mothur

Chimera.uchime command not working

Hello,
I’m using mothur v.1.42.0 and I was running command chimera.uchime as follows:
mothur> chimera.uchime(fasta=/home/heba/New/fileList.paired.trim.contigs.good.unique.filter.precluster.fasta, count=/home/heba/New/fileList.paired.trim.contigs.good.unique.filter.precluster.count_table, dereplicate=T)

Using 1 processors.
and I got the following error: [ERROR]: /home/heba/New/fileList.paired.trim.contigs.good.unique.filter.precluster.fasta is blank. Please correct.

00:00 31Mb 0.1% Reading /home/heba/New/fileList.paired.trim.contigs.good.uni00:00 31Mb 0.1% Reading /home/heba/New/fileList.paired.trim.contigs.good.uni00:00 31Mb 100.0% Reading /home/heba/New/fileList.paired.trim.contigs.good.unique.filter.precluster.temp
Floating point exception (core dumped)
[ERROR]: /home/heba/New/fileList.paired.trim.contigs.good.unique.filter.precluster.denovo.uchime.chimeras is blank. Please correct.

It took 0 secs to check 0 sequences. 0 chimeras were found.

Output File Names:
/home/heba/New/fileList.paired.trim.contigs.good.unique.filter.precluster.denovo.uchime.chimeras
/home/heba/New/fileList.paired.trim.contigs.good.unique.filter.precluster.denovo.uchime.accnos

Can you help me find chimeras in my sequences?
I also tried dereplicate=F and not adding the dereplicate parameter, and I got the same outcome.

Thank you!

Can you post the output of what you get when you run…

summary.seqs(fasta=/home/heba/New/fileList.paired.trim.contigs.good.unique.filter.precluster.fasta, count=/home/heba/New/fileList.paired.trim.contigs.good.unique.filter.precluster.count_table)

This is what happened:
mothur > summary.seqs(fasta=/home/heba/New/fileList.paired.trim.contigs.good.unique.filter.precluster.fasta, count=/home/heba/New/fileList.paired.trim.contigs.good.unique.filter.precluster.count_table)
[ERROR]: /home/heba/New/fileList.paired.trim.contigs.good.unique.filter.precluster.fasta is blank, aborting.
You have no current fastafile and the fasta parameter is required.

Using 1 processors.
[ERROR]: did not complete summary.seqs.

I checked and the precluster.fasta is blank, while all other fasta files (good fasta and unique fasta) are normal and include sequences!

Can you post the output from when you do the following?

summary.seqs(fasta=/home/heba/New/fileList.paired.trim.contigs.good.unique.fasta)

You might also post the output of what you did when you ran screen.seqs and the output from

summary.seqs(fasta=/home/heba/New/fileList.paired.trim.contigs.align)

This is the output of the first command:

mothur > summary.seqs(fasta=/home/heba/fileList.paired.trim.contigs.good.unique.fasta)

Using 1 processors.

		Start	End	NBases	Ambigs	Polymer	NumSeqs
Minimum:	1	35	35	0	3	1
2.5%-tile:	1	439	439	0	4	6201
25%-tile:	1	443	443	0	5	62009
Median: 	1	460	460	0	5	124018
75%-tile:	1	460	460	0	6	186027
97.5%-tile:	1	465	465	0	6	241835
Maximum:	1	470	470	0	8	248035
Mean:	1	452.215	452.215	0	5.19994
number of Seqs:	248035

Output File Names: 
/home/heba/fileList.paired.trim.contigs.good.unique.summary

It took 4 secs to summarize 248035 sequences.

I didn’t find a fle named /home/heba/New/fileList.paired.trim.contigs.align but I ran the command using "/home/heba/New/fileList.paired.trim.contigs.good.unique.align
and here is its output:

mothur > summary.seqs(fasta=/home/heba/fileList.paired.trim.contigs.good.unique.align)

Using 1 processors.

		Start	End	NBases	Ambigs	Polymer	NumSeqs
Minimum:	1	1231	1	0	1	1
2.5%-tile:	        1	13422	290	0	3	6201
25%-tile:	        1	13422	290	0	4	62009
Median:  	       1	13422	291	0	4	124018
75%-tile:	       1	13422	291	0	5	186027
97.5%-tile:      1	13422	292	0	6	241835
Maximum:	13425	13425	301	0	8	248035
Mean:	65.6023	13419.1	289.425	0	4.23962
number of Seqs:	248035

Output File Names: 
/home/heba/fileList.paired.trim.contigs.good.unique.summary

It took 80 secs to summarize 248035 sequences.

It looks like you probably didn’t run screen.seqs, right? You’ll want to run something like this before running filter.seqs, unique.seqs, pre.cluster, and then chimera.uchime

screen.seqs(fasta=fileList.paired.trim.contigs.good.unique.align, count=fileList.paired.trim.contigs.good.count_table, start=1, end=13422)
filter.seqs(fasta=current, vertical=T, trump=.)
unique.seqs(fasta=current, count=current)
pre.cluster(fasta=current, count=current, diffs=2)
etc.
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