Clearcut truncates sequence names to 7 characters

mothur bugs
1

I’m running mothur v. 47 on windows.
Description of problem:

clearcut(fasta=BacPop10.chop.unique.good.filter.unique.precluster.fasta, DNA=T, verbose=t)
unifrac.weighted(tree=BacPop10.chop.unique.good.filter.unique.precluster.tre, count=BacPop10.chop.unique.good.filter.unique.precluster.count_table, distance=lt)

generates the following error:
[ERROR]: M02058_ is not in your count table. Please correct.
[ERROR]: M06066_ is not in your count table. Please correct.
etc
etc
Here what the first few lines of the tree file generated by clearcut look like:
((((((((((((((((((((((((((((((((((M06066_:-0.000208,(M02058_:-0.000202,(M06066_:-0.000196,(M06066_:-0.000191,(((((((((((((M06066_:0.004497,(((((((M06066_:0.000307,(M06066_:0.000955,(((M06066_:0.010741,M06066_:0.016657):0.005434,(((((M06066_:0.011 etc.

As indicated by the error message, the seqs names are truncated.

If I run clearcut on our galaxy instance, download the tree file and run unifrac.weighted in windows (v.47), unifrac runs fine. Here is what the first few lines of the tree file generated in galaxy look like:
((((((M02058_549_000000000-BNC88_1_1101_21424_19684:0.004682,M06066_61_000000000-C4YPK_1_1102_24380_21149:0.004752):-0.000000,((((M02058_520_000000000-BKCRD_1_1111_16117_29088:0.004713,M06066_91_000000000-CCMK3_1_1104_18642_7041:0.004721):-0.000000,((M06066_91_000000000-CCMK3_1_2103_16948_13817:0.002374,M06066_91_000000000-

The seq names are complete. Galaxy runs mothur v. 39.5
|Galaxy Tool ID:|toolshed.g2.bx.psu.edu/repos/iuc/mothur_clearcut/mothur_clearcut/1.39.5.0|
|Galaxy Tool Version:|1.39.5.0|
|Tool Version:|v.1.39.5|

Just to be sure, I replaced the hyphens in the seq names with underscores, which did not solve the problem.

thanks for your help,

Giovanni

2

Thanks for reporting this issue. I have fixed the bug and the change will be part of our next release. In the meantime try this:

mothur > dist.seqs(fasta=BacPop10.chop.unique.good.filter.unique.precluster.fasta, output=lt)
mothur > clearcut(phylip=current)

3

This topic was automatically closed 10 days after the last reply. New replies are no longer allowed.