mothur

Filter.seqs Error (Unable to open)

Hi, I am getting the following error messages when using the filter.seqs command, but I am unsure how to fix it. I used the get.current() command to make sure the fasta being used was the trim.unique.good.align file however I am not sure why it is saying unable to open.

mothur > set.current(fasta=R_2021_10_05_12_00_01_user_S5-70-10-05-2021_Chip.trim.unique.good.align)

Using 8 processors.

Current files saved by mothur:
accnos=R_2021_10_05_12_00_01_user_S5-70-10-05-2021_Chip.trim.unique.bad.accnos
fasta=R_2021_10_05_12_00_01_user_S5-70-10-05-2021_Chip.trim.unique.good.align
group=R_2021_10_05_12_00_01_user_S5-70-10-05-2021_Chip.groups
name=R_2021_10_05_12_00_01_user_S5-70-10-05-2021_Chip.trim.names
oligos=CXMicroMothurOligos.txt
qfile=R_2021_10_05_12_00_01_user_S5-70-10-05-2021_Chip.qual
count=R_2021_10_05_12_00_01_user_S5-70-10-05-2021_Chip.trim.good.count_table
processors=8
summary=R_2021_10_05_12_00_01_user_S5-70-10-05-2021_Chip.trim.unique.good.summary

Output File Names:
current_files.summary

mothur > summary.seqs(fasta=current, count=current, processors=8)
Using R_2021_10_05_12_00_01_user_S5-70-10-05-2021_Chip.trim.good.count_table as input file for the count parameter.
Using R_2021_10_05_12_00_01_user_S5-70-10-05-2021_Chip.trim.unique.good.align as input file for the fasta parameter.

Using 8 processors.

	Start	End	NBases	Ambigs	Polymer	NumSeqs

Minimum: 2 11549 265 0 4 1
2.5%-tile: 2 11549 265 0 4 1
25%-tile: 2 11549 266 0 4 3
Median: 1238 11549 268 0 5 6
75%-tile: 1963 11549 270 0 5 9
97.5%-tile: 1963 11549 272 0 6 11
Maximum: 1963 11549 272 0 6 11
Mean: 1100 11549 267 0 4

of unique seqs: 11

total # of seqs: 11

It took 1 secs to summarize 11 sequences.

Output File Names:
R_2021_10_05_12_00_01_user_S5-70-10-05-2021_Chip.trim.unique.good.summary

mothur > filter.seqs(fasta=current, vertical=T, trump=.)
Using R_2021_10_05_12_00_01_user_S5-70-10-05-2021_Chip.trim.unique.good.align as input file for the fasta parameter.
Unable to open R_2021_10_05_12_00_01_user_S5. Trying default /usr/bin/R_2021_10_05_12_00_01_user_S5.
Unable to open /usr/bin/R_2021_10_05_12_00_01_user_S5. Trying mothur’s executable location /usr/bin/R_2021_10_05_12_00_01_user_S5.
Unable to open /usr/bin/R_2021_10_05_12_00_01_user_S5.
Unable to open 70. Trying default /usr/bin/70.
Unable to open /usr/bin/70. Trying mothur’s executable location /usr/bin/70.
Unable to open /usr/bin/70.
Unable to open 10. Trying default /usr/bin/10.
Unable to open /usr/bin/10. Trying mothur’s executable location /usr/bin/10.
Unable to open /usr/bin/10.
Unable to open 05. Trying default /usr/bin/05.
Unable to open /usr/bin/05. Trying mothur’s executable location /usr/bin/05.
Unable to open /usr/bin/05.
Unable to open 2021_Chip.trim.unique.good.align. Trying default /usr/bin/2021_Chip.trim.unique.good.align.
Unable to open /usr/bin/2021_Chip.trim.unique.good.align. Trying mothur’s executable location /usr/bin/2021_Chip.trim.unique.good.align.
Unable to open /usr/bin/2021_Chip.trim.unique.good.align.
no valid files.

Using 8 processors.
[ERROR]: did not complete filter.seqs.

Okay so I believe this is occurring because of the bashes in the file name. Does this mean I should rename all the current files without the dashes and use set.current() command to each parameter with the new file name that does not contain the dashes?

Yeah - you can change the dashes to underscores and that should solve the problems

Pat

Removing all the dashes and underscores fixed the issue :smiley:

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