Hello,
I am a beginner of Mothur, without any experience for data analysis.
Some samples have the same barcode, and the oligos_all is:
primer ACTCCTACGGGAGGCAGCAG GGACTACHVGGGTWTCTAAT V3-4
barcode TAATCG ACTTGA F61
barcode ATCACG TACAGC F62
barcode GAGATA CTAGCT F63
barcode CGCGGT GAGTGG F91
barcode TCGGCA AGTCAA F92
barcode ATCGTA TCTACC F93
barcode AGTTCC TGAATG F94
barcode GTACTT CCAGCT F95
barcode CAGATC GTGAAA F96
barcode GGTTGT CGATGT F101
barcode CCACAA GCCAAT F102
barcode TCGAAG AGTGGA F103
barcode ACAGTG TTCAGA F121
barcode GTTGAA CATCGT F122
barcode CGTACG GCCGCG F123
barcode TCCCGA ATGTCA F152
barcode GTTTCG CTATAC F154
barcode CGGAAT GGTAGC F171
barcode TAACGA ATATGT F172
barcode AGAGTA TTAGGC F173
barcode TAATCG ACTTGA F105
barcode ATCACG TACAGC F106
barcode GAGATA CTAGCT F125
barcode CGCGGT GAGTGG F155
barcode TCGGCA AGTCAA F156
barcode ATCGTA TCTACC F174
barcodes of sample F61 and sample F105 (TAATCG ACTTGA), sample F62 and sample F106 (ATCACG TACAGC), sample F63 and sample F125 (GAGATA CTAGCT) et al. are the same.
I know that it is NOT correct to run one make.contigs(file=hm.files, oligos=oligos_all.txt). Therefore, I split the data into two groups, putting them into two places, making two oligos files as below, and running make.contigs two times.
one is:
make.contigs(file=hm1.files, oligos=oligos_file_hm1.txt)
primer ACTCCTACGGGAGGCAGCAG GGACTACHVGGGTWTCTAAT V3-4
barcode TAATCG ACTTGA F61
barcode ATCACG TACAGC F62
barcode GAGATA CTAGCT F63
barcode CGCGGT GAGTGG F91
barcode TCGGCA AGTCAA F92
barcode ATCGTA TCTACC F93
barcode AGTTCC TGAATG F94
barcode GTACTT CCAGCT F95
barcode CAGATC GTGAAA F96
barcode GGTTGT CGATGT F101
barcode CCACAA GCCAAT F102
barcode TCGAAG AGTGGA F103
barcode ACAGTG TTCAGA F121
barcode GTTGAA CATCGT F122
barcode CGTACG GCCGCG F123
barcode TCCCGA ATGTCA F152
barcode GTTTCG CTATAC F154
barcode CGGAAT GGTAGC F171
barcode TAACGA ATATGT F172
barcode AGAGTA TTAGGC F173
and another one is:
make.contigs(file=hm2.files, oligos=oligos_file_hm2.txt)
primer ACTCCTACGGGAGGCAGCAG GGACTACHVGGGTWTCTAAT V3-4
barcode TAATCG ACTTGA F105
barcode ATCACG TACAGC F106
barcode GAGATA CTAGCT F125
barcode CGCGGT GAGTGG F155
barcode TCGGCA AGTCAA F156
barcode ATCGTA TCTACC F174
The two runs had two results. Then I tried to merge.files() those files:
merge.files(input=hm1.trim.contigs.fasta-hm2.trim.contigs.fasta, output=hm.trim.contigs.fasta)
merge.files(input=hm1.scrap.contigs.fasta-hm2.scrap.contigs.fasta, output=hm.scrap.contigs.fasta)
merge.files(input=hm1.contigs_report-hm2.contigs_report, output=hm.contigs_report)
merge.files(input=hm1.contigs.count_table-hm2.contigs.count_table, output=hm.contigs.count_table)
However, the summary.seqs show a wrong information.
mothur > summary.seqs(fasta=hm.trim.contigs.fasta, count=hm.contigs.count_table)
[ERROR]: Your count table contains a sequence named #Compressed with a total=0. Please correct.
[ERROR]: Your count table contains a sequence named #Compressed with a total=0. Please correct.
[ERROR]: Your count table contains more than 1 sequence named #Compressed, sequence names must be unique. Please correct.
[ERROR]: Your count table contains a sequence named #Compressed with a total=0. Please correct.
[ERROR]: Your count table contains more than 1 sequence named #Compressed, sequence names must be unique. Please correct.
[ERROR]: Your count table contains a sequence named #Compressed with a total=0. Please correct.
[ERROR]: Your count table contains more than 1 sequence named #Compressed, sequence names must be unique. Please correct.
[ERROR]: Your count table contains a sequence named #Compressed with a total=0. Please correct.
[ERROR]: Your count table contains more than 1 sequence named #Compressed, sequence names must be unique. Please correct.
[ERROR]: Your count table contains a sequence named #Compressed with a total=0. Please correct.
**** Exceeded maximum allowed command errors, quitting ****
[ERROR]: Your count table contains more than 1 sequence named #Compressed, sequence names must be unique. Please correct.
Can anybody explain it and direct me to resolve the problem? Many thanks!
Zhenghua
