Good day to you Dr Rivers
I am a beginner with qiime2 and I am trying to analyse ITS 1 and 2 for a read from a sequencing facility (MRDNA USA). I have a paired-end-demux.qza file.
I followed this tutorial for my reads. I tried to trim the qza file and get this error message:
qiime itsxpress trim-pair-output-unmerged \
--i-per-sample-sequences demux-full.qza
--p-region ALL
--p-taxa F
--o-trimmed trimmed.qza
Plugin error from itsxpress:
Command '['bbmerge.sh', 'in=/tmp/qiime2-archive-21xz919x/8e2eaab4-8c65-44cf-abac-aa8b890c2c6d/data/101A_8_L001_R1_001.fastq.gz', 'in2=/tmp/qiime2-archive-21xz919x/8e2eaab4-8c65-44cf-abac-aa8b890c2c6d/data/101A_8_L001_R2_001.fastq.gz', 'out=/tmp/itsxpress_o0oh31fp/seq.fq.gz', 't=1', 'maxmismatches=40', 'maxratio=0.3']' returned non-zero exit status 1.
Debug info has been saved to /tmp/qiime2-q2cli-err-lb1gyl7a.log
Can you please help with this?
Do I have to install bbmerge and HMMsearch on qiime2? How do I go about it?
Have you seen this topic, @bettya ? It looks very similar to your error, and might help get you on the right track before @Adam_Rivers gets a chance to look your question over. The search tool is mighty mighty!
Side note - if you ever find yourself posting a question about an error message with a debugging logfile, please consider sharing that file's contents in your post. They're often useful in figuring out what's going on.
Thanks for your help
I did tried all the suggestions in the searched topic, I still get the same error:
qiime itsxpress trim-pair-output-unmerged \
--i-per-sample-sequences demux-full.qza
--p-region ALL
--p-taxa F
--o-trimmed trimmed.qza
Plugin error from itsxpress:
Command '['bbmerge.sh', 'in=/tmp/qiime2-archive-_jy02pke/8e2eaab4-8c65-44cf-abac-aa8b890c2c6d/data/101A_8_L001_R1_001.fastq.gz', 'in2=/tmp/qiime2-archive-_jy02pke/8e2eaab4-8c65-44cf-abac-aa8b890c2c6d/data/101A_8_L001_R2_001.fastq.gz', 'out=/tmp/itsxpress_z_hyqqni/seq.fq.gz', 't=1', 'maxmismatches=40', 'maxratio=0.3']' returned non-zero exit status 1.
Debug info has been saved to /tmp/qiime2-q2cli-err-_bw_d929.log
How do I get the error debug file on qiime2?
Please note that I am working with a virtual box and I am a beginner.
Can someone please help me with a step by step suggestion?
/tmp/qiime2-q2cli-err-lb1gyl7a.log is an absolute file path to the log file. Working from the command line, you can use any text editor to open it. e.g. nano /tmp/qiime2-q2cli-err-lb1gyl7a.log
Notes:
Temp files are usually removed automatically shortly after they are created. If you get a file not found error, try re-running the command and then opening it immediately.
VirtualBox may handle temp files differently than the systems I'm used to. If that doesn't work, you may have to google how to open a temp file in virtualbox, or even how to change where the guest operating system you're running (e.g. Ubuntu) saves temp files so that they don't get automatically removed.
Hi Chris
Just like you described. The error log file:
ERROR:root:Could not perform read merging with BBmerge. Error from BBmerge was>
java -Djava.library.path=/home/qiime2/miniconda/envs/qiime2-2020.11/opt/bbma>
Executing jgi.BBMerge [in=/tmp/qiime2-archive-zd8zpdnx/8e2eaab4-8c65-44cf-abac>
Version 38.18
Set threads to 1
Exception in thread "main" java.lang.RuntimeException: Unknown parameter maxmi>
at jgi.BBMerge.(BBMerge.java:644)
at jgi.BBMerge.main(BBMerge.java:49)
Traceback (most recent call last):
File "/home/qiime2/miniconda/envs/qiime2-2020.11/lib/python3.6/site-packages>
p1.check_returncode()
File "/home/qiime2/miniconda/envs/qiime2-2020.11/lib/python3.6/subprocess.py>
self.stderr)
subprocess.CalledProcessError: Command '['bbmerge.sh', 'in=/tmp/qiime2-archive>
Traceback (most recent call last):
File "/home/qiime2/miniconda/envs/qiime2-2020.11/lib/python3.6/site-packages>
results = action(**arguments)
File "", line 2, in trim_pair_output_unmerged
File "/home/qiime2/miniconda/envs/qiime2-2020.11/lib/python3.6/site-packages>
output_types, provenance)
File "/home/qiime2/miniconda/envs/qiime2-2020.11/lib/python3.6/site-packages>
[ Read 37 lines ]
Thank you for your help.
Anything named bbtools or bbmap should be removed with conda (assuming that was how it was installed)
Run
conda remove bbmap
if present, also run
conda remove bbtools
Then reinstall the latest version of bbtools (under the package name bbmap)
conda install -c bioconda bbmap
Why this is happening:
It appears that newer versions of qiime2 are installing an older version of bbtools that is not compatible with Itsxpress. I need to test out installing Itsxpress on these newer versions and see if I can modify my bioconda manifest file in a way that is compatible with the new Qiime2 conda environment. There is a conflict with the way we specify dependencies.
Hi Dr Rivers
I tried your suggestion and this is what I got:
qiime itsxpress trim-pair-output-unmerged \
--i-per-sample-sequences demux-full.qza
--p-region ALL
--p-taxa F
--o-trimmed trimmed.qza
Traceback (most recent call last):
File "/home/qiime2/miniconda/envs/qiime2-2020.11/lib/python3.6/site-packages/q2cli/click/type.py", line 112, in _convert_input
result = qiime2.sdk.Result.load(value)
File "/home/qiime2/miniconda/envs/qiime2-2020.11/lib/python3.6/site-packages/qiime2/sdk/result.py", line 66, in load
archiver = archive.Archiver.load(filepath)
File "/home/qiime2/miniconda/envs/qiime2-2020.11/lib/python3.6/site-packages/qiime2/core/archive/archiver.py", line 307, in load
return cls(path, Format(rec))
File "/home/qiime2/miniconda/envs/qiime2-2020.11/lib/python3.6/site-packages/qiime2/core/archive/format/v1.py", line 29, in init
super().init(archive_record)
File "/home/qiime2/miniconda/envs/qiime2-2020.11/lib/python3.6/site-packages/qiime2/core/archive/format/v0.py", line 73, in init
self.format = sdk.parse_format(format)
File "/home/qiime2/miniconda/envs/qiime2-2020.11/lib/python3.6/site-packages/qiime2/sdk/util.py", line 88, in parse_format
pm = qiime2.sdk.PluginManager()
File "/home/qiime2/miniconda/envs/qiime2-2020.11/lib/python3.6/site-packages/qiime2/sdk/plugin_manager.py", line 54, in new
self._init(add_plugins=add_plugins)
File "/home/qiime2/miniconda/envs/qiime2-2020.11/lib/python3.6/site-packages/qiime2/sdk/plugin_manager.py", line 81, in _init
plugin = entry_point.load()
File "/home/qiime2/miniconda/envs/qiime2-2020.11/lib/python3.6/site-packages/pkg_resources/init.py", line 2471, in load
self.require(*args, **kwargs)
File "/home/qiime2/miniconda/envs/qiime2-2020.11/lib/python3.6/site-packages/pkg_resources/init.py", line 2494, in require
items = working_set.resolve(reqs, env, installer, extras=self.extras)
File "/home/qiime2/miniconda/envs/qiime2-2020.11/lib/python3.6/site-packages/pkg_resources/init.py", line 785, in resolve
raise DistributionNotFound(req, requirers)
pkg_resources.DistributionNotFound: The 'itsxpress>=1.8.0' distribution was not found and is required by the application
There was a problem loading demux-full.qza as a QIIME 2 Result:
The 'itsxpress>=1.8.0' distribution was not found and is required by the application
Currently, itsxpress and q2-itsxpress are two packages, that will be changing in version 2 because it is confusing. You can make sure both are installed with these commands
Thank you, Dr Rivers for your response.
I tried all your suggestions and more.
I have errors again. This is the error and the error log:
Plugin error from itsxpress:
Command '['bbmerge.sh', 'in=/tmp/qiime2-archive-svmsfmkj/8e2eaab4-8c65-44cf-abac-aa8b890c2c6d/data/101A_8_L001_R1_001.fastq.gz', 'in2=/tmp/qiime2-archive-svmsfmkj/8e2eaab4-8c65-44cf-abac-aa8b890c2c6d/data/101A_8_L001_R2_001.fastq.gz', 'out=/tmp/itsxpress_5ny3brkf/seq.fq.gz', 't=1', 'maxmismatches=40', 'maxratio=0.3']' returned non-zero exit status 1.
Error log:
GNU nano 4.8 /tmp/qiime2-q2cli-err-rat58zqb.log
ERROR:root:Could not perform read merging with BBmerge. Error from BBmerge was>
java -Djava.library.path=/home/qiime2/miniconda/envs/qiime2-2020.11/opt/bbma>
Executing jgi.BBMerge [in=/tmp/qiime2-archive-qstqyua0/8e2eaab4-8c65-44cf-abac>
Version 38.18
Set threads to 1
Exception in thread "main" java.lang.RuntimeException: Unknown parameter maxmi>
at jgi.BBMerge.(BBMerge.java:644)
at jgi.BBMerge.main(BBMerge.java:49)
Traceback (most recent call last):
File "/home/qiime2/miniconda/envs/qiime2-2020.11/lib/python3.6/site-packages>
p1.check_returncode()
File "/home/qiime2/miniconda/envs/qiime2-2020.11/lib/python3.6/subprocess.py>
self.stderr)
subprocess.CalledProcessError: Command '['bbmerge.sh', 'in=/tmp/qiime2-archive>
Traceback (most recent call last):
File "/home/qiime2/miniconda/envs/qiime2-2020.11/lib/python3.6/site-packages>
results = action(**arguments)
File "", line 2, in trim_pair_output_unmerged
File "/home/qiime2/miniconda/envs/qiime2-2020.11/lib/python3.6/site-packages>
output_types, provenance)
File "/home/qiime2/miniconda/envs/qiime2-2020.11/lib/python3.6/site-packages>
output_views = self._callable(**view_args)
File "/home/qiime2/miniconda/envs/qiime2-2020.11/lib/python3.6/site-packages>
cluster_id=cluster_id)
search tool is mighty mighty! 
