It passed using the dist.seqs command. Dos anyone knows how to fix it?
I need to perform the dist.seqs with these sequences but I can not.
My summary.seqs of the file was:
Using 6 processors.
Start End NBases Ambigs Polymer NumSeqs
Minimum: 1 654 232 0 3 1
2.5%-tile: 1 654 242 0 3 198
25%-tile: 1 654 252 0 4 1971
Median: 1 654 253 0 4 3941
75%-tile: 1 654 253 0 5 5911
97.5%-tile: 1 654 255 0 6 7684
Maximum: 1 654 261 0 8 7880
Mean: 1 654 252.16 0 4.61751
Sorry, I don’t understand your question or what you are trying to do. Also, what version of mothur are you using?
Hi Schloss,
Mothur version 1.37
I explain you.
I obtained the OTUs abundance table (last count table), subsampled (sub.sample) it to the smallest sample and eliminated the singletons and null rows (R script).
After to obtain the resulting table, I extracted the OTUs sequences from the .fasta to calculate the distance (dist.seqs) using those sequences to follow the further steps (make.shared, otu.rep, alpha diversity, etc)
What happend was an ERROR telling me that the sequences have different lengths. To turn around this, I used the screen.seqs to eliminate the sequences with different start/end and preserve those whit start=1 and end=654. After this I thought that all sequnces would have the same size, but the ERROR occurred again.
Thank you in advance.
Can you retry it with v1.39? We’ve made a number of changes in the last year that may effect this problem.
Hi Patrick,
I tried the new version, 1.39.2, and the ERROR message is the same.
mothur > summary.seqs(fasta=alfonso220.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.selected)
Start End NBases Ambigs Polymer NumSeqs
Minimum: 1 654 235 0 3 1
2.5%-tile: 1 654 242 0 3 140
25%-tile: 1 654 252 0 4 1395
Median: 1 654 253 0 5 2789
75%-tile: 1 654 253 0 5 4183
97.5%-tile: 6 654 255 0 6 5438
Maximum: 6 654 261 0 8 5577
Mean: 1.23041 654 252.007 0 4.60893
mothur > dist.seqs(fasta=alfonso220.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.selected)
“[ERROR]: your sequences are not the same length, aborting.”
May I send you my sequence file to try?
The problem is caused by a few sequences in the file. Here’s an example:
Sequence Name length of alignment this sequences length
M02255_76_000000000-ADUNE_1_1103_6841_18121 654 656
M02255_76_000000000-ADUNE_1_1103_6841_18121
T----AC—GG-AG-GGG--------GCT-A-G------C–G–T—T–GT-T-CGG-AA------TT-A–C-T–GG-GC-------GT–A-----AA-GC-GC-AC-------G-TA-G-G-C-G-------------G–C-TT-T-G-C-----------AA----G-T-T-A--------G-A-G–G–TG–A-AA-GC–C-T-GG-G-G-----CT-C-AA------C-T-C-C-A-G-A–A-T----T-G–C-C—T–T-------T–AA-G-A—C-------T–G-C–AT–C-G-C----T-T-G-A-A-T–C—C-GG-----GA-G-A--------G-G-T-G—AG-T------GG–A–ATT----C-C-G-A-GT–GT-A-G-AG-GT–G—A–A-A—TT-C-GT-AG–AT-A-TT–C-G–G-A-A-G-A-AC-A-CC—AG–T–G–GC-GAA-G–G-C–G-------G–C-T-C-A—CTG–G–AC-C-G---------------------G-T—A-T-T–GA–CG-C-T-G–A-GG–T-G-CG-A–AA-G-C—G-TG–GG-G–AG-C-A-AA--------CA–GG
–
The red dashes are on their own line and are adding the additional length. All the sequences that are causing the issue have the same problem. How was this file created?
You can use the filter.seqs command in debug mode to tell you the lengths.
mothur > set.dir(debug=t)
mothur > filter.seqs(inputdir=…/…/felipe, fasta=alfonso220.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.selected)
[DEBUG]: removed /Users/sarahwestcott/Desktop/felipe/temp1487956445
[DEBUG]: removed /Users/sarahwestcott/Desktop/felipe/temp1487956445
Setting input directory to: /Users/sarahwestcott/Desktop/felipe/
Using 1 processors.
Creating Filter…
[DEBUG]: M02255_77_000000000-ADUT3_1_1101_13422_10668 length = 654
[DEBUG]: M02255_77_000000000-ADUT3_1_1101_25799_6575 length = 654
[DEBUG]: M02255_77_000000000-ADUT3_1_1101_12569_9643 length = 654
[DEBUG]: M02255_77_000000000-ADUT3_1_1101_27087_10900 length = 654
[DEBUG]: M02255_76_000000000-ADUNE_1_1103_6841_18121 length = 656
[ERROR]: Sequences are not all the same length, please correct.
[DEBUG]: M02255_77_000000000-ADUT3_1_1101_13769_20532 length = 654
[DEBUG]: M02255_77_000000000-ADUT3_1_1101_9421_20643 length = 654
[DEBUG]: M02255_77_000000000-ADUT3_1_1103_15125_18615 length = 654
[DEBUG]: M02255_76_000000000-ADUNE_1_1101_6744_17104 length = 654
[DEBUG]: M02255_76_000000000-ADUNE_1_1101_28569_13911 length = 654
…
[DEBUG]: M02255_76_000000000-ADUNE_1_1104_8166_19001 length = 656
[ERROR]: Sequences are not all the same length, please correct.
[DEBUG]: M02255_76_000000000-ADUNE_1_1117_27229_8253 length = 656
[ERROR]: Sequences are not all the same length, please correct.
[DEBUG]: M02255_77_000000000-ADUT3_1_1101_27484_17238 length = 654
[DEBUG]: M02255_76_000000000-ADUNE_1_1116_14170_7406 length = 656
[ERROR]: Sequences are not all the same length, please correct.
[DEBUG]: M02255_77_000000000-ADUT3_1_2101_26186_13235 length = 654