Hello,
I want to perform Picrust2. I have imported my data using following command -
qiime tools import --type SampleData[PairedEndSequencesWithQuality] --input-path my-pared-end --output-path my_paired-end-demux.qza
I using the output of this process my_paired-end-demux.qza
as a input for vsearch join-pairs using following commands - I tried two different commands
1
qiime vsearch join-pairs --i-demultiplexed-seqs my_paired-end-demux.qza --p-allowmergestagger --p-minlen 50 --p-maxns 250 --p-minovlen 125 --o-joined-sequences my_paired-end_joined_vsearch.qza
2
qiime vsearch join-pairs --i-demultiplexed-seqs my_paired-end-demux.qza --p-allowmergestagger --o-joined-sequences my_paired-end_joined_vsearch.qza
after running this I am getting following error message in log file
/home/amol2/volume/software/miniconda/miniconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/q2_vsearch/_join_pairs.py:90: YAMLLoadWarning: calling yaml.load() without Loader=... is dep$
demultiplexed_seqs.metadata.pathspec)))['phred-offset']
Traceback (most recent call last):
File "/home/amol2/volume/software/miniconda/miniconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/q2cli/commands.py", line 327, in __call__
results = action(**arguments)
File "</home/amol2/volume/software/miniconda/miniconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/decorator.py:decorator-gen-131>", line 2, in join_pairs
File "/home/amol2/volume/software/miniconda/miniconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/qiime2/sdk/action.py", line 240, in bound_callable
output_types, provenance)
File "/home/amol2/volume/software/miniconda/miniconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/qiime2/sdk/action.py", line 383, in _callable_executor_
output_views = self._callable(**view_args)
File "/home/amol2/volume/software/miniconda/miniconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/q2_vsearch/_join_pairs.py", line 57, in join_pairs
qmax, qmaxout)
File "/home/amol2/volume/software/miniconda/miniconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/q2_vsearch/_join_pairs.py", line 90, in _join_pairs_w_command_output
demultiplexed_seqs.metadata.pathspec)))['phred-offset']
TypeError: list indices must be integers or slices, not str
I tried to search on google but could not find any post with similar error. Can someone please help me with this?
Thanks in advance.