get.sharedseqs error

Commands in mothur
1

I’m trying to run get.sharedseqs, but I keep getting the same basic error. I’ve tried running it a few different ways:
get.sharedseqs(list=VFmultiple2.final.an.list, group=VFmultiple2.final.groups)
get.sharedseqs(shared=VFmultiple2.final.an.shared, label=0.03-0.05)
get.sharedseqs(list=VFmultiple2.final.an.list, group=VFmultiple2.final.groups, label=0.03-0.05, fasta=VFmultiple2.final.fasta)
etc.

Each time it spits back something to this effect:
0.03[ERROR]: Could not open VFmultiple2.final.an.0.03.unique.001WI-003WI-005WI-006WI-007WI-008WI-009WI-012WI-013WI-014WI-015WI-016WI-017WI-019WI-020WI-Control-G1-G10-G11-G12-G14-G15-G16-G17-G20-G21-G23-G25-G27-G28-G29-G30-G31-G32-G35-G38-G39-G40-G42-G44-G48-G49-G50-G51-G53-G6-G9.shared.seqs

It does tell me that it creates an output file, but I can’t actually find that file anywhere to see what is in it.
What am I doing wrong?
Thanks,
Alissa

2

I wonder if the length of the filename is becoming an issue. Could you send your input files to mothur.bugs@gmail.com?

3

Thanks for reporting this bug. It is caused by the length of the filename mothur is creating. The combination of all your group names creates a filename too long for the operating system. I have corrected this issue in mothur and the fix will be part of our next release.

4

I am encountering a different issue with get.sharedseqs. The .shared.seqs output is not giving the sequence ID, instead its just giving the OTU number and group names.
Is there a way to tackle this problem?

I am using Mac version 1.32.1

Thanks for your support.

5

Can you post the command you are running? The different parameters given provide different outputs.

6

I am having this same issue. Here is my input and output:


mothur > get.sharedseqs(shared=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.proks.wang.pick.2.subsample.tx.unique_list.shared, uniquegroups=BlueNG)

1 9

Output File Names:
stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.proks.wang.pick.2.subsample.tx.unique_list.1.unique.BlueNG.shared.seqs

mothur > system(less stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.proks.wang.pick.2.subsample.tx.unique_list.1.unique.BlueNG.shared.seqs)

Otu281|BlueNG|39
Otu341|BlueNG|10
Otu342|BlueNG|4
Otu366|BlueNG|4
Otu463|BlueNG|1
Otu466|BlueNG|1
Otu506|BlueNG|1
Otu508|BlueNG|3
Otu513|BlueNG|1

The same type of problem arose whether I used uniquegroups or sharedgroups.

Thanks!

7

Hi Westcott,

Here is the command which I used:

get.sharedseqs(shared=EX.filter.shared)

Prior to running this command, I used filter.shared to sort out my OTUs, and the resultant .filter.shared file was used for get.sharedseqs command as mentioned above.

Thanks.

8

If you want the sequence IDs, you need to use a list file as the input. Something like:

get.sharedseqs(list=abrecovery.an.list, sharedgroups=A-B, label=0.03, group=abrecovery.groups)

AY457885|A|Otu001
AY457884|A|Otu001
AY457811|B|Otu001
AY457771|B|Otu001
AY457827|B|Otu001
AY457821|B|Otu001
…

The shared file does not contain any sequence IDs so mothur can not report any to you.

9

Great, thanks!