mothur > sffinfo(sff=454Reads_archaea.sff, flow=T)
Extracting info from 454Reads_archaea.sff …
10000
20000
30000
40000
50000
60000
70000
80000
90000
92115
It took 68 secs to extract 92115.
Output File Names:
454Reads_archaea.fasta
454Reads_archaea.qual
454Reads_archaea.flow
mothur > trim.flows(flow=454Reads_archaea.flow, oligos=oligos_LXY.txt, pdiffs=2, bdiffs=1, processors=2)
Appending files from process 15674
Output File Names:
454Reads_archaea.trim.flow
454Reads_archaea.scrap.flow
454Reads_archaea.GZ_ARC.flow
454Reads_archaea.GZ1122_ARC.flow
454Reads_archaea.GZ1122cellulose_ARC.flow
454Reads_archaea.GZ_xylan_ARC.flow
454Reads_archaea.GZ_cellulose55_ARC.flow
454Reads_archaea.SHX_xylan_ARC.flow
454Reads_archaea.GZ_xylose_ARC.flow
454Reads_archaea.Eric_ARC.flow
454Reads_archaea.Milk_D_ARC.flow
454Reads_archaea.Milk_E_ARC.flow
454Reads_archaea.ST1219_ARC.flow
454Reads_archaea.YL_ARC.flow
454Reads_archaea.SHX_xylose_ARC.flow
454Reads_archaea.SHX_cellulose55_ARC.flow
454Reads_archaea.TP_1201_ARC.flow
454Reads_archaea.ST_ARC.flow
454Reads_archaea.YL0203cellulose_ARC.flow
454Reads_archaea.TP_xylan_ARC.flow
454Reads_archaea.ST0303cellulose_ARC.flow
454Reads_archaea.SHX_ARC.flow
454Reads_archaea.ST_xylan_ARC.flow
454Reads_archaea.YL_xylan_ARC.flow
454Reads_archaea.SHX1219_ARC.flow
454Reads_archaea.SHX1125cellulose_ARC.flow
454Reads_archaea.flow.files
mothur > shhh.flows(file=454Reads_archaea.flow.files, processors=4)
mothur > trim.seqs(fasta=454Reads_archaea.shhh.fasta, name=454Reads_archaea.shhh.names, oligos=oligos_LXY.txt, pdiffs=2, bdiffs=1, maxhomop=8, minlength=150, flip=T, processors=2)
Total of all groups is 44091
Output File Names:
454Reads_archaea.shhh.trim.fasta
454Reads_archaea.shhh.scrap.fasta
454Reads_archaea.shhh.trim.names
454Reads_archaea.shhh.scrap.names
454Reads_archaea.shhh.groups
mothur > summary.seqs(fasta=454Reads_archaea.shhh.trim.fasta, name=454Reads_archaea.shhh.trim.names)
Using 2 processors.
Start End NBases Ambigs Polymer NumSeqs
Minimum: 1 218 218 0 3 1
2.5%-tile: 1 251 251 0 3 1103
25%-tile: 1 268 268 0 4 11023
Median: 1 274 274 0 4 22046
75%-tile: 1 281 281 0 4 33069
97.5%-tile: 1 297 297 0 5 42989
Maximum: 1 333 333 0 8 44091
Mean: 1 273.837 273.837 0 4.15944
# of unique seqs: 12780
total # of seqs: 44091
Output File Name:
454Reads_archaea.shhh.trim.summary
mothur > unique.seqs(fasta=454Reads_archaea.shhh.trim.fasta, name=454Reads_archaea.shhh.trim.names)
1000 959
2000 1691
3000 2431
4000 3358
5000 4352
6000 5335
7000 6328
8000 7261
9000 8187
10000 9082
11000 9963
12000 10859
12780 11449
Output File Names:
454Reads_archaea.shhh.trim.unique.fasta
454Reads_archaea.shhh.trim.unique.names
mothur > summary.seqs(fasta=454Reads_archaea.shhh.trim.unique.fasta, name=454Reads_archaea.shhh.trim.unique.names)
Using 2 processors.
Start End NBases Ambigs Polymer NumSeqs
Minimum: 1 218 218 0 3 1
2.5%-tile: 1 251 251 0 3 1103
25%-tile: 1 268 268 0 4 11023
Median: 1 274 274 0 4 22046
75%-tile: 1 281 281 0 4 33069
97.5%-tile: 1 297 297 0 5 42989
Maximum: 1 333 333 0 8 44091
Mean: 1 273.837 273.837 0 4.15944
# of unique seqs: 11449
total # of seqs: 44091
Output File Name:
454Reads_archaea.shhh.trim.unique.summary
Submit to RDP database, check and filter bacteria sequences!
http://rdp.cme.msu.edu/classifier/cl_status.jsp
domain Bacteria (1435 sequences)
shenzy@shenzy-ubuntu:/winxp_disk2/shenzy/xiaoying_work_archaea/16s_archaea_allsamples/shhh_pipe2$ wc allrank_454Reads_archaea.shhh.trim.unique.fasta_classified.txt
1435 1520 200784 allrank_454Reads_archaea.shhh.trim.unique.fasta_classified.txt
./filter_bacterseqs_for_align.py -i allrank_454Reads_archaea.shhh.trim.unique.fasta_classified.txt -f 454Reads_archaea.shhh.trim.unique.fasta -n 454Reads_archaea.shhh.trim.unique.names -g 454Reads_archaea.shhh.groups
shenzy@shenzy-ubuntu:/winxp_disk2/shenzy/xiaoying_work_archaea/16s_archaea_allsamples/shhh_pipe2$ wc 454Reads_archaea.shhh.groups.filter
42187 84374 1224728 454Reads_archaea.shhh.groups.filter
shenzy@shenzy-ubuntu:/winxp_disk2/shenzy/xiaoying_work_archaea/16s_archaea_allsamples/shhh_pipe2$ wc 454Reads_archaea.shhh.groups
44091 88182 1270431 454Reads_archaea.shhh.groups
mothur > summary.seqs(fasta=454Reads_archaea.shhh.trim.unique.fasta.filter, name=454Reads_archaea.shhh.trim.unique.names.filter)
Using 2 processors.
Start End NBases Ambigs Polymer NumSeqs
Minimum: 1 218 218 0 3 1
2.5%-tile: 1 256 256 0 3 1055
25%-tile: 1 268 268 0 4 10547
Median: 1 274 274 0 4 21094
75%-tile: 1 282 282 0 4 31641
97.5%-tile: 1 297 297 0 5 41133
Maximum: 1 333 333 0 8 42187
Mean: 1 274.543 274.543 0 4.15355
# of unique seqs: 10014
total # of seqs: 42187
mothur > screen.seqs(fasta=454Reads_archaea.shhh.trim.unique.fasta.align, name=454Reads_archaea.shhh.trim.unique.names.filter, group=454Reads_archaea.shhh.groups.filter, processors=2)
Output File Name:
454Reads_archaea.shhh.trim.unique.fasta.summary
###mothur > align.seqs(candidate=454Reads_archaea.shhh.trim.unique.fasta.filter, template=core_set_aligned.imputed.fasta, flip=T, ksize=9, align=needleman, gapopen=-1, processors=3)
###
mothur > align.seqs(fasta=454Reads_archaea.shhh.trim.unique.fasta.filter, reference=core_set_aligned.fasta.imputed, flip=T, processors=3)
Using 3 processors.
Reading in the core_set_aligned.fasta.imputed template sequences… DONE.
It took 1 to read 4938 sequences.
Aligning sequences from 454Reads_archaea.shhh.trim.unique.fasta.filter …
100
…
3338
Some of you sequences generated alignments that eliminated too many bases, a list is provided in 454Reads_archaea.shhh.trim.unique.fasta.flip.accnos. If the reverse compliment proved to be better it was reported.
It took 60 secs to align 10014 sequences.
Output File Names:
454Reads_archaea.shhh.trim.unique.fasta.align
454Reads_archaea.shhh.trim.unique.fasta.align.report
454Reads_archaea.shhh.trim.unique.fasta.flip.accnos
mothur > summary.seqs(fasta=454Reads_archaea.shhh.trim.unique.fasta.align, name=454Reads_archaea.shhh.trim.unique.names.filter)
Using 3 processors.
Start End NBases Ambigs Polymer NumSeqs
Minimum: 86 98 2 0 1 1
2.5%-tile: 132 1746 51 0 3 1055
25%-tile: 136 1822 268 0 4 10547
Median: 136 1834 274 0 4 21094
75%-tile: 136 1850 282 0 4 31641
97.5%-tile: 194 1887 297 0 5 41133
Maximum: 6858 6885 313 0 8 42187
Mean: 284.168 1920.46 266.145 0 4.10781
# of unique seqs: 10014
total # of seqs: 42187
Output File Name:
454Reads_archaea.shhh.trim.unique.fasta.summary
##mothur > screen.seqs(fasta=454Reads_archaea.shhh.trim.unique.fasta.align, name=454Reads_archaea.shhh.trim.unique.names.filter, group=454Reads_archaea.shhh.groups.filter, ##start=136, optimize=end, criteria=90, processors=2)
#The optimize and criteria parameters allow you set the start, end, maxabig, maxhomop, minlength and maxlength parameters relative to your set of sequences .
#For example optimize=start-end, criteria=90, would set the start and end values to the position 90% of your sequences started and ended.
mothur > screen.seqs(fasta=454Reads_archaea.shhh.trim.unique.fasta.align, name=454Reads_archaea.shhh.trim.unique.names.filter, group=454Reads_archaea.shhh.groups.filter, optimize=start-end, criteria=90, processors=4)
…
Output File Names:
454Reads_archaea.shhh.trim.unique.fasta.good.align
454Reads_archaea.shhh.trim.unique.fasta.bad.accnos
454Reads_archaea.shhh.trim.unique.names.good.filter
454Reads_archaea.shhh.groups.good.filter
It took 4 secs to screen 10014 sequences.
mothur > summary.seqs(fasta=454Reads_archaea.shhh.trim.unique.fasta.good.align, name=454Reads_archaea.shhh.trim.unique.names.good.filter)
Using 4 processors.
Start End NBases Ambigs Polymer NumSeqs
Minimum: 107 1819 243 0 3 1
2.5%-tile: 133 1821 263 0 3 925
25%-tile: 136 1831 269 0 4 9242
Median: 136 1836 274 0 4 18484
75%-tile: 136 1853 283 0 4 27725
97.5%-tile: 136 1871 298 0 5 36042
Maximum: 136 1920 313 0 8 36966
Mean: 135.731 1840.24 276.401 0 4.14224
# of unique seqs: 7703
total # of seqs: 36966
Output File Name:
454Reads_archaea.shhh.trim.unique.fasta.good.summary
mothur > filter.seqs(fasta=454Reads_archaea.shhh.trim.unique.fasta.good.align, vertical=T, trump=., processors=2)
3700
3800
3851
Length of filtered alignment: 486
Number of columns removed: 7196
Length of the original alignment: 7682
Number of sequences used to construct filter: 7703
Output File Names:
454Reads_archaea.filter
454Reads_archaea.shhh.trim.unique.fasta.good.filter.fasta
mothur > unique.seqs(fasta=454Reads_archaea.shhh.trim.unique.fasta.good.filter.fasta, name=454Reads_archaea.shhh.trim.unique.names.good.filter)
1000 974
2000 1887
3000 2768
4000 3604
5000 4424
6000 5238
7000 6017
7703 6573
Output File Names:
454Reads_archaea.shhh.trim.unique.fasta.good.filter.unique.fasta
454Reads_archaea.shhh.trim.unique.fasta.good.filter.names
mothur > shhh.seqs(fasta=454Reads_archaea.shhh.trim.unique.fasta.good.filter.unique.fasta, name=454Reads_archaea.shhh.trim.unique.fasta.good.filter.names, group=454Reads_archaea.shhh.groups.good.filter, processors=3)
Output File Names:
454Reads_archaea.shhh.trim.unique.fasta.good.filter.unique.shhh_seqs.unique.fasta
454Reads_archaea.shhh.trim.unique.fasta.good.filter.unique.shhh_seqs.unique.names
/******************************************/
Output File Names:
454Reads_archaea.shhh.trim.unique.fasta.good.filter.unique.shhh.Eric_ARC.map
454Reads_archaea.shhh.trim.unique.fasta.good.filter.unique.shhh.GZ1122_ARC.map
454Reads_archaea.shhh.trim.unique.fasta.good.filter.unique.shhh.GZ1122cellulose_ARC.map
…….
mothur > summary.seqs(fasta=454Reads_archaea.shhh.trim.unique.fasta.good.filter.unique.shhh_seqs.fasta, name=454Reads_archaea.shhh.trim.unique.fasta.good.filter.unique.shhh_seqs.names)
Using 2 processors.
Start End NBases Ambigs Polymer NumSeqs
Minimum: 1 484 219 0 3 1
2.5%-tile: 1 486 260 0 3 925
25%-tile: 1 486 261 0 4 9242
Median: 1 486 261 0 4 18484
75%-tile: 1 486 266 0 4 27725
97.5%-tile: 1 486 266 0 5 36042
Maximum: 3 486 282 0 7 36966
Mean: 1.00103 486 262.434 0 4.1387
# of unique seqs: 2911
total # of seqs: 36966
Output File Name:
454Reads_archaea.shhh.trim.unique.fasta.good.filter.unique.shhh_seqs.summary
mothur > chimera.uchime(fasta=454Reads_archaea.shhh.trim.unique.fasta.good.filter.unique.shhh_seqs.fasta, name=454Reads_archaea.shhh.trim.unique.fasta.good.filter.unique.shhh_seqs.names, group=454Reads_archaea.shhh.groups.good.filter, processors=3)
It took 0 secs to check 46 sequences from group YL_xylan_ARC.
It took 43 secs to check 3276 sequences. 362 chimeras were found.
The number of sequences checked may be larger than the number of unique sequences because some sequences are found in several samples.
Output File Names:
454Reads_archaea.shhh.trim.unique.fasta.good.filter.unique.shhh_seqs.uchime.chimeras
454Reads_archaea.shhh.trim.unique.fasta.good.filter.unique.shhh_seqs.uchime.accnos
##############################3
shenzy@shenzy-ubuntu:/winxp_disk2/shenzy/xiaoying_work_archaea/16s_archaea_allsamples/shhh_pipe2$ mv 454Reads_archaea.shhh.trim.unique.fasta.good.filter.unique.shhh_seqs.uchime.accnos 454Reads_archaea.shhh.trim.unique.fasta.good.filter.unique.shhh_seqs.uchime.accnos.self
shenzy@shenzy-ubuntu:/winxp_disk2/shenzy/xiaoying_work_archaea/16s_archaea_allsamples/shhh_pipe2$ mv 454Reads_archaea.shhh.trim.unique.fasta.good.filter.unique.shhh_seqs.uchime.chimeras 454Reads_archaea.shhh.trim.unique.fasta.good.filter.unique.shhh_seqs.uchime.chimeras.self
################################
mothur >chimera.uchime(fasta=454Reads_archaea.shhh.trim.unique.fasta.good.filter.unique.shhh_seqs.fasta, reference=core_set_aligned.fasta.imputed, processors=3)
05:04 26Mb 100.0% 30/969 chimeras found (3.1%)
05:11 26Mb 100.0% 88/970 chimeras found (9.1%)
It took 311 secs to check 2911 sequences. 213 chimeras were found.
Output File Names:
454Reads_archaea.shhh.trim.unique.fasta.good.filter.unique.shhh_seqs.uchime.chimeras
454Reads_archaea.shhh.trim.unique.fasta.good.filter.unique.shhh_seqs.uchime.accnos
###################################
shenzy@shenzy-ubuntu:/winxp_disk2/shenzy/xiaoying_work_archaea/16s_archaea_allsamples/shhh_pipe2$ wc 454Reads_archaea.shhh.trim.unique.fasta.good.filter.unique.shhh_seqs.uchime.accnos
213 213 3195 454Reads_archaea.shhh.trim.unique.fasta.good.filter.unique.shhh_seqs.uchime.accnos
shenzy@shenzy-ubuntu:/winxp_disk2/shenzy/xiaoying_work_archaea/16s_archaea_allsamples/shhh_pipe2$ wc 454Reads_archaea.shhh.trim.unique.fasta.good.filter.unique.shhh_seqs.uchime.accnos.self
362 362 5430 454Reads_archaea.shhh.trim.unique.fasta.good.filter.unique.shhh_seqs.uchime.accnos.self
cat 454Reads_archaea.shhh.trim.unique.fasta.good.filter.unique.shhh_seqs.uchime.accnos 454Reads_archaea.shhh.trim.unique.fasta.good.filter.unique.shhh_seqs.uchime.accnos.self > 454Reads_archaea.shhh.trim.unique.fasta.good.filter.unique.shhh_seqs.uchime.accnos.sum
sort 454Reads_archaea.shhh.trim.unique.fasta.good.filter.unique.shhh_seqs.uchime.accnos.sum > 454Reads_archaea.shhh.trim.unique.fasta.good.filter.unique.shhh_seqs.uchime.accnos.sum.sort
merge 2 predict results of chimera and del repeat!
shenzy@shenzy-ubuntu:/winxp_disk2/shenzy/xiaoying_work_archaea/16s_archaea_allsamples/shhh_pipe2$ sed ‘$!N; /^\(.*\)\n\1$/!P; D’ 454Reads_archaea.shhh.trim.unique.fasta.good.filter.unique.shhh_seqs.uchime.accnos.sum.sort > 454Reads_archaea.shhh.trim.unique.fasta.good.filter.unique.shhh_seqs.uchime.accnos.sum.sort.uniq
shenzy@shenzy-ubuntu:/winxp_disk2/shenzy/xiaoying_work_archaea/16s_archaea_allsamples/shhh_pipe2$ wc 454Reads_archaea.shhh.trim.unique.fasta.good.filter.unique.shhh_seqs.uchime.accnos.sum.sort.uniq
382 382 5730 454Reads_archaea.shhh.trim.unique.fasta.good.filter.unique.shhh_seqs.uchime.accnos.sum.sort.uniq
####################################
get_fasta_from_seqname.py -i 454Reads_archaea.shhh.trim.unique.fasta.good.filter.unique.shhh_seqs.uchime.accnos.sum.sort.uniq -j 454Reads_archaea.fasta > 454Reads_archaea.shhh.trim.unique.fasta.good.filter.unique.shhh_seqs.uchime.accnos.sum.sort.uniq.fasta
chimera seqs RDP checking (http://rdp.cme.msu.edu/classifier/classifier.jsp)
Check the last genus id percent, if percent >=90%, (keep it and merge it to the non-chimera reads of each sample)
shenzy@shenzy-ubuntu:/winxp_disk2/shenzy/xiaoying_work_archaea/16s_archaea_allsamples/shhh_pipe2$ more allrank_454Reads_archaea.shhh.trim.unique.fasta.good.filter.unique.shhh_seqs.uchime.accnos.sum.sort.uniq.fasta_classified.txt
HQ93PQ301A0ZHW;;Root;100%;Archaea;100%;”Euryarchaeota”;100%;”Methanomicrobia”;100%;Methanomicrobiales;100%;Methanospirillaceae;100%;Methanospirillum;100%
HQ93PQ301A1JYN;;Root;100%;Archaea;100%;”Euryarchaeota”;100%;”Methanomicrobia”;100%;Methanosarcinales;100%;Methanosarcinaceae;100%;Methanosarcina;100%
shenzy@shenzy-ubuntu:/winxp_disk2/shenzy/xiaoying_work_archaea/16s_archaea_allsamples/shhh_pipe2$ check_real_chimera_seq.py -i allrank_454Reads_archaea.shhh.trim.unique.fasta.good.filter.unique.shhh_seqs.uchime.accnos.sum.sort.uniq.fasta_classified.txt -d 90 | wc
221 221 3315
The 221 sequences should be merged to non-chimera results!!
-rwxrwxrwx 1 root root 2.4K 2012-08-14 11:19 chimera.seqs.name
shenzy@shenzy-ubuntu:/winxp_disk2/shenzy/xiaoying_work_archaea/16s_archaea_allsamples/shhh_pipe2$ wc chimera.seqs.name
161 161 2415 chimera.seqs.name
######################################################################
Removing chimeras (the total predict chimera seqs by two approaches!)
######################################################################
mothur > remove.seqs(accnos=chimera.seqs.name, fasta=454Reads_archaea.shhh.trim.unique.fasta.good.filter.unique.shhh_seqs.fasta, name=454Reads_archaea.shhh.trim.unique.fasta.good.filter.unique.shhh_seqs.names, group=454Reads_archaea.shhh.groups.good.filter)
Removed 1197 sequences from your name file.
Removed 161 sequences from your fasta file.
Removed 1197 sequences from your group file.
Output File Names:
454Reads_archaea.shhh.trim.unique.fasta.good.filter.unique.shhh_seqs.pick.names
454Reads_archaea.shhh.trim.unique.fasta.good.filter.unique.shhh_seqs.pick.fasta
454Reads_archaea.shhh.groups.good.pick.filter
mothur > summary.seqs(name=current)
Using 454Reads_archaea.shhh.trim.unique.fasta.good.filter.unique.shhh_seqs.pick.names as input file for the name parameter.
Using 454Reads_archaea.shhh.trim.unique.fasta.good.filter.unique.shhh_seqs.pick.fasta as input file for the fasta parameter.
Using 3 processors.
Start End NBases Ambigs Polymer NumSeqs
Minimum: 1 484 219 0 3 1
2.5%-tile: 1 486 260 0 3 895
25%-tile: 1 486 261 0 4 8943
Median: 1 486 261 0 4 17885
75%-tile: 1 486 266 0 4 26827
97.5%-tile: 1 486 266 0 5 34875
Maximum: 3 486 278 0 7 35769
Mean: 1.00106 486 262.504 0 4.16914
# of unique seqs: 2750
total # of seqs: 35769
Output File Name:
454Reads_archaea.shhh.trim.unique.fasta.good.filter.unique.shhh_seqs.pick.summary
#############################
chimera number
##############################
./compute_chimera_for_singlesample.py -i 454Reads_Bacteria.Eric_BAC.shhh.groups -j chimera.seqs.name
GZ1122_ARC: 10
GZ1122cellulose_ARC: 3
GZ_ARC: 1
GZ_cellulose55_ARC: 1
GZ_xylan_ARC: 7
GZ_xylose_ARC: 4
SHX1125cellulose_ARC: 0
SHX1219_ARC: 0
SHX_ARC: 5
SHX_cellulose55_ARC: 8
SHX_xylan_ARC: 3
SHX_xylose_ARC: 35
ST0303cellulose_ARC: 15
ST1219_ARC: 5
ST_ARC: 21
ST_xylan_ARC: 11
TP_1201_ARC: 0
TP_xylan_ARC: 19
YL0203cellulose_ARC: 7
YL_ARC: 2
YL_xylan_ARC: 3
#######################
Removing “contaminants”
#######################
wget http://www.mothur.org/w/images/5/59/Trainset9_032012.pds.zip
shenzy@shenzy-ubuntu:/winxp_disk2/shenzy/xiaoying_work_archaea/16s_archaea_allsamples/shhh_pipe2$ unzip Trainset9_032012.pds.zip
Archive: Trainset9_032012.pds.zip
inflating: trainset9_032012.pds.tax
inflating: trainset9_032012.pds.fasta
mothur > classify.seqs(fasta=454Reads_archaea.shhh.trim.unique.fasta.good.filter.unique.shhh_seqs.pick.fasta, name=454Reads_archaea.shhh.trim.unique.fasta.good.filter.unique.shhh_seqs.pick.names, group=454Reads_archaea.shhh.groups.good.pick.filter, template=trainset9_032012.pds.fasta, taxonomy=trainset9_032012.pds.tax, cutoff=80, processors=2)
….
Processing sequence: 1300
Processing sequence: 1300
[WARNING]: HQ93PQ301C4CTV could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.
[WARNING]: HQ93PQ301CK6YP could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.
[WARNING]: HQ93PQ301DJMTI could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.
[WARNING]: HQ93PQ301ERRC6 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.
Processing sequence: 1372
Processing sequence: 1371
It took 25 secs to classify 2750 sequences.
Reading 454Reads_archaea.shhh.trim.unique.fasta.good.filter.unique.shhh_seqs.pick.names… Done.
It took 3 secs to create the summary file for 2750 sequences.
Output File Names:
454Reads_archaea.shhh.trim.unique.fasta.good.filter.unique.shhh_seqs.pick.pds.taxonomy
454Reads_archaea.shhh.trim.unique.fasta.good.filter.unique.shhh_seqs.pick.pds.flip.accnos
454Reads_archaea.shhh.trim.unique.fasta.good.filter.unique.shhh_seqs.pick.pds.tax.summary
mothur > remove.lineage(fasta=454Reads_archaea.shhh.trim.unique.fasta.good.filter.unique.shhh_seqs.pick.fasta, name=454Reads_archaea.shhh.trim.unique.fasta.good.filter.unique.shhh_seqs.pick.names, group=454Reads_archaea.shhh.groups.good.pick.filter, taxonomy=454Reads_archaea.shhh.trim.unique.fasta.good.filter.unique.shhh_seqs.pick.pds.taxonomy, taxon=Mitochondria-Cyanobacteria_Chloroplast-Eukarya-Bacteria-unknown)
Output File Names:
454Reads_archaea.shhh.trim.unique.fasta.good.filter.unique.shhh_seqs.pick.pds.pick.taxonomy
454Reads_archaea.shhh.trim.unique.fasta.good.filter.unique.shhh_seqs.pick.pick.names
454Reads_archaea.shhh.trim.unique.fasta.good.filter.unique.shhh_seqs.pick.pick.fasta
454Reads_archaea.shhh.groups.good.pick.pick.filter
mothur > summary.seqs(name=current)
Using 454Reads_archaea.shhh.trim.unique.fasta.good.filter.unique.shhh_seqs.pick.pick.names as input file for the name parameter.
Using 454Reads_archaea.shhh.trim.unique.fasta.good.filter.unique.shhh_seqs.pick.pick.fasta as input file for the fasta parameter.
Using 2 processors.
Start End NBases Ambigs Polymer NumSeqs
Minimum: 1 484 219 0 3 1
2.5%-tile: 1 486 260 0 3 852
25%-tile: 1 486 261 0 4 8519
Median: 1 486 261 0 4 17037
75%-tile: 1 486 266 0 4 25555
97.5%-tile: 1 486 266 0 5 33221
Maximum: 1 486 278 0 7 34072
Mean: 1 486 262.598 0 4.21437
# of unique seqs: 2644
total # of seqs: 34072
Output File Name:
454Reads_archaea.shhh.trim.unique.fasta.good.filter.unique.shhh_seqs.pick.pick.summary
############################################################################################
mothur > system(cp 454Reads_archaea.shhh.trim.unique.fasta.good.filter.unique.shhh_seqs.pick.pds.pick.taxonomy archaea_16s_final.taxonomy)
mothur > system(cp 454Reads_archaea.shhh.trim.unique.fasta.good.filter.unique.shhh_seqs.pick.pick.names archaea_16s_final.names)
mothur > system(cp 454Reads_archaea.shhh.trim.unique.fasta.good.filter.unique.shhh_seqs.pick.pick.fasta archaea_16s_final.fasta)
mothur > system(cp 454Reads_archaea.shhh.groups.good.pick.pick.filter archaea_16s_final.groups)
mothur > dist.seqs(fasta=archaea_16s_final.fasta, cutoff=0.1, processors=3)
Output File Name:
archaea_16s_final.dist
It took 25 to calculate the distances for 2644 sequences.
mothur > cluster(column=archaea_16s_final.dist, name=archaea_16s_final.names)
changed cutoff to 0.0392497
Output File Names:
archaea_16s_final.an.sabund
archaea_16s_final.an.rabund
archaea_16s_final.an.list
It took 9 seconds to cluster
mothur > make.shared(list=archaea_16s_final.an.list, group=archaea_16s_final.groups)
unique
0.01
0.02
0.03
Output File Names:
archaea_16s_final.an.shared
archaea_16s_final.an.Eric_ARC.rabund
archaea_16s_final.an.GZ1122_ARC.rabund
archaea_16s_final.an.GZ1122cellulose_ARC.rabund
archaea_16s_final.an.GZ_ARC.rabund
archaea_16s_final.an.GZ_cellulose55_ARC.rabund
archaea_16s_final.an.GZ_xylan_ARC.rabund
archaea_16s_final.an.GZ_xylose_ARC.rabund
archaea_16s_final.an.Milk_D_ARC.rabund
archaea_16s_final.an.Milk_E_ARC.rabund
archaea_16s_final.an.SHX1125cellulose_ARC.rabund
archaea_16s_final.an.SHX1219_ARC.rabund
archaea_16s_final.an.SHX_ARC.rabund
archaea_16s_final.an.SHX_cellulose55_ARC.rabund
archaea_16s_final.an.SHX_xylan_ARC.rabund
archaea_16s_final.an.SHX_xylose_ARC.rabund
archaea_16s_final.an.ST0303cellulose_ARC.rabund
archaea_16s_final.an.ST1219_ARC.rabund
archaea_16s_final.an.ST_ARC.rabund
archaea_16s_final.an.ST_xylan_ARC.rabund
archaea_16s_final.an.TP_1201_ARC.rabund
archaea_16s_final.an.TP_xylan_ARC.rabund
archaea_16s_final.an.YL0203cellulose_ARC.rabund
archaea_16s_final.an.YL_ARC.rabund
archaea_16s_final.an.YL_xylan_ARC.rabund
mothur > count.groups()
Using archaea_16s_final.an.shared as input file for the shared parameter.
Eric_ARC contains 14.
GZ1122_ARC contains 1780.
GZ1122cellulose_ARC contains 1063.
GZ_ARC contains 53.
GZ_cellulose55_ARC contains 1997.
GZ_xylan_ARC contains 1509.
GZ_xylose_ARC contains 1241.
Milk_D_ARC contains 19.
Milk_E_ARC contains 434.
SHX1125cellulose_ARC contains 2568.
SHX1219_ARC contains 2012.
SHX_ARC contains 1594.
SHX_cellulose55_ARC contains 2235.
SHX_xylan_ARC contains 944.
SHX_xylose_ARC contains 1932.
ST0303cellulose_ARC contains 1815.
ST1219_ARC contains 1597.
ST_ARC contains 774.
ST_xylan_ARC contains 1755.
TP_1201_ARC contains 1952.
TP_xylan_ARC contains 1849.
YL0203cellulose_ARC contains 1762.
YL_ARC contains 1154.
YL_xylan_ARC contains 2019.
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^old^^^^^^^^^^^^^
Using archaea_16s_final.an.shared as input file for the shared parameter.
Eric_ARC contains 15.***********
GZ1122_ARC contains 1815.
GZ1122cellulose_ARC contains 1081.
GZ_ARC contains 54.
GZ_cellulose55_ARC contains 1997.
GZ_xylan_ARC contains 1547.
GZ_xylose_ARC contains 1245.
Milk_D_ARC contains 18. *********
Milk_E_ARC contains 434. ********
SHX1125cellulose_ARC contains 2570.
SHX1219_ARC contains 2012.
SHX_ARC contains 1593.
SHX_cellulose55_ARC contains 2236.
SHX_xylan_ARC contains 947.
SHX_xylose_ARC contains 1932.
ST0303cellulose_ARC contains 1810.
ST1219_ARC contains 1597.
ST_ARC contains 759.
ST_xylan_ARC contains 1755.
TP_1201_ARC contains 1952.
TP_xylan_ARC contains 1849.
YL0203cellulose_ARC contains 1762.
YL_ARC contains 1164.
YL_xylan_ARC contains 2019.
mothur > count.groups()
Using archaea_16s_final.an.shared as input file for the shared parameter.
Eric_ARC contains 569.
GZ1122_ARC contains 2103.
GZ1122cellulose_ARC contains 1594.
GZ_ARC contains 530.
GZ_cellulose55_ARC contains 2001.
GZ_xylan_ARC contains 1889.
GZ_xylose_ARC contains 2015.
Milk_D_ARC contains 598.
Milk_E_ARC contains 1753.
SHX1125cellulose_ARC contains 2831.
SHX1219_ARC contains 2247.
SHX_ARC contains 1660.
SHX_cellulose55_ARC contains 2249.
SHX_xylan_ARC contains 1213.
SHX_xylose_ARC contains 1991.
ST0303cellulose_ARC contains 1845.
ST1219_ARC contains 1621.
ST_ARC contains 1859.
ST_xylan_ARC contains 1769.
TP_1201_ARC contains 1969.
TP_xylan_ARC contains 1890.
YL0203cellulose_ARC contains 1785.
YL_ARC contains 1285.
YL_xylan_ARC contains 2025.
mothur > sub.sample(shared=archaea_16s_final.an.shared, size=759)
Eric_ARC contains 15. Eliminating.
GZ_ARC contains 54. Eliminating.
Milk_D_ARC contains 18. Eliminating.
Milk_E_ARC contains 434. Eliminating.
Sampling 759 from each group.
unique
0.01
0.02
0.03
Output File Names:
archaea_16s_final.an.uniquesubsample.shared
archaea_16s_final.an.0.01subsample.shared
archaea_16s_final.an.0.02subsample.shared
archaea_16s_final.an.0.03subsample.shared
mothur > classify.otu(list=archaea_16s_final.an.list, name=archaea_16s_final.names, taxonomy=archaea_16s_final.taxonomy)
reftaxonomy is not required, but if given will keep the rankIDs in the summary file static.
unique 2636
0.01 1940
0.02 1033
0.03 634
Output File Names:
archaea_16s_final.an.uniquecons.taxonomy
archaea_16s_final.an.uniquecons.tax.summary
archaea_16s_final.an.0.01cons.taxonomy
archaea_16s_final.an.0.01cons.tax.summary
archaea_16s_final.an.0.02cons.taxonomy
archaea_16s_final.an.0.02cons.tax.summary
archaea_16s_final.an.0.03cons.taxonomy
archaea_16s_final.an.0.03cons.tax.summary
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