I ran the same command as my last message (itsxpress) with the
--verbose flag and this is what I get:
Usage: qiime itsxpress trim-single [OPTIONS]
ITSxpress trimSingle is used for qza types with SquencesWithQuality or
JoinedSequencesWithQuality. This means the qza must be in the
SingleLanePerSampleSingleEndFastqDirFmt, and only contain one fastq file.
The taxa list and variable for it:
A = Alveolata
B = Bryophyta
C = Bacillariophyta
D = Amoebozoa
E = Euglenozoa
F = Fungi
G = Chlorophyta (green algae)
H = Rhodophyta (red algae)
I = Phaeophyceae (brown algae)
L = Marchantiophyta (liverworts)
M = Metazoa
O = Oomycota
P = Haptophyceae (prymnesiophytes)
Q = Raphidophyceae
R = Rhizaria
S = Synurophyceae
T = Tracheophyta (higher plants)
U = Eustigmatophyceae
ALL = All
--i-per-sample-sequences ARTIFACT SampleData[SequencesWithQuality]
The artifact that contains the sequence file(s).
Either Joined Paired or just a single fastq. One file
sequences in the qza data folder. [required]
--p-region TEXT Choices('ITS2', 'ITS1', 'ALL')
The regions ITS2, ITS1, and ALL that can be selected
--p-taxa TEXT Choices('A', 'B', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'L',
'M', 'ALL', 'O', 'P', 'Q', 'R', 'S', 'T', 'U')
The selected taxonomic group sequenced that can be
selected from. [default: 'F']
--p-threads INTEGER The number of processor threads to use in the run.
--p-cluster-id NUMBER Range(0.97, 1.0, inclusive_end=True)
The percent identity for clustering reads, set to 1
for exact dereplication. [default: 0.995]
--o-trimmed ARTIFACT SampleData[SequencesWithQuality]
The trimmed sequences from ITSxpress. [required]
--output-dir PATH Output unspecified results to a directory
--verbose / --quiet Display verbose output to stdout and/or stderr
during execution of this action. Or silence output if
execution is successful (silence is golden).
--example-data PATH Write example data and exit.
--citations Show citations and exit.
--help Show this message and exit.
There was a problem with the command:
(1/1) Invalid value for '--o-trimmed': '' is not a writable directory, cannot write output to it.
I notice now that I've put the text into the preformatted HTML, there is no space like you were talking about in the above post:
In my block of text, it's formatted as '' but looks like ' '.
I also wonder if what the message talks about with "SingleLanePerSampleSingleEndFastqDirFmt" is important. I'm not sure what format the file I have is in, but I know it is SampleData[SequencesWithQuality] so it should work.
I also wanted to include the bash report, since this was something interesting I noticed as well. I run it with
bash -x to troubleshoot, and got this:
I'm not sure which line would be line 4, but something seems to be stopping my code from running in the first place. And this makes me think it might be a permissions issue as well––is line 4 the --i-per-sample-sequences command? It could be something to do with not reading my file in the first place––but since it's the right file type, I have no clue why that would be!
This is all so weird!! Thank you again for all of your continued help on this.