MaestSi
commented
1 year ago Hi, I don't get what you edited. In any case, you are running diversity analyses at taxonomy level 1 (which probably is just "Bacteria" and could not be very meaningful). Moreover, diversityAnalyses process requires more than one sample to produce alpha and beta-diversity metrics. I just edited metontiime2.nf script to prevent running diversity metrics with a single sample, which previously resulted in an error. Please let me know if everything runs smoothly on your side. Please note that you should also have at least 10k reads for this process to complete successfully (numReadsDiversity parameter). SM
it look wrong at line 529 in metontiime2.nf make me cannot run diverrsity step. So, i fixed it and run it is successfull. Please, check it. this is my error: Caused by: Process
diversityAnalyses (1)terminated with an error exit status (1)Command executed:
mkdir -p /home/caothithuylinh/Desktop/testOntimeV2/diversityAnalyses mkdir -p /home/caothithuylinh/Desktop/testOntimeV2/diversityAnalyses/taxa-Bacteria-samplingDepth-10000-level1
qiime diversity core-metrics --i-table /home/caothithuylinh/Desktop/testOntimeV2/filterTaxa/table-Bacteria-min-freq-1-collapsed-absfreq-level1.qza --p-sampling-depth 10000 --m-metadata-file /home/caothithuylinh/Desktop/testOntimeV2/MetONTIIME/sample-metadata.tsv --o-rarefied-table /home/caothithuylinh/Desktop/testOntimeV2/diversityAnalyses/taxa-Bacteria-samplingDepth-10000-level1/rarefied-table.qza --o-observed-features-vector /home/caothithuylinh/Desktop/testOntimeV2/diversityAnalyses/taxa-Bacteria-samplingDepth-10000-level1/observed-features-vector.qza --o-shannon-vector /home/caothithuylinh/Desktop/testOntimeV2/diversityAnalyses/taxa-Bacteria-samplingDepth-10000-level1/shannon-vector.qza --o-evenness-vector /home/caothithuylinh/Desktop/testOntimeV2/diversityAnalyses/taxa-Bacteria-samplingDepth-10000-level1/evenness-vector.qza --o-jaccard-distance-matrix /home/caothithuylinh/Desktop/testOntimeV2/diversityAnalyses/taxa-Bacteria-samplingDepth-10000-level1/jaccard-distance-matrix.qza --o-bray-curtis-distance-matrix /home/caothithuylinh/Desktop/testOntimeV2/diversityAnalyses/samplingDepth-10000-level1/bray-curtis-distance-matrix.qza --o-jaccard-pcoa-results /home/caothithuylinh/Desktop/testOntimeV2/diversityAnalyses/taxa-Bacteria-samplingDepth-10000-level1/jaccard-pcoa-results.qza --o-bray-curtis-pcoa-results /home/caothithuylinh/Desktop/testOntimeV2/diversityAnalyses/taxa-Bacteria-samplingDepth-10000-level1/bray-curtis-pcoa-results.qza --o-jaccard-emperor /home/caothithuylinh/Desktop/testOntimeV2/diversityAnalyses/taxa-Bacteria-samplingDepth-10000-level1/jaccard-emperor.qzv --o-bray-curtis-emperor /home/caothithuylinh/Desktop/testOntimeV2/diversityAnalyses/taxa-Bacteria-samplingDepth-10000-level1/bray-curtis-emperor.qzv
for f in $(find /home/caothithuylinh/Desktop/testOntimeV2/diversityAnalyses/taxa-Bacteria-samplingDepth-10000-level1 | grep "qza" | grep -v "distance-matrix"); do
done
qiime diversity alpha-rarefaction --i-table /home/caothithuylinh/Desktop/testOntimeV2/filterTaxa/table-Bacteria-min-freq-1-collapsed-absfreq-level1.qza --p-max-depth 10000 --m-metadata-file /home/caothithuylinh/Desktop/testOntimeV2/MetONTIIME/sample-metadata.tsv --o-visualization /home/caothithuylinh/Desktop/testOntimeV2/diversityAnalyses/taxa-Bacteria-samplingDepth-10000-level1/alpha-rarefaction.qzv
Command exit status: 1
Command output: (empty)
Command error: --o-bray-curtis-distance-matrix ARTIFACT DistanceMatrix Matrix of Bray-Curtis distances between pairs of samples. [required] --o-jaccard-pcoa-results ARTIFACT PCoAResults PCoA matrix computed from Jaccard distances between samples. [required] --o-bray-curtis-pcoa-results ARTIFACT PCoAResults PCoA matrix computed from Bray-Curtis distances between samples. [required] --o-jaccard-emperor VISUALIZATION Emperor plot of the PCoA matrix computed from Jaccard. [required] --o-bray-curtis-emperor VISUALIZATION Emperor plot of the PCoA matrix computed from Bray-Curtis. [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). --recycle-pool TEXT Use a cache pool for pipeline resumption. QIIME 2 will cache your results in this pool for reuse by future invocations. These pool are retained until deleted by the user. If not provided, QIIME 2 will create a pool which is automatically reused by invocations of the same action and removed if the action is successful. Note: these pools are local to the cache you are using. --no-recycle Do not recycle results from a previous failed pipeline run or save the results from this run for future recycling. --parallel Execute your action in parallel. This flag will use your default parallel config. --parallel-config FILE Execute your action in parallel using a config at the indicated path. --use-cache DIRECTORY Specify the cache to be used for the intermediate work of this pipeline. If not provided, the default cache under $TMP/qiime2/ will be used.
IMPORTANT FOR HPC USERS: If you are on an HPC system
and are using parallel execution it is important to
set this to a location that is globally accessible
to all nodes in the cluster.
--example-data PATH Write example data and exit.
--citations Show citations and exit.
--help Show this message and exit.
(1/1) Invalid value for '--o-bray-curtis-distance-matrix': Directory '/home/c aothithuylinh/Desktop/testOntimeV2/diversityAnalyses/samplingDepth-10000-lev el1' does not exist, cannot save 'bray-curtis-distance-matrix.qza' into it.
Work dir: /home/caothithuylinh/Desktop/testOntimeV2/MetONTIIME/work/41/289bc9e25b780abf155c1196aea5d7
Tip: view the complete command output by changing to the process work dir and entering the command
cat .command.out-- Check '.nextflow.log' file for details