mothur

Combining raw data with multiple Illumina MiSeq runs with overlapping barcodes

#1

Dear Mothur user

I have problem in combining MiSeq Illumina data from two different runs. I ran trim seq command but since many of the barcodes were same between two runs, trim seq command is disregarding many samples. As a result, though my two runs have a total of 522 samples, but after trim seq only 323 samples are coming. Details of the problem can be seen below.

Your help and advise will be highy appreciated.

thank you

Windows version

mothur v.1.41.1

Last updated: 11/26/18

mothur >

 trim.seqs(fasta= merge.fasta, oligos=combined.oligos, checkorient=t)

Using 4 processors.

[WARNING]: barcode TACCGGAT is in your oligos file already, disregarding.

[WARNING]: barcode TACGCGAT is in your oligos file already, disregarding.

[WARNING]: barcode TAGGATCC is in your oligos file already, disregarding.

[WARNING]: barcode TATACGGC is in your oligos file already, disregarding.

[WARNING]: barcode TCACCACT is in your oligos file already, disregarding.

[WARNING]: barcode TAATCGCG is in your oligos file already, disregarding.

[WARNING]: barcode TACCGGTA is in your oligos file already, disregarding.

[WARNING]: barcode TACGCGTA is in your oligos file already, disregarding.

[WARNING]: barcode TAGCCGTA is in your oligos file already, disregarding.

[WARNING]: barcode TAGGATGG is in your oligos file already, disregarding.

and so on......................


Below is my oilgo file.
|Barcode|TAATCCGG|799F_1|
|---|---|---|
|Barcode|TACCATGG|799F_10|
|Barcode|TCAGTGTG|799F_100|
|Barcode|TCCAACCT|799F_101|
|BARCODE|TCCAACCT|799F_101|
|Barcode|TCCAACGA|799F_102|
|BARCODE|TCCAACGA|799F_102|
|Barcode|TCCAAGCA|799F_103|
|BARCODE|TCCAAGCA|799F_103|
|Barcode|TCCAAGGT|799F_104|
|BARCODE|TCCAAGGT|799F_104|
|Barcode|TCCACAAG|799F_105|
|BARCODE|TCCACAAG|799F_105|
|Barcode|TCCACATC|799F_106|
|BARCODE|TCCACATC|799F_106|
|Barcode|TCCACTAC|799F_107|
|BARCODE|TCCACTAC|799F_107|
|Barcode|TCCACTTG|799F_108|
|BARCODE|TCCACTTG|799F_108|
|Barcode|TCCAGAAC|799F_109|
|BARCODE|TCCAGAAC|799F_109|
|Barcode|TACCGCAA|799F_11|
|BARCODE|TACCGCAA|799F_11|
|Barcode|TCCAGATG|799F_110|
|BARCODE|TCCAGATG|799F_110|
|Barcode|TCCAGTAG|799F_111|
|BARCODE|TCCAGTAG|799F_111|
|Barcode|TCCAGTTC|799F_112|
|BARCODE|TCCAGTTC|799F_112|
|Barcode|TCCATCCA|799F_113|
|BARCODE|TCCATCCA|799F_113|
|Barcode|TCCATCGT|799F_114|
|BARCODE|TCCATCGT|799F_114|
|Barcode|TCCATGCT|799F_115|
|BARCODE|TCCATGCT|799F_115|
|Barcode|TCCATGGA|799F_116|
|BARCODE|TCCATGGA|799F_116|
|Barcode|TCCTACCA|799F_117|
|BARCODE|TCCTACCA|799F_117|
|Barcode|TCCTACGT|799F_118|
|BARCODE|TCCTACGT|799F_118|
|Barcode|TCCTAGCT|799F_119|
|BARCODE|TCCTAGCT|799F_119|
|Barcode|TACCGCTT|799F_12|
|BARCODE|TACCGCTT|799F_12|
|Barcode|TCCTAGGA|799F_120|
|BARCODE|TCCTAGGA|799F_120|
|Barcode|TCCTCAAC|799F_121|
|BARCODE|TCCTCAAC|799F_121|
|Barcode|TCCTCATG|799F_122|
|BARCODE|TCCTCATG|799F_122|
|Barcode|TCCTCTAG|799F_123|
|BARCODE|TCCTCTAG|799F_123|
|Barcode|TCCTCTTC|799F_124|
|BARCODE|TCCTCTTC|799F_124|
|Barcode|TCCTGAAG|799F_125|
|BARCODE|TCCTGAAG|799F_125|
|Barcode|TCCTGATC|799F_126|
|BARCODE|TCCTGATC|799F_126|
|Barcode|TCCTGTAC|799F_127|
|BARCODE|TCCTGTAC|799F_127|
|Barcode|TCCTGTTG|799F_128|
|BARCODE|TCCTGTTG|799F_128|
|Barcode|TCCTTCCT|799F_129|
|BARCODE|TCCTTCCT|799F_129|
|Barcode|TACCGGAT|799F_13|
|BARCODE|TACCGGAT|799F_13|
|Barcode|TCCTTCGA|799F_130|
|BARCODE|TCCTTCGA|799F_130|
|Barcode|TCCTTGCA|799F_131|
|BARCODE|TCCTTGCA|799F_131|
|Barcode|TCCTTGGT|799F_132|
|BARCODE|TCCTTGGT|799F_132|
|Barcode|TCGAACCA|799F_133|
|BARCODE|TCGAACCA|799F_133|
|Barcode|TCGAACGT|799F_134|
|BARCODE|TCGAACGT|799F_134|
|Barcode|TCGAAGCT|799F_135|
|BARCODE|TCGAAGCT|799F_135|
|Barcode|TCGAAGGA|799F_136|
|BARCODE|TCGAAGGA|799F_136|
|Barcode|TCGACAAC|799F_137|
|BARCODE|TCGACAAC|799F_137|
|Barcode|TCGACATG|799F_138|
|BARCODE|TCGACATG|799F_138|
|Barcode|TCGACTAG|799F_139|
|BARCODE|TCGACTAG|799F_139|
|Barcode|TACCGGTA|799F_14|
|BARCODE|TACCGGTA|799F_14|
|Barcode|TCGACTTC|799F_140|
|BARCODE|TCGACTTC|799F_140|
|Barcode|TCGAGAAG|799F_141|
|BARCODE|TCGAGAAG|799F_141|
|Barcode|TCGAGATC|799F_142|
|BARCODE|TCGAGATC|799F_142|
|Barcode|TCGAGTAC|799F_143|
|BARCODE|TCGAGTAC|799F_143|
|Barcode|TCGAGTTG|799F_144|
|BARCODE|TCGAGTTG|799F_144|
|Barcode|TCGATCCT|799F_145|
|BARCODE|TCGATCCT|799F_145|
|Barcode|TCGATCGA|799F_146|
|BARCODE|TCGATCGA|799F_146|
|Barcode|TCGATGCA|799F_147|
|BARCODE|TCGATGCA|799F_147|
|Barcode|TCGATGGT|799F_148|
|Barcode|TCGTACCT|799F_149|
|BARCODE|TCGTACCT|799F_149|
|Barcode|TACCTACC|799F_15|
|BARCODE|TACCTACC|799F_15|
|Barcode|TCGTACGA|799F_150|
|BARCODE|TCGTACGA|799F_150|
|Barcode|TCGTAGCA|799F_151|
|BARCODE|TCGTAGCA|799F_151|
|Barcode|TCGTAGGT|799F_152|
|BARCODE|TCGTAGGT|799F_152|
|Barcode|TCGTCAAG|799F_153|
|BARCODE|TCGTCAAG|799F_153|
|Barcode|TCGTCATC|799F_154|
|BARCODE|TCGTCATC|799F_154|
|Barcode|TCGTCTAC|799F_155|
|BARCODE|TCGTCTAC|799F_155|
|Barcode|TCGTCTTG|799F_156|
|BARCODE|TCGTCTTG|799F_156|
|Barcode|TCGTGAAC|799F_157|
|BARCODE|TCGTGAAC|799F_157|
|Barcode|TCGTGATG|799F_158|
|BARCODE|TCGTGATG|799F_158|
|Barcode|TCGTGTAG|799F_159|
|BARCODE|TCGTGTAG|799F_159|
|Barcode|TACCTAGG|799F_16|
|BARCODE|TACCTAGG|799F_16|
|Barcode|TCGTGTTC|799F_160|
|BARCODE|TCGTGTTC|799F_160|
|Barcode|TCGTTCCA|799F_161|
|BARCODE|TCGTTCCA|799F_161|
|Barcode|TCGTTCGT|799F_162|
|BARCODE|TCGTTGCT|799F_163|
|Barcode|TCGTTGGA|799F_164|
|BARCODE|TCGTTGGA|799F_164|
|Barcode|TCTCACAC|799F_165|
|BARCODE|TCTCACAC|799F_165|
|Barcode|TCTCACTG|799F_166|
|BARCODE|TCTCACTG|799F_166|
|Barcode|TCTCAGAG|799F_167|
|BARCODE|TCTCAGAG|799F_167|
|Barcode|TCTCAGTC|799F_168|
|BARCODE|TCTCAGTC|799F_168|
|Barcode|TCTCCACA|799F_169|
|BARCODE|TCTCCACA|799F_169|
|Barcode|TACCTTCG|799F_17|
|BARCODE|TACCTTCG|799F_17|
|Barcode|TCTCCAGT|799F_170|
|BARCODE|TCTCCAGT|799F_170|
|Barcode|TCTCCTCT|799F_171|
|BARCODE|TCTCCTCT|799F_171|
|Barcode|TCTCCTGA|799F_172|
|BARCODE|TCTCCTGA|799F_172|
|Barcode|TCTCGACT|799F_173|
|BARCODE|TCTCGACT|799F_173|
|Barcode|TCTCGAGA|799F_174|
|BARCODE|TCTCGAGA|799F_174|
|Barcode|TCTCGTCA|799F_175|
|BARCODE|TCTCGTCA|799F_175|
|Barcode|TCTCGTGT|799F_176|
|BARCODE|TCTCGTGT|799F_176|
|Barcode|TCTCTCAG|799F_177|
|BARCODE|TCTCTCAG|799F_177|
|Barcode|TCTCTCTC|799F_178|
|BARCODE|TCTCTCTC|799F_178|
|Barcode|TCTCTGAC|799F_179|
|BARCODE|TCTCTGAC|799F_179|
|Barcode|TACCTTGC|799F_18|
|BARCODE|TACCTTGC|799F_18|
|Barcode|TCTCTGTG|799F_180|
|BARCODE|TCTCTGTG|799F_180|
|Barcode|TCTGACAG|799F_181|
|BARCODE|TCTGACAG|799F_181|
|Barcode|TCTGACTC|799F_182|
|BARCODE|TCTGACTC|799F_182|
|Barcode|TCTGAGAC|799F_183|
|BARCODE|TCTGAGAC|799F_183|
|Barcode|TCTGAGTG|799F_184|
|BARCODE|TCTGAGTG|799F_184|
|Barcode|TCTGCACT|799F_185|
|BARCODE|TCTGCACT|799F_185|
|Barcode|TCTGCAGA|799F_186|
|BARCODE|TCTGCAGA|799F_186|
|Barcode|TCTGCTCA|799F_187|
|BARCODE|TCTGCTCA|799F_187|
|Barcode|TCTGCTGT|799F_188|
|BARCODE|TCTGCTGT|799F_188|
|Barcode|TCTGGACA|799F_189|
|BARCODE|TCTGGACA|799F_189|
|Barcode|TACGAACC|799F_19|
|BARCODE|TACGAACC|799F_19|
|Barcode|TCTGGAGT|799F_190|
|BARCODE|TCTGGAGT|799F_190|
|Barcode|TCTGGTCT|799F_191|
|BARCODE|TCTGGTCT|799F_191|
|Barcode|TCTGGTGA|799F_192|
|BARCODE|TCTGGTGA|799F_192|
|Barcode|TCTGTCAC|799F_193|
|BARCODE|TCTGTCAC|799F_193|
|Barcode|TCTGTCTG|799F_194|
|BARCODE|TCTGTCTG|799F_194|
|Barcode|TCTGTGAG|799F_195|
|BARCODE|TCTGTGAG|799F_195|
|Barcode|TCTGTGTC|799F_196|
|BARCODE|TCTGTGTC|799F_196|
|Barcode|TGACACAC|799F_197|
|BARCODE|TGACACAC|799F_197|
|BARCODE|TGACACTG|799F_198|
|BARCODE|TGACAGAG|799F_199|
|Barcode|TAATCGCG|799F_2|
|BARCODE|TAATCGCG|799F_2|
|Barcode|TACGAAGG|799F_20|
|BARCODE|TACGAAGG|799F_20|
|BARCODE|TGACAGTC|799F_200|
|BARCODE|TGACCACA|799F_201|
|BARCODE|TGACCAGT|799F_202|
|BARCODE|TGACCTCT|799F_203|
|BARCODE|TGACCTGA|799F_204|
|Barcode|TGACGACT|799F_205|
|BARCODE|TGACGACT|799F_205|
|Barcode|TGACGAGA|799F_206|
|BARCODE|TGACGAGA|799F_206|
|Barcode|TGACGTCA|799F_207|
|BARCODE|TGACGTCA|799F_207|
|Barcode|TGACGTGT|799F_208|
|BARCODE|TGACGTGT|799F_208|
|Barcode|TGACTCAG|799F_209|
|BARCODE|TGACTCAG|799F_209|
|Barcode|TACGATCG|799F_21|
|BARCODE|TACGATCG|799F_21|
|BARCODE|TGACTCTC|799F_210|
|BARCODE|TGACTGAC|799F_211|
|BARCODE|TGACTGTG|799F_212|
|BARCODE|TGAGACAG|799F_213|
|BARCODE|TGAGACTC|799F_214|
|BARCODE|TGAGAGAC|799F_215|
|BARCODE|TGAGAGTG|799F_216|
|Barcode|TGAGCACT|799F_217|
|BARCODE|TGAGCACT|799F_217|
|Barcode|TGAGCAGA|799F_218|
|BARCODE|TGAGCAGA|799F_218|
|Barcode|TGAGCTCA|799F_219|
|BARCODE|TGAGCTCA|799F_219|
|Barcode|TACGATGC|799F_22|
|Barcode|TGAGCTGT|799F_220|
|BARCODE|TGAGCTGT|799F_220|
|Barcode|TGAGGACA|799F_221|
|BARCODE|TGAGGACA|799F_221|
|BARCODE|TGAGGAGT|799F_222|
|BARCODE|TGAGGTCT|799F_223|
|BARCODE|TGAGGTGA|799F_224|
|BARCODE|TGAGTCAC|799F_225|
|BARCODE|TGAGTCTG|799F_226|
|BARCODE|TGAGTGAG|799F_227|
|BARCODE|TGAGTGTC|799F_228|
|Barcode|TGCAACCA|799F_229|
|BARCODE|TGCAACCA|799F_229|
|Barcode|TACGCCAA|799F_23|
|BARCODE|TACGCCAA|799F_23|
|Barcode|TGCAACGT|799F_230|
|BARCODE|TGCAACGT|799F_230|
|Barcode|TGCAAGCT|799F_231|
|BARCODE|TGCAAGCT|799F_231|
|Barcode|TGCAAGGA|799F_232|
|BARCODE|TGCAAGGA|799F_232|
|BARCODE|TGCACAAC|799F_233|
|BARCODE|TGCACATG|799F_234|
|BARCODE|TGCACTAG|799F_235|
|BARCODE|TGCACTTC|799F_236|
|BARCODE|TGCAGAAG|799F_237|
|BARCODE|TGCAGATC|799F_238|
|BARCODE|TGCAGTAC|799F_239|
|Barcode|TACGCCTT|799F_24|
|BARCODE|TACGCCTT|799F_24|
|BARCODE|TGCAGTTG|799F_240|
|Barcode|TGCATCCT|799F_241|
|BARCODE|TGCATCCT|799F_241|
|Barcode|TGCATCGA|799F_242|
|BARCODE|TGCATCGA|799F_242|
|Barcode|TGCATGCA|799F_243|
|BARCODE|TGCATGCA|799F_243|
|Barcode|TGCATGGT|799F_244|
|BARCODE|TGCATGGT|799F_244|
|BARCODE|TGCTACCT|799F_245|
|BARCODE|TGCTACGA|799F_246|
|BARCODE|TGCTAGCA|799F_247|
|BARCODE|TGCTAGGT|799F_248|
|BARCODE|TGCTCAAG|799F_249|
|Barcode|TACGCGAT|799F_25|
|BARCODE|TACGCGAT|799F_25|
|BARCODE|TGCTCATC|799F_250|
|BARCODE|TGCTCTAC|799F_251|
|BARCODE|TGCTCTTG|799F_252|
|Barcode|TGCTGAAC|799F_253|
|BARCODE|TGCTGAAC|799F_253|
|Barcode|TGCTGATG|799F_254|
|BARCODE|TGCTGATG|799F_254|
|Barcode|TGCTGTAG|799F_255|
|BARCODE|TGCTGTAG|799F_255|
|Barcode|TGCTGTTC|799F_256|
|BARCODE|TGCTGTTC|799F_256|
|BARCODE|TGCTTCCA|799F_257|
|BARCODE|TGCTTCGT|799F_258|
|BARCODE|TGCTTGCT|799F_259|
|Barcode|TACGCGTA|799F_26|
|BARCODE|TACGCGTA|799F_26|
|BARCODE|TGCTTGGA|799F_260|
|BARCODE|TGGAACCT|799F_261|
|BARCODE|TGGAACGA|799F_262|
|BARCODE|TGGAAGCA|799F_263|
|BARCODE|TGGAAGGT|799F_264|
|Barcode|TGGACAAG|799F_265|
|BARCODE|TGGACAAG|799F_265|
|Barcode|TGGACATC|799F_266|
|BARCODE|TGGACATC|799F_266|
|Barcode|TGGACTAC|799F_267|
|BARCODE|TGGACTAC|799F_267|
|Barcode|TGGACTTG|799F_268|
|BARCODE|TGGAGAAC|799F_269|
|Barcode|TACGGCAT|799F_27|
|BARCODE|TACGGCAT|799F_27|
|BARCODE|TGGAGATG|799F_270|
|BARCODE|TGGAGTAG|799F_271|
|BARCODE|TGGAGTTC|799F_272|
|BARCODE|TGGATCCA|799F_273|
|Barcode|TGGATGCT|799F_275|
|Barcode|TGGTACCA|799F_277|
|Barcode|TGGTACGT|799F_278|
|Barcode|TGGTAGCT|799F_279|
|BARCODE|TGGTAGCT|799F_279|
|Barcode|TACGGCTA|799F_28|
|BARCODE|TACGGCTA|799F_28|
|Barcode|TGGTAGGA|799F_280|
|BARCODE|TGGTCTAG|799F_283|
|BARCODE|TGGTCTTC|799F_284|
|BARCODE|TGGTGATC|799F_286|
|BARCODE|TGGTGTTG|799F_288|
|BARCODE|GATCAGCT|799F_289|
|Barcode|TACGTACG|799F_29|
|BARCODE|TACGTACG|799F_29|
|BARCODE|GATCGTTG|799F_298|
|Barcode|TAATCGGC|799F_3|
|BARCODE|TAATCGGC|799F_3|
|Barcode|TACGTAGC|799F_30|
|BARCODE|TACGTAGC|799F_30|
|BARCODE|GATCTCGA|799F_300|
|BARCODE|GATGCAAG|799F_307|
|BARCODE|GATGCATC|799F_308|
|Barcode|TACGTTCC|799F_31|
|BARCODE|TACGTTCC|799F_31|
|BARCODE|GATGTCGT|799F_316|
|Barcode|TACGTTGG|799F_32|
|BARCODE|TACGTTGG|799F_32|
|BARCODE|GCAACGAA|799F_321|
|BARCODE|GCAACGTT|799F_322|
|Barcode|TAGCAACC|799F_33|
|BARCODE|TAGCAACC|799F_33|
|BARCODE|GCATAACC|799F_331|
|BARCODE|GCATAAGG|799F_332|
|BARCODE|GCATGCAT|799F_339|
|Barcode|TAGCAAGG|799F_34|
|BARCODE|GCCGAATT|799F_345|
|BARCODE|GCCGATAT|799F_346|
|BARCODE|GCCGATTA|799F_347|
|BARCODE|GCCGTAAT|799F_348|
|Barcode|TAGCATCG|799F_35|
|BARCODE|TAGCATCG|799F_35|
|BARCODE|GCGCTAAT|799F_354|
|BARCODE|GCGCTTAA|799F_356|
|Barcode|TAGCATGC|799F_36|
|BARCODE|TAGCATGC|799F_36|
|BARCODE|GCTAATCG|799F_361|
|BARCODE|GCTACCAA|799F_363|
|Barcode|TAGCCGAT|799F_37|
|BARCODE|GCTATACG|799F_371|
|BARCODE|GCTATAGC|799F_372|
|BARCODE|GCTTATCC|799F_377|
|BARCODE|GCTTCCAT|799F_379|
|Barcode|TAGCCGTA|799F_38|
|BARCODE|TAGCCGTA|799F_38|
|BARCODE|ATAACCGC|799F_385|
|BARCODE|ATAACGCC|799F_386|
|Barcode|TAGCGCAT|799F_39|
|BARCODE|TAGCGCAT|799F_39|
|BARCODE|ATATGCGC|799F_393|
|BARCODE|ATCCAACG|799F_395|
|Barcode|TAATGCCG|799F_4|
|Barcode|TAGCGCTA|799F_40|
|BARCODE|ATCCGCTT|799F_400|
|Barcode|TAGCGGAA|799F_41|
|BARCODE|TAGCGGAA|799F_41|
|BARCODE|ATGGCCTA|799F_412|
|BARCODE|ATGGCGAA|799F_413|
|BARCODE|ATGGCGTT|799F_414|
|Barcode|TAGCGGTT|799F_42|
|BARCODE|TAGCGGTT|799F_42|
|BARCODE|ATTACGGC|799F_421|
|BARCODE|CAACACGT|799F_426|
|BARCODE|CAACAGCT|799F_427|
|BARCODE|CAACAGGA|799F_428|
|BARCODE|CAACCAAC|799F_429|
|Barcode|TAGCTACG|799F_43|
|BARCODE|TAGCTACG|799F_43|
|BARCODE|CAACCATG|799F_430|
|Barcode|TAGCTAGC|799F_44|
|BARCODE|TAGCTAGC|799F_44|
|Barcode|TAGCTTCC|799F_45|
|BARCODE|TAGCTTCC|799F_45|
|Barcode|TAGCTTGG|799F_46|
|Barcode|TAGGAACG|799F_47|
|BARCODE|TAGGAACG|799F_47|
|Barcode|TAGGAAGC|799F_48|
|Barcode|TAGGATCC|799F_49|
|BARCODE|TAGGATCC|799F_49|
|Barcode|TAATGCGC|799F_5|
|BARCODE|TAATGCGC|799F_5|
|Barcode|TAGGATGG|799F_50|
|BARCODE|TAGGATGG|799F_50|
|Barcode|TAGGCCAT|799F_51|
|BARCODE|TAGGCCAT|799F_51|
|Barcode|TAGGCCTA|799F_52|
|BARCODE|TAGGCCTA|799F_52|
|Barcode|TAGGCGAA|799F_53|
|BARCODE|TAGGCGAA|799F_53|
|Barcode|TAGGCGTT|799F_54|
|BARCODE|TAGGCGTT|799F_54|
|Barcode|TAGGTACC|799F_55|
|BARCODE|TAGGTACC|799F_55|
|Barcode|TAGGTAGG|799F_56|
|BARCODE|TAGGTAGG|799F_56|
|Barcode|TAGGTTCG|799F_57|
|BARCODE|TAGGTTCG|799F_57|
|Barcode|TAGGTTGC|799F_58|
|Barcode|TATACCGG|799F_59|
|BARCODE|TATACCGG|799F_59|
|Barcode|TAATGGCC|799F_6|
|BARCODE|TAATGGCC|799F_6|
|Barcode|TATACGCG|799F_60|
|BARCODE|TATACGCG|799F_60|
|Barcode|TATACGGC|799F_61|
|BARCODE|TATACGGC|799F_61|
|Barcode|TATAGCCG|799F_62|
|BARCODE|TATAGCCG|799F_62|
|Barcode|TATAGCGC|799F_63|
|BARCODE|TATAGCGC|799F_63|
|Barcode|TATAGGCC|799F_64|
|BARCODE|TATAGGCC|799F_64|
|Barcode|TATTCCGC|799F_65|
|BARCODE|TATTCCGC|799F_65|
|Barcode|TATTCGCC|799F_66|
|Barcode|TATTGCGG|799F_67|
|Barcode|TATTGGCG|799F_68|
|BARCODE|TATTGGCG|799F_68|
|Barcode|TCACACAG|799F_69|
|BARCODE|TCACACAG|799F_69|
|Barcode|TACCAACG|799F_7|
|BARCODE|TACCAACG|799F_7|
|Barcode|TCACACTC|799F_70|
|Barcode|TCACAGAC|799F_71|
|Barcode|TCACAGTG|799F_72|
|BARCODE|TCACAGTG|799F_72|
|Barcode|TCACCACT|799F_73|
|BARCODE|TCACCACT|799F_73|
|Barcode|TCACCAGA|799F_74|
|BARCODE|TCACCAGA|799F_74|
|Barcode|TCACCTCA|799F_75|
|BARCODE|TCACCTCA|799F_75|
|Barcode|TCACCTGT|799F_76|
|Barcode|TCACGACA|799F_77|
|BARCODE|TCACGACA|799F_77|
|Barcode|TCACGAGT|799F_78|
|BARCODE|TCACGAGT|799F_78|
|Barcode|TCACGTCT|799F_79|
|BARCODE|TCACGTCT|799F_79|
|Barcode|TACCAAGC|799F_8|
|BARCODE|TACCAAGC|799F_8|
|Barcode|TCACGTGA|799F_80|
|Barcode|TCACTCAC|799F_81|
|BARCODE|TCACTCAC|799F_81|
|Barcode|TCACTCTG|799F_82|
|Barcode|TCACTGAG|799F_83|
|Barcode|TCACTGTC|799F_84|
|BARCODE|TCACTGTC|799F_84|
|Barcode|TCAGACAC|799F_85|
|Barcode|TCAGACTG|799F_86|
|BARCODE|TCAGACTG|799F_86|
|Barcode|TCAGAGAG|799F_87|
|BARCODE|TCAGAGAG|799F_87|
|Barcode|TCAGAGTC|799F_88|
|BARCODE|TCAGAGTC|799F_88|
|Barcode|TCAGCACA|799F_89|
|BARCODE|TCAGCACA|799F_89|
|Barcode|TACCATCC|799F_9|
|BARCODE|TACCATCC|799F_9|
|Barcode|TCAGCAGT|799F_90|
|Barcode|TCAGCTCT|799F_91|
|BARCODE|TCAGCTCT|799F_91|
|Barcode|TCAGCTGA|799F_92|
|BARCODE|TCAGCTGA|799F_92|
|Barcode|TCAGGACT|799F_93|
|BARCODE|TCAGGACT|799F_93|
|Barcode|TCAGGAGA|799F_94|
|Barcode|TCAGGTCA|799F_95|
|BARCODE|TCAGGTCA|799F_95|
|Barcode|TCAGGTGT|799F_96|
|BARCODE|TCAGGTGT|799F_96|
|Barcode|TCAGTCAG|799F_97|
|BARCODE|TCAGTCAG|799F_97|
|Barcode|TCAGTCTC|799F_98|
|BARCODE|TCAGTCTC|799F_98|
|Barcode|TCAGTGAC|799F_99|
|BARCODE|TCAGTGAC|799F_99|
|BARCODE|CAACGATC|799F_NTC1|
|BARCODE|CAACGTAC|799F_NTC2|
|BARCODE|CAACGTTG|799F_NTC3|
|BARCODE|CAACTCCT|799F_NTC4|
|BARCODE|TCAGTGTG|799F_100|
#2

Looking at the first error…

[WARNING]: barcode TACCGGAT is in your oligos file already, disregarding.

and then looking in your oligos file you have…

barcode   TACCGGAT   799F_13
barcode   TACCGGAT   799F_13

What happens if you only include one copy of that line? I assume that if you ran this across two runs, that 799F_13 was the same sample in both runs, right? If they are different, then you need to give them different names. If you have the same barcode, but different names, then you need to run make.contigs on each set of samples separately

#3

Thanks for your reply .

Since 799f_13 is a different sample in both run : I need to rename sample name. This I will do.

But I want to analyze samples of both illumina runs together as they are part of one experiment. Thus, running separately make.contig on each run data will not serve my purpose.

Kindly advise.

Thanks

Gurdeep

#4

Right - after running make.contigs, you’ll need to pool all of the files together. Alternatively, it would be better to give your samples meaningful names that are unique across sequencing runs. This will make your life easier down the road when you want to analyze the output of mothur.

#5

Thank you.

dear Dr. Schloss

I have renamed barcode names and now barcode names (391 in total) are unique (but just to recall you, barcode sequences are not unique) and now my .oligo file is as below.

forward AGAACMGGATTAGATACCCKG
reverse ACGTCATCCCCACCTTCC
BARCODE 799F_1000 TCAGCACA
BARCODE 799F_1001 ATCCAACG
BARCODE 799F_1002 TCAGCTCT
BARCODE 799F_1003 TCAGCTGA
BARCODE 799F_1004 TCAGGACT
BARCODE 799F_1005 TCAGGTCA
BARCODE 799F_1006 TCAGGTGT
BARCODE 799F_1007 TCAGTCAG
BARCODE 799F_1008 TCAGTCTC
BARCODE 799F_1009 TCAGTGAC
BARCODE 799F_1010 TCAGTGTG
BARCODE 799F_1011 TCCAACCT
BARCODE 799F_1012 TCCAACGA
BARCODE 799F_1013 TCCAAGCA
BARCODE 799F_1014 TCCAAGGT
BARCODE 799F_1015 TCCACAAG
BARCODE 799F_1016 TCCACATC
BARCODE 799F_1017 TCCACTAC
BARCODE 799F_1018 TCCACTTG
BARCODE 799F_1019 TCCAGAAC
BARCODE 799F_1020 TCCAGATG
BARCODE 799F_1021 TCCAGTAG
BARCODE 799F_1022 TCCAGTTC
BARCODE 799F_1023 TCCATCCA
BARCODE 799F_1024 TCCATCGT
BARCODE 799F_1025 TCCATGCT
BARCODE 799F_1026 TCCATGGA
BARCODE 799F_1027 TCCTACCA
BARCODE 799F_1028 TCCTACGT
BARCODE 799F_1029 TCCTAGCT
BARCODE 799F_1030 TCCTAGGA
BARCODE 799F_1031 TCCTCAAC
BARCODE 799F_1032 TCCTCATG
BARCODE 799F_1033 TCCTCTAG
BARCODE 799F_1034 TCCTCTTC
BARCODE 799F_1035 TCCTGAAG
BARCODE 799F_1036 TCCTGATC
BARCODE 799F_1037 TCCTGTAC
BARCODE 799F_1038 TCCTGTTG
BARCODE 799F_1039 TCCTTCCT
BARCODE 799F_1040 TCCTTCGA
BARCODE 799F_1041 TCCTTGCA
BARCODE 799F_1042 TCCTTGGT
BARCODE 799F_1043 TCGAACCA
BARCODE 799F_1044 TCGAACGT
BARCODE 799F_1045 TCGAAGCT
BARCODE 799F_1046 TCGAAGGA
BARCODE 799F_1047 TCGACAAC
BARCODE 799F_1048 TCGACATG
BARCODE 799F_1049 TCGACTAG
BARCODE 799F_1050 TCGACTTC
BARCODE 799F_1051 TCGAGAAG
BARCODE 799F_1052 TCGAGATC
BARCODE 799F_1053 TCGAGTAC
BARCODE 799F_1054 TCGAGTTG
BARCODE 799F_1055 TCGATCCT
BARCODE 799F_1056 TCGATCGA
BARCODE 799F_1057 TCGATGCA
BARCODE 799F_1058 TCGTACCT
BARCODE 799F_1059 TCGTACGA
BARCODE 799F_1060 TCGTAGCA
BARCODE 799F_1061 TCGTAGGT
BARCODE 799F_1062 TCGTCAAG
BARCODE 799F_1063 TCGTCATC
BARCODE 799F_1064 TCGTCTAC
BARCODE 799F_1065 TCGTCTTG
BARCODE 799F_1066 TCGTGAAC
BARCODE 799F_1067 TCGTGATG
BARCODE 799F_1068 TCGTGTAG
BARCODE 799F_1069 TCGTGTTC
BARCODE 799F_1070 TCGTTCCA
BARCODE 799F_1071 TCGTTGCT
BARCODE 799F_1072 TCGTTGGA
BARCODE 799F_1073 TCTCACAC
BARCODE 799F_1074 TCTCACTG
BARCODE 799F_1075 TCTCAGAG
BARCODE 799F_1076 TCTCAGTC
BARCODE 799F_1077 TCTCCACA
BARCODE 799F_1078 TCTCCAGT
BARCODE 799F_1079 TCTCCTCT
BARCODE 799F_1080 TCTCCTGA
BARCODE 799F_1081 TCTCGACT
BARCODE 799F_1082 TCTCGAGA
BARCODE 799F_1083 TCTCGTCA
BARCODE 799F_1084 TCTCGTGT
BARCODE 799F_1085 TCTCTCAG
BARCODE 799F_1086 TCTCTCTC
BARCODE 799F_1087 TCTCTGAC
BARCODE 799F_1088 TCTCTGTG
BARCODE 799F_1089 TCTGACAG
BARCODE 799F_1090 TCTGACTC
BARCODE 799F_1091 TCTGAGAC
BARCODE 799F_1092 TCTGAGTG
BARCODE 799F_1093 TCTGCACT
BARCODE 799F_1094 TCTGCAGA
BARCODE 799F_1095 TCTGCTCA
BARCODE 799F_1096 TCTGCTGT
BARCODE 799F_1097 TCTGGACA
BARCODE 799F_1098 TCTGGAGT
BARCODE 799F_1099 TCTGGTCT
BARCODE 799F_1100 TCTGGTGA
BARCODE 799F_1101 TCTGTCAC
BARCODE 799F_1102 TCTGTCTG
BARCODE 799F_1103 TCTGTGAG
BARCODE 799F_1104 TCTGTGTC
BARCODE 799F_1105 TGACACAC
BARCODE 799F_1106 TGACACTG
BARCODE 799F_1107 TGACAGAG
BARCODE 799F_1108 TGACAGTC
BARCODE 799F_1109 TGACCACA
BARCODE 799F_1110 TGACCAGT
BARCODE 799F_1111 TGACCTCT
BARCODE 799F_1112 TGACCTGA
BARCODE 799F_1113 TGACGACT
BARCODE 799F_1114 TGACGAGA
BARCODE 799F_1115 TGACGTCA
BARCODE 799F_1116 TGACGTGT
BARCODE 799F_1117 TGACTCAG
BARCODE 799F_1118 TGACTCTC
BARCODE 799F_1119 TGACTGAC
BARCODE 799F_1120 TGACTGTG
BARCODE 799F_1121 TGAGACAG
BARCODE 799F_1122 TGAGACTC
BARCODE 799F_1123 TGAGAGAC
BARCODE 799F_1124 TGAGAGTG
BARCODE 799F_1125 TGAGCACT
BARCODE 799F_1126 TGAGCAGA
BARCODE 799F_1127 TGAGCTCA
BARCODE 799F_1128 TGAGCTGT
BARCODE 799F_1129 TGAGGACA
BARCODE 799F_1130 TGAGGAGT
BARCODE 799F_1131 TGAGGTCT
BARCODE 799F_1132 TGAGGTGA
BARCODE 799F_1133 TGAGTCAC
BARCODE 799F_1134 TGAGTCTG
BARCODE 799F_1135 TGAGTGAG
BARCODE 799F_1136 TGAGTGTC
BARCODE 799F_1137 TGCAACCA
BARCODE 799F_1138 TGCAACGT
BARCODE 799F_1139 TGCAAGCT
BARCODE 799F_1140 TGCAAGGA
BARCODE 799F_1141 TGCACAAC
BARCODE 799F_1142 TGCACATG
BARCODE 799F_1143 TGCACTAG
BARCODE 799F_1144 TGCACTTC
BARCODE 799F_1145 TGCAGAAG
BARCODE 799F_1146 TGCAGATC
BARCODE 799F_1147 TGCAGTAC
BARCODE 799F_1148 TGCAGTTG
BARCODE 799F_1149 TGCATCCT
BARCODE 799F_1150 TGCATCGA
BARCODE 799F_1151 TGCATGCA
BARCODE 799F_1152 TGCATGGT
BARCODE 799F_1153 TGCTACCT
BARCODE 799F_1154 TGCTACGA
BARCODE 799F_1155 TGCTAGCA
BARCODE 799F_1156 TGCTAGGT
BARCODE 799F_1157 TGCTCAAG
BARCODE 799F_1158 TGCTCATC
BARCODE 799F_1159 TGCTCTAC
BARCODE 799F_1160 TGCTCTTG
BARCODE 799F_1161 TGCTGAAC
BARCODE 799F_1162 TGCTGATG
BARCODE 799F_1163 TGCTGTAG
BARCODE 799F_1164 TGCTGTTC
BARCODE 799F_1165 TGCTTCCA
BARCODE 799F_1166 TGCTTCGT
BARCODE 799F_1167 TGCTTGCT
BARCODE 799F_1168 TGCTTGGA
BARCODE 799F_1169 TGGAACCT
BARCODE 799F_1170 TGGAACGA
BARCODE 799F_1171 TGGAAGCA
BARCODE 799F_1172 TGGAAGGT
BARCODE 799F_1173 TGGACAAG
BARCODE 799F_1174 TGGACATC
BARCODE 799F_1175 TGGACTAC
BARCODE 799F_1176 TGGAGAAC
BARCODE 799F_1177 TGGAGATG
BARCODE 799F_1178 CAACGATC
BARCODE 799F_1179 CAACGTAC
BARCODE 799F_1180 CAACGTTG
BARCODE 799F_1181 CAACTCCT
BARCODE 799F_1182 TAATCCGG
BARCODE 799F_1183 TACCGGAT
BARCODE 799F_1184 TACGCGAT
BARCODE 799F_1185 TAGCCGAT
BARCODE 799F_1186 TAGGATCC
BARCODE 799F_1187 TATACGGC
BARCODE 799F_1188 TCACCACT
BARCODE 799F_1189 TCAGACAC
BARCODE 799F_1190 TAATCGCG
BARCODE 799F_1191 TACCGGTA
BARCODE 799F_1192 TACGCGTA
BARCODE 799F_1193 TAGCCGTA
BARCODE 799F_1194 TAGGATGG
BARCODE 799F_1195 TATAGCCG
BARCODE 799F_1196 TCACCAGA
BARCODE 799F_1197 TCAGACTG
BARCODE 799F_1198 TAATCGGC
BARCODE 799F_1199 TACCTACC
BARCODE 799F_1200 TACGGCAT
BARCODE 799F_1201 TAGCGCAT
BARCODE 799F_1202 TAGGCCAT
BARCODE 799F_1203 TATAGCGC
BARCODE 799F_1204 TCACCTCA
BARCODE 799F_1205 TCAGAGAG
BARCODE 799F_1206 TAATGCCG
BARCODE 799F_1207 TACCTAGG
BARCODE 799F_1208 TACGGCTA
BARCODE 799F_1209 TAGCGCTA
BARCODE 799F_1210 TAGGCCTA
BARCODE 799F_1211 TATAGGCC
BARCODE 799F_1212 TCACCTGT
BARCODE 799F_1213 TCAGAGTC
BARCODE 799F_1214 TAATGCGC
BARCODE 799F_1215 TACCTTCG
BARCODE 799F_1216 TACGTACG
BARCODE 799F_1217 TAGCGGAA
BARCODE 799F_1218 TAGGCGAA
BARCODE 799F_1219 TATTCCGC
BARCODE 799F_1220 TCACGACA
BARCODE 799F_1221 TCAGCACA
BARCODE 799F_1222 TAATGGCC
BARCODE 799F_1223 TACCTTGC
BARCODE 799F_1224 TACGTAGC
BARCODE 799F_1225 TAGCGGTT
BARCODE 799F_1226 TAGGCGTT
BARCODE 799F_1227 TATTCGCC
BARCODE 799F_1228 TCACGAGT
BARCODE 799F_1229 TCAGCAGT
BARCODE 799F_1230 TACCAACG
BARCODE 799F_1231 TACGAACC
BARCODE 799F_1232 TACGTTCC
BARCODE 799F_1233 TAGCTACG
BARCODE 799F_1234 TAGGTACC
BARCODE 799F_1235 TATTGCGG
BARCODE 799F_1236 TCACGTCT
BARCODE 799F_1237 TCAGCTCT
BARCODE 799F_1238 TACCAAGC
BARCODE 799F_1239 TACGAAGG
BARCODE 799F_1240 TACGTTGG
BARCODE 799F_1241 TAGCTAGC
BARCODE 799F_1242 TAGGTAGG
BARCODE 799F_1243 TATTGGCG
BARCODE 799F_1244 TCACGTGA
BARCODE 799F_1245 TCAGCTGA
BARCODE 799F_1246 TACCATCC
BARCODE 799F_1247 TACGATCG
BARCODE 799F_1248 TAGCAACC
BARCODE 799F_1249 TAGCTTCC
BARCODE 799F_1250 TAGGTTCG
BARCODE 799F_1251 TCACACAG
BARCODE 799F_1252 TCACTCAC
BARCODE 799F_1253 TCAGGACT
BARCODE 799F_1254 TACCATGG
BARCODE 799F_1255 TACGATGC
BARCODE 799F_1256 TAGCAAGG
BARCODE 799F_1257 TAGCTTGG
BARCODE 799F_1258 TAGGTTGC
BARCODE 799F_1259 TCACACTC
BARCODE 799F_1260 TCACTCTG
BARCODE 799F_1261 TCAGGAGA
BARCODE 799F_1262 TACCGCAA
BARCODE 799F_1263 TACGCCAA
BARCODE 799F_1264 TAGCATCG
BARCODE 799F_1265 TAGGAACG
BARCODE 799F_1266 TATACCGG
BARCODE 799F_1267 TCACAGAC
BARCODE 799F_1268 TCACTGAG
BARCODE 799F_1269 TCAGGTCA
BARCODE 799F_1270 TACCGCTT
BARCODE 799F_1271 TACGCCTT
BARCODE 799F_1272 TAGCATGC
BARCODE 799F_1273 TAGGAAGC
BARCODE 799F_1274 TATACGCG
BARCODE 799F_1275 TCACAGTG
BARCODE 799F_1276 TCACTGTC
BARCODE 799F_1277 TCAGGTGT
BARCODE 799F_1278 TCAGTCAG
BARCODE 799F_1279 TCCAGAAC
BARCODE 799F_1280 TCCTCAAC
BARCODE 799F_1281 TCGAACCA
BARCODE 799F_1282 TCGATCCT
BARCODE 799F_1283 TCGTGAAC
BARCODE 799F_1284 TCTCCACA
BARCODE 799F_1285 TCTGACAG
BARCODE 799F_1286 TCAGTCTC
BARCODE 799F_1287 TCCAGATG
BARCODE 799F_1288 TCCTCATG
BARCODE 799F_1289 TCGAACGT
BARCODE 799F_1290 TCGATCGA
BARCODE 799F_1291 TCGTGATG
BARCODE 799F_1292 TCTCCAGT
BARCODE 799F_1293 TCTGACTC
BARCODE 799F_1294 TCAGTGAC
BARCODE 799F_1295 TCCAGTAG
BARCODE 799F_1296 TCCTCTAG
BARCODE 799F_1297 TCGAAGCT
BARCODE 799F_1298 TCGATGCA
BARCODE 799F_1299 TCGTGTAG
BARCODE 799F_1300 TCTCCTCT
BARCODE 799F_1301 TCTGAGAC
BARCODE 799F_1302 TCAGTGTG
BARCODE 799F_1303 TCCAGTTC
BARCODE 799F_1304 TCCTCTTC
BARCODE 799F_1305 TCGAAGGA
BARCODE 799F_1306 TCGATGGT
BARCODE 799F_1307 TCGTGTTC
BARCODE 799F_1308 TCTCCTGA
BARCODE 799F_1309 TCTGAGTG
BARCODE 799F_1310 TCCAACCT
BARCODE 799F_1311 TCCATCCA
BARCODE 799F_1312 TCCTGAAG
BARCODE 799F_1313 TCGACAAC
BARCODE 799F_1314 TCGTACCT
BARCODE 799F_1315 TCGTTCCA
BARCODE 799F_1316 TCTCGACT
BARCODE 799F_1317 TCTGCACT
BARCODE 799F_1318 TCCAACGA
BARCODE 799F_1319 TCCATCGT
BARCODE 799F_1320 TCCTGATC
BARCODE 799F_1321 TCGACATG
BARCODE 799F_1322 TCGTACGA
BARCODE 799F_1323 TCGTTCGT
BARCODE 799F_1324 TCTCGAGA
BARCODE 799F_1325 TCTGCAGA
BARCODE 799F_1326 TCCAAGCA
BARCODE 799F_1327 TCCATGCT
BARCODE 799F_1328 TCCTGTAC
BARCODE 799F_1329 TCGACTAG
BARCODE 799F_1330 TCGTAGCA
BARCODE 799F_1331 TCTCGTCA
BARCODE 799F_1332 TCTGCTCA
BARCODE 799F_1333 TCCAAGGT
BARCODE 799F_1334 TCCATGGA
BARCODE 799F_1335 TCCTGTTG
BARCODE 799F_1336 TCGACTTC
BARCODE 799F_1337 TCGTAGGT
BARCODE 799F_1338 TCGTTGGA
BARCODE 799F_1339 TCTCGTGT
BARCODE 799F_1340 TCTGCTGT
BARCODE 799F_1341 TCCACAAG
BARCODE 799F_1342 TCCTACCA
BARCODE 799F_1343 TCCTTCCT
BARCODE 799F_1344 TCGAGAAG
BARCODE 799F_1345 TCGTCAAG
BARCODE 799F_1346 TCTCACAC
BARCODE 799F_1347 TCTCTCAG
BARCODE 799F_1348 TCTGGACA
BARCODE 799F_1349 TCCACATC
BARCODE 799F_1350 TCCTACGT
BARCODE 799F_1351 TCCTTCGA
BARCODE 799F_1352 TCGAGATC
BARCODE 799F_1353 TCGTCATC
BARCODE 799F_1354 TCTCACTG
BARCODE 799F_1355 TCTCTCTC
BARCODE 799F_1356 TCTGGAGT
BARCODE 799F_1357 TCCACTAC
BARCODE 799F_1358 TCCTAGCT
BARCODE 799F_1359 TCCTTGCA
BARCODE 799F_1360 TCGAGTAC
BARCODE 799F_1361 TCGTCTAC
BARCODE 799F_1362 TCTCAGAG
BARCODE 799F_1363 TCTCTGAC
BARCODE 799F_1364 TCTGGTCT
BARCODE 799F_1365 TCCACTTG
BARCODE 799F_1366 TCCTAGGA
BARCODE 799F_1367 TCCTTGGT
BARCODE 799F_1368 TCGAGTTG
BARCODE 799F_1369 TCGTCTTG
BARCODE 799F_1370 TCTCAGTC
BARCODE 799F_1371 TCTCTGTG
BARCODE 799F_1372 TCTGGTGA
BARCODE 799F_1373 TCTGTCAC
BARCODE 799F_1374 TGACGACT
BARCODE 799F_1375 TGAGCACT
BARCODE 799F_1376 TGCAACCA
BARCODE 799F_1377 TGCATCCT
BARCODE 799F_1378 TGCTGAAC
BARCODE 799F_1379 TGGACAAG
BARCODE 799F_1380 TGGTACCA
BARCODE 799F_1381 TCTGTCTG
BARCODE 799F_1382 TGACGAGA
BARCODE 799F_1383 TGAGCAGA
BARCODE 799F_1384 TGCAACGT
BARCODE 799F_1385 TGCATCGA
BARCODE 799F_1386 TGCTGATG
BARCODE 799F_1387 TGGACATC
BARCODE 799F_1388 TGGTACGT
BARCODE 799F_1389 TCTGTGAG
BARCODE 799F_1390 TGACGTCA
BARCODE 799F_1391 TGAGGACA
BARCODE 799F_1392 TGGATGCT

Windows version

mothur v.1.41.1

Last updated: 11/26/18

mothur >

merge.files(input=GR_run3_S1_L001_R1_001.trim.contigs.groups-Tube2_S1_L001_R1_001.trim.contigs.groups, output=merge.fasta)

Output File Names:

merge.fasta

mothur >

trim.seqs(fasta= merge.fasta, oligos=combined.oligos, checkorient=t)

Using 4 processors.

It took 1135 secs to trim 26660383 sequences.

Group count:

TCAGCACA 11445

Total of all groups is 11445

Output File Names:

merge.trim.fasta

merge.scrap.fasta

merge.groups

As you can see from above, there is some error and I am not able to get trimmed data properly for each sample.. Kindly help me in resolving the issue.

thank you
Gurdeep

#6

If you look at merge.scrap.fasta you should see some letters after the sequence names. Can you tell what most of those are? When you look at those sequences, can you see the sequences start with the barcode? I suspect you don’t have the right barcodes or the sequences aren’t starting with those you have listed.

#7

I am trying to look at the merge.scrap.fasta file but unable to open the file so far in the notepad/word because of large size 13.4 GB.
So seems like all data is getting in to scarp file.
need to look again.
thanks

#8

Is there a way that you can use the linux capabilities of windows to use the head command to see the first lines of the scrap file?

#9

Thanks for your suggestion. I do not have linux capability so I chose to re-run the entire analysis. Renaming of barcodes solved the issue. And right now I am at cluster split command on miseq sop. Processed two runs together and generated 4000000 reads from 390 samples using SOP. Thanks much for your advise. Without mothur life will be very difficult.

Gurdeep

closed #10

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