Checking sequences from 03092012Lanoil.txt.shhh.trim.unique.good.filter.unique.precluster.fasta …
[ERROR]: Could not open 03092012Lanoil.txt.shhh.trim.unique.good.filter.unique.precluster.uchime.chimeraD10SUPRA
[ERROR]: Could not open 03092012Lanoil.txt.shhh.trim.unique.good.filter.unique.precluster.uchime.chimera1.tempI.19
When you run chimera.uchime with a group file, mothur uses the group names in the temporary files. What do your group names look like? Do they contain any special characters that could cause problems for the OS?
Thanks for your fast response
I don’t think that there are any problematic characters, just letters and numbers
Example:
HK2JE2401ERFRF D10SUPRA
HK2JE2401CODH5 D10SUPRA
HK2JE2401DVB32 D10SUPRA
HK2JE2401EGY8U D10SUPRA
HK2JE2401CAO1S D10SUPRA
HK2JE2401DPYTY D10SUPRA
Do you have read and write permissions on the folder the files are in? Is the uchime executable able to run? If the uchime executable ran you should see something like:
Indeed I have read and write permissions on the folder, I have performed all of the analysis up to the chimera.uchime step in the same folder all the other commands ran fine.
The uchime executable is able to run, I ran it against the silva bd and it seems to run fine.
Here is the output from it so far
C:\sff>uchime --input 03092012Lanoil.txt.shhh.trim.unique.good.filter.unique.pre
cluster.fasta --db silva.gold.ng.fasta
uchime v4.2.40
by Robert C. Edgar http://drive5.com/uchime
This code is donated to the public domain.
Here is the end of the run
C:\sff>uchime --input 03092012Lanoil.txt.shhh.trim.unique.good.filter.unique.pre
cluster.fasta --db silva.gold.ng.fasta
uchime v4.2.40
by Robert C. Edgar http://drive5.com/uchime
This code is donated to the public domain.
Unable to open 03092012Lanoil.txt.shhh.trim.unique.good.filter.unique.precluster
.unique.fasta. It will be disregarded.
[ERROR]: no valid files.
[ERROR]: did not complete chimera.uchime.
Sorry this is turning out to be so frustrating. This second error is different than the first. I did notice that you gave mothur a different filename than you gave the uchime directly, prehaps a typo?
Can you try running the first chimera.uchime command with 1 processor? The first error could mean that one of the child processes died unexpectedly and therefore did not write out the files mothur is looking for.
Ok I ran it with one processor got same result
mothur > chimera.uchime(fasta=03092012Lanoil.txt.shhh.trim.unique.good.filter.un
ique.precluster.fasta, name=03092012Lanoil.txt.shhh.trim.unique.good.filter.uniq
ue.precluster.names, group=03092012Lanoil.txt.shhh.good.pick.groups)
uchime by Robert C. Edgar
http://drive5.com/uchime
This code is donated to the public domain.
Checking sequences from 03092012Lanoil.txt.shhh.trim.unique.good.filter.unique.p
recluster.fasta …
[ERROR]: Could not open 03092012Lanoil.txt.shhh.trim.unique.good.filter.unique.p
recluster.uchime.chimeraD10SUPRA
you where right about the typo so I tried the silva again
chimera.uchime(fasta=03092012Lanoil.txt.shhh.trim.unique.good.filter
ique.precluster.fasta, reference=silva.gold.ng.fasta)
uchime by Robert C. Edgar
http://drive5.com/uchime
This code is donated to the public domain.
Checking sequences from 03092012Lanoil.txt.shhh.trim.unique.good.filter.uniqu
recluster.fasta …
It took 0 secs to check 1 sequences. 0 chimeras were found.
Output File Names:
03092012Lanoil.txt.shhh.trim.unique.good.filter.unique.precluster.uchime.chim
03092012Lanoil.txt.shhh.trim.unique.good.filter.unique.precluster.uchime.accn
and again…
mothur > chimera.uchime(fasta=03092012Lanoil.txt.shhh.trim.unique.good.filter
ique.precluster.fasta, reference=silva.gold.ng.fasta)
Checking sequences from 03092012Lanoil.txt.shhh.trim.unique.good.filter.uniqu
recluster.fasta …
It took 0 secs to check 2 sequences. 0 chimeras were found.
Output File Names:
03092012Lanoil.txt.shhh.trim.unique.good.filter.unique.precluster.uchime.chim
03092012Lanoil.txt.shhh.trim.unique.good.filter.unique.precluster.uchime.accn
mothur > chimera.uchime(fasta=03092012Lanoil.txt.shhh.trim.unique.good.filter
ique.precluster.fasta, reference=silva.gold.ng.fasta)
uchime by Robert C. Edgar http://drive5.com/uchime
This code is donated to the public domain.
Checking sequences from 03092012Lanoil.txt.shhh.trim.unique.good.filter.uniqu
recluster.fasta …
It took 0 secs to check 3 sequences. 0 chimeras were found.
Output File Names:
03092012Lanoil.txt.shhh.trim.unique.good.filter.unique.precluster.uchime.chim
03092012Lanoil.txt.shhh.trim.unique.good.filter.unique.precluster.uchime.accn
So I got pissed and changed the name of the file to test.fasta (I thought it might be to early in the morning for me to work on such long names :))
mothur > chimera.uchime(fasta=test.fasta, reference=silva.gold.ng.fasta)
uchime by Robert C. Edgar
http://drive5.com/uchime
This code is donated to the public domain.
Checking sequences from test.fasta …
[ERROR]: Could not open test.uchime.chimera
Did you find the error for this person? I’m having the same issue (same errors in mothur but works outside mothur). I’d like to try it without the database though to see how my chimera #s change
I’m still running 1.24 (haven’t gotten around to upgrading). I’m having all sort of errors with the same fasta, so I’m trying to figure out if there’s just something weird with this file. it’s the same file that I sent you for the pre.cluster error. This weekend I tried shortening the sequence names and rerunning the SOP-seemed fine till screening seqs after aligning (which worked the first time around) and I only have 10% of my sequences after that command. I’m still trying to figure out what’s going on with that
For the screen.seqs issue, you want screen.seqs(fasta=current, name=current, group=bac.groups, end=5705, start=1046, processors=4). The start parameter removes sequences that start AFTER the position you specify.
I am having the same “ignoring gaps in FASTA file” message than previous posting. I have tried with only one processor and I have the same results. Could you please let me know if there was a solution for this in the past?
Checking sequences from 28F.shhh.trim.unique.good.filter.unique.precluster.fasta …
uchime v4.2.40
by Robert C. Edgar http://drive5.com/uchime
This code is donated to the public domain.
00:00 569.3 0.1% Reading 28F.shhh.trim.unique.good.filter.unique.precluster.temp
WARNING: Ignoring gaps in FASTA file ‘28F.shhh.trim.unique.good.filter.unique.precluster.temp’
00:00 684.0 100.0% Reading 28F.shhh.trim.unique.good.filter.unique.precluster.temp
00:00 684.0 76 sequences
00:00 1.4Mb 100.0% 0/75 chimeras found (0.0%)
It took 0 secs to check 76 sequences from group A41_B.28F.
uchime v4.2.40
by Robert C. Edgar http://drive5.com/uchime
This code is donated to the public domain.
00:00 573.4 0.1% Reading 28F.shhh.trim.unique.good.filter.unique.precluster.temp
WARNING: Ignoring gaps in FASTA file ‘28F.shhh.trim.unique.good.filter.unique.precluster.temp’
00:00 696.3 100.0% Reading 28F.shhh.trim.unique.good.filter.unique.precluster.temp
00:00 696.3 87 sequences
00:01 1.4Mb 100.0% 3/86 chimeras found (3.4%)
You can ignore that warning. Uchime does not require sequences to be aligned, so it is just reporting that it is ignoring the gaps in the aligned sequence.
Checking sequences from Methods.unique.good.filter.unique.precluster.fasta …
[ERROR]: Could not open Methods.unique.good.filter.unique.precluster.uchime.chimeras27167.tempC_7
[ERROR]: Could not open Methods.unique.good.filter.unique.precluster.uchime.chimeras27163.temp39_09
[ERROR]: Could not open Methods.unique.good.filter.unique.precluster.uchime.chimeras27166.tempC_31
[ERROR]: Could not open Methods.unique.good.filter.unique.precluster.uchime.chimeras27165.tempC_21
[ERROR]: Could not open Methods.unique.good.filter.unique.precluster.uchime.chimeras27162.temp26_09
[ERROR]: Could not open Methods.unique.good.filter.unique.precluster.uchime.chimeras10_09
[ERROR]: Could not open Methods.unique.good.filter.unique.precluster.uchime.chimeras27164.tempC_10
[ERROR]: Could not open Methods.unique.good.filter.unique.precluster.uchime.chimeras27161.temp1_09
I don't see a reply or a solution from this old post, so not sure what can be done.
To add to this old thread, I too have an error with chimera.uchime not finding files. (logfile). This command on this same file worked previously in another directory, and the new directory has a longer path which led me to think that maybe the file path is too long and causing the error.
To test this I renamed the files to something nice and short (BFWGZ.an.count_table and BFWGZ.an.fasta) and sure enough chimera.uchime now works. I see this fix is perhaps inconsistent with the OP who renamed their fasta file to something shorter and it still failed… but perhaps if it was a path length issue their path was still over some threshold even with the shorter file name??
To add information, the old path before renaming (threw the error) was 211 characters (including separators); the new path after renaming (ran fine) was 166 characters.
Thanks for posting such a detailed response! Mothur does not have a limit on the length of filenames, but the chimera.uchime command is a wrapper for the uchime program. I suspect that uchime may failing do the the length of the filename which is why mothur can’t find the output files generated by uchime.
