HELP what does this ERROR mean

meghanS · October 6, 2022, 4:24pm

/******************************************/

Running command: remove.seqs(accnos=/Users/meghanstern/Desktop/mothur 2.0/SRR830919.bad.accnos.temp, count=/Users/meghanstern/Desktop/mothur 2.0/SRR830919.full.count_table)

[ERROR]: SRR830919.1.2 is not in your count table. Please correct.

/******************************************/

zsh: segmentation fault /Users/meghanstern/Desktop/mothur\ 2.0/mothur

Saving session...

...copying shared history...

...saving history...truncating history files...

...completed.

[Process completed]

mothur > get.current()

Current RAM usage: 0.00491714 Gigabytes. Total Ram: 16 Gigabytes.

Current files saved by mothur:
processors=8

Current default directories saved by mothur:
	/Users/meghanstern/Desktop/mothur 2.0/


Current working directory: /Users/meghanstern/

Output File Names: 
current_files.summary


mothur > pcr.seqs(fasta=silva.bacteria.fasta, start=11895, end=25318, keepdotsF)
Unable to open silva.bacteria.fasta. Trying MOTHUR_FILES directory /Users/meghanstern/Desktop/mothur 2.0/silva.bacteria.fasta.

Using 8 processors.
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[NOTE]: no sequences were bad, removing /Users/meghanstern/Desktop/mothur 2.0/silva.bacteria.bad.accnos

It took 5 secs to screen 14956 sequences.

Output File Names: 
/Users/meghanstern/Desktop/mothur 2.0/silva.bacteria.pcr.fasta


                                                                                [ERROR]: You are missing (
[ERROR]: Invalid.

mothur > pcr.seqs(fasta=silva.bacteria.fasta, start=11895, end=25318, keepdotsF)
Unable to open silva.bacteria.fasta. Trying MOTHUR_FILES directory /Users/meghanstern/Desktop/mothur 2.0/silva.bacteria.fasta.

Using 8 processors.
1000
1000
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1870
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[NOTE]: no sequences were bad, removing /Users/meghanstern/Desktop/mothur 2.0/silva.bacteria.bad.accnos

It took 4 secs to screen 14956 sequences.

Output File Names: 
/Users/meghanstern/Desktop/mothur 2.0/silva.bacteria.pcr.fasta


                                                                                [ERROR]: You are missing (
[ERROR]: Invalid.
                                                                              s=Fothur > pcr.seqs(fasta=silva.bacteria.fasta, start=11895, end=25318, keepdotsF)
Unable to open silva.bacteria.fasta. Trying MOTHUR_FILES directory /Users/meghanstern/Desktop/mothur 2.0/silva.bacteria.fasta.

Using 8 processors.
pcr.seqs(fasta=silva.bacteria.fasta, start=11895, end=25318, keepdots=F)^[[D1000
1000
1000
1000
1000
1000
1000
1000
1870
1870
1869
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1869
1869
[NOTE]: no sequences were bad, removing /Users/meghanstern/Desktop/mothur 2.0/silva.bacteria.bad.accnos

It took 4 secs to screen 14956 sequences.

Output File Names: 
/Users/meghanstern/Desktop/mothur 2.0/silva.bacteria.pcr.fasta



mothur > pcr.seqs(fasta=silva.bacteria.fasta, start=11895, end=25318, keepdots=F)
Unable to open silva.bacteria.fasta. Trying MOTHUR_FILES directory /Users/meghanstern/Desktop/mothur 2.0/silva.bacteria.fasta.

Using 8 processors.
1000
1000
1000
1000
1000
1000
1000
1000
1870
1869
1870
1869
1870
1869
1870
1869
[NOTE]: no sequences were bad, removing /Users/meghanstern/Desktop/mothur 2.0/silva.bacteria.bad.accnos

It took 5 secs to screen 14956 sequences.

Output File Names: 
/Users/meghanstern/Desktop/mothur 2.0/silva.bacteria.pcr.fasta



mothur > rename.file(input=silva.bacteria.pcr.fasta, new=silva.v4.fasta)
Unable to open silva.bacteria.pcr.fasta. Trying MOTHUR_FILES directory /Users/meghanstern/Desktop/mothur 2.0/silva.bacteria.pcr.fasta.

Current files saved by mothur:
fasta=/Users/meghanstern/Desktop/mothur 2.0/silva.bacteria.pcr.fasta
processors=8

mothur > summary.seqs(fasta=silva.v4.fasta)

Using 8 processors.

		Start	End	NBases	Ambigs	Polymer	NumSeqs
Minimum:	1	13424	269	0	3	1
2.5%-tile:	1	13424	291	0	4	374
25%-tile:	1	13424	292	0	4	3740
Median: 	1	13424	292	0	4	7479
75%-tile:	1	13424	292	0	5	11218
97.5%-tile:	1	13424	293	1	6	14583
Maximum:	3	13424	350	5	9	14956
Mean:	1	13424	291	0	4
# of Seqs:	14956

It took 2 secs to summarize 14956 sequences.

Output File Names:
silva.v4.summary


mothur > count.seqs(name=SRR830919.fasta)
Unable to open SRR830919.fasta. Trying MOTHUR_FILES directory /Users/meghanstern/Desktop/mothur 2.0/SRR830919.fasta.

It took 4 secs to create a table for 257043 sequences.

Total number of sequences: 257043

Output File Names: 
/Users/meghanstern/Desktop/mothur 2.0/SRR830919.count_table


mothur > count.seqs(count=SRR830919.count_table, compress=f)
Unable to open SRR830919.count_table. Trying MOTHUR_FILES directory /Users/meghanstern/Desktop/mothur 2.0/SRR830919.count_table.

Output File Names: 
/Users/meghanstern/Desktop/mothur 2.0/SRR830919.full.count_table


mothur > screen.seqs(fasta=SRR830919.fasta, count=SRR830919.full.count_table,mambig=0, maxlength=275, maxhomop=8)
[WARNING]: mxambig is not a valid parameter, ignoring.
The valid parameters are: fasta, contigsreport, alignreport, summary, name, count, group, qfile, taxonomy, start, end, maxambig, maxhomop, minlength, maxlength, processors, criteria, optimize, seed, inputdir, outputdir, minoverlap, ostart, oend, mismatches, maxn, minscore, maxinsert, and minsim.
Unable to open SRR830919.fasta. Trying MOTHUR_FILES directory /Users/meghanstern/Desktop/mothur 2.0/SRR830919.fasta.
Unable to open SRR830919.full.count_table. Trying MOTHUR_FILES directory /Users/meghanstern/Desktop/mothur 2.0/SRR830919.full.count_table.

Using 8 processors.
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It took 1 secs to screen 257043 sequences, removed 256110.

/******************************************/
Running command: remove.seqs(accnos=/Users/meghanstern/Desktop/mothur 2.0/SRR830919.bad.accnos.temp, count=/Users/meghanstern/Desktop/mothur 2.0/SRR830919.full.count_table)
[ERROR]: SRR830919.10.2 is not in your count table. Please correct.
/******************************************/
zsh: segmentation fault  /Users/meghanstern/Desktop/mothur\ 2.0/mothur

Saving session...
...copying shared history...
...saving history...truncating history files...
...completed.

[Process completed]

I am getting this error and I’m not sure what it means

pschloss · October 6, 2022, 5:46pm

First - be sure to notice that you used mxambig as an argument rather than maxambig.

Second - your count file has a name that wouldn’t be generated by mothur (i.e., the .full. part). Did you generate these files outside of mothur? I wonder if your fasta file was generated the same way as your count file. You might double check that the same sequences are getting into both files.

leocadio · October 7, 2022, 8:19pm

Pat - the “full” part is added by mothur when inflating the new count file. They do it in the line above

mothur > count.seqs(count=SRR830919.count_table, compress=f)

(I inflate mine too if I want to trace what happens to each sample)

But, I am a bit lost in the code; I think with all renaming and changing fastas, there is a point the count and the fasta file do not correspond to each other.

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HELP what does this ERROR mean

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