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