TGGTTT
ATGATGATAGAGACGGCTTGGTAA
+
1=DFFFFHHHHHGIJJJJJJJCGH
Les parametres
Input Parameter 	Value 	Note for rerun
Single or Paired-end reads 	single 	
Select reads 	11: FASTQ Groomer on data 10 	
Filter out chimeric clusters 	false 	
Length of prefix to be used in the analysis 	0 	
Match length 	True 	
Maximum number/percent of mismatches allowed 	None 	
Description length 	0
Les erreurs:
Fatal error: Exit code 134 ()
cd-hit-dup: cdhit-dup.cxx:159: int HashingDepth(int, int): Assertion `len >= min' failed.
Aborted
 From input: /data/galaxy.prabi.fr/database/files/025/dataset_25721.dat
Total number of sequences: 39
Longest: 30
Shortest: 22
Sorted by length ...
Start clustering duplicated sequences ...
primer = 0

Re: [galaxy-dev] probleme tool galaxy

navratil

Curtis Hendrickson (Campus)

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