Trouble with filepaths and q2-dada2

(Clara) #1

Hi @thermokarst and @ebolyen, after I reinstalled the latest QIIME2, i encounter an error as follow which I never encounter before I reinstalled, are they related?

Usage: qiime dada2 denoise-paired [OPTIONS]

This method denoises paired-end sequences, dereplicates them, and filters
chimeras.

Inputs:
–i-demultiplexed-seqs ARTIFACT SampleData[PairedEndSequencesWithQuality]
The paired-end demultiplexed sequences to be
denoised. [required]
Parameters:
–p-trunc-len-f INTEGER
Position at which forward read sequences should be
truncated due to decrease in quality. This truncates
the 3’ end of the of the input sequences, which will
be the bases that were sequenced in the last cycles.
Reads that are shorter than this value will be
discarded. After this parameter is applied there must
still be at least a 20 nucleotide overlap between the
forward and reverse reads. If 0 is provided, no
truncation or length filtering will be performed
[required]
–p-trunc-len-r INTEGER
Position at which reverse read sequences should be
truncated due to decrease in quality. This truncates
the 3’ end of the of the input sequences, which will
be the bases that were sequenced in the last cycles.
Reads that are shorter than this value will be
discarded. After this parameter is applied there must
still be at least a 20 nucleotide overlap between the
forward and reverse reads. If 0 is provided, no
truncation or length filtering will be performed
[required]
–p-trim-left-f INTEGER
Position at which forward read sequences should be
trimmed due to low quality. This trims the 5’ end of
the input sequences, which will be the bases that
were sequenced in the first cycles. [default: 0]
–p-trim-left-r INTEGER
Position at which reverse read sequences should be
trimmed due to low quality. This trims the 5’ end of
the input sequences, which will be the bases that
were sequenced in the first cycles. [default: 0]
–p-max-ee NUMBER Reads with number of expected errors higher than
this value will be discarded. [default: 2.0]
–p-trunc-q INTEGER Reads are truncated at the first instance of a
quality score less than or equal to this value. If
the resulting read is then shorter than trunc-len-f
or trunc-len-r (depending on the direction of the
read) it is discarded. [default: 2]
–p-chimera-method TEXT Choices(‘none’, ‘pooled’, ‘consensus’)
The method used to remove chimeras. “none”: No
chimera removal is performed. “pooled”: All reads are
pooled prior to chimera detection. “consensus”:
Chimeras are detected in samples individually, and
sequences found chimeric in a sufficient fraction of
samples are removed. [default: ‘consensus’]
–p-min-fold-parent-over-abundance NUMBER
The minimum abundance of potential parents of a
sequence being tested as chimeric, expressed as a
fold-change versus the abundance of the sequence
being tested. Values should be greater than or equal
to 1 (i.e. parents should be more abundant than the
sequence being tested). This parameter has no effect
if chimera-method is “none”. [default: 1.0]
–p-n-threads INTEGER The number of threads to use for multithreaded
processing. If 0 is provided, all available cores
will be used. [default: 1]
–p-n-reads-learn INTEGER
The number of reads to use when training the error
model. Smaller numbers will result in a shorter run
time but a less reliable error model.
[default: 1000000]
–p-hashed-feature-ids / --p-no-hashed-feature-ids
If true, the feature ids in the resulting table will
be presented as hashes of the sequences defining each
feature. The hash will always be the same for the
same sequence so this allows feature tables to be
merged across runs of this method. You should only
merge tables if the exact same parameters are used
for each run. [default: True]
Outputs:
–o-table ARTIFACT FeatureTable[Frequency]
The resulting feature table. [required]
–o-representative-sequences ARTIFACT FeatureData[Sequence]
The resulting feature sequences. Each feature in the
feature table will be represented by exactly one
sequence, and these sequences will be the joined
paired-end sequences. [required]
–o-denoising-stats ARTIFACT SampleData[DADA2Stats]
[required]
Miscellaneous:
–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).
–citations Show citations and exit.
–help Show this message and exit.

                There was a problem with the command:

(1/1) Invalid value for “–i-demultiplexed-seqs”: ‘demux-paired-end.qza’ is
not a QIIME 2 Artifact (.qza)

Here is my command:
qiime dada2 denoise-paired
–i-demultiplexed-seqs demux-paired-end.qza
–p-trim-left-f 6
–p-trunc-len-f 278
–p-trim-left-r 6
–p-trunc-len-r 223
–o-representative-sequences rep-seqs-dada2.qza
–o-table table-dada2.qza
–o-denoising-stats stats-dada2
–p-n-threads 0

Thanks.

QIIME 2 2019.4.0 has faulty OpenBLAS results on certain CPUs
(Matthew Ryan Dillon) #2

Hi @Clara

Nope! I split this into a new topic for that reason.

Can you run ls in that same directory? How about

qiime tools validate demux-paired-end.qza

Thanks! :t_rex:

(Clara) #3

Hi @thermokarst, thanks for the guilde, here are the results:

with -ls

So means my "demux-paired-end.qza file is available. Next,
with -qiime tools validate demux-paired-end.qza,

There was a problem loading demux-paired-end.qza as a QIIME 2 Result:

[Errno 28] No space left on device

See above for debug info.

By looking at these info, I think is because I do not have enough space in the root, and I am using another directory now and it has run for 20 mins so far, should be fine. I will reply again if I having an error again. Thanks @thermokarst .

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