Itsxpress bbmerge error

I tried running the itsxpress plugin using a conda install in qiime 2020.6, and received the error pasted below. I then tried downloading and running the dataset from the tutorial page, and received the same error. Looking at this error message, I suspect the problem is that the function bbmerge has been updated, causing a parameter name to be changed from “maxmismatches” to “mismatches.” Has anyone else had this problem? Is it possible this plugin needs to be updated to match the current bbmerge function?
Thanks!
Tori

export PATH=/miniconda3/bin:$PATH
source activate qiime2-2020.6
qiime itsxpress trim-pair-output-unmerged
–i-per-sample-sequences apple_demux_ITS.qza
–p-region ITS2
–p-taxa F
–o-trimmed apple_demux_ITS_trim.qza
–verbose

ERROR:root:Could not perform read merging with BBmerge. Error from BBmerge was:
java -Djava.library.path=/miniconda3/envs/qiime2-2020.6/opt/bbmap-38.18/jni/ -ea -Xmx1000m -Xms1000m -cp /miniconda3/envs/qiime2-2020.6/opt/bbmap-38.18/current/ jgi.BBMerge in=/tmp/qiime2-archive-j59v3jb4/cd8af088-d77f-4da7-bb0e-f36452a4546a/data/S1_0_L001_R1_001.fastq.gz in2=/tmp/qiime2-archive-j59v3jb4/cd8af088-d77f-4da7-bb0e-f36452a4546a/data/S1_1_L001_R2_001.fastq.gz out=/tmp/itsxpress_chq9fald/seq.fq.gz t=1 maxmismatches=40 maxratio=0.3
Executing jgi.BBMerge [in=/tmp/qiime2-archive-j59v3jb4/cd8af088-d77f-4da7-bb0e-f36452a4546a/data/S1_0_L001_R1_001.fastq.gz, in2=/tmp/qiime2-archive-j59v3jb4/cd8af088-d77f-4da7-bb0e-f36452a4546a/data/S1_1_L001_R2_001.fastq.gz, out=/tmp/itsxpress_chq9fald/seq.fq.gz, t=1, maxmismatches=40, maxratio=0.3]
Version 38.18

Set threads to 1
Exception in thread “main” java.lang.RuntimeException: Unknown parameter maxmismatches=40
at jgi.BBMerge.(BBMerge.java:644)
at jgi.BBMerge.main(BBMerge.java:49)
Traceback (most recent call last):
File “/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/itsxpress/main.py”, line 650, in _merge_reads
p1.check_returncode()
File “/miniconda3/envs/qiime2-2020.6/lib/python3.6/subprocess.py”, line 389, in check_returncode
self.stderr)
subprocess.CalledProcessError: Command ‘[‘bbmerge.sh’, ‘in=/tmp/qiime2-archive-j59v3jb4/cd8af088-d77f-4da7-bb0e-f36452a4546a/data/S1_0_L001_R1_001.fastq.gz’, ‘in2=/tmp/qiime2-archive-j59v3jb4/cd8af088-d77f-4da7-bb0e-f36452a4546a/data/S1_1_L001_R2_001.fastq.gz’, ‘out=/tmp/itsxpress_chq9fald/seq.fq.gz’, ‘t=1’, ‘maxmismatches=40’, ‘maxratio=0.3’]’ returned non-zero exit status 1.
Traceback (most recent call last):
File “/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/q2cli/commands.py”, line 329, in call
results = action(**arguments)
File “”, line 2, in trim_pair_output_unmerged
File “/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 245, in bound_callable
output_types, provenance)
File “/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 390, in callable_executor
output_views = self._callable(**view_args)
File “/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/q2_itsxpress/_itsxpress.py”, line 158, in trim_pair_output_unmerged
cluster_id=cluster_id)
File “/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/q2_itsxpress/_itsxpress.py”, line 203, in main
threads=threads)
File “/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/q2_itsxpress/_itsxpress.py”, line 83, in _set_fastqs_and_check
sobj._merge_reads(threads=threads)
File “/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/itsxpress/main.py”, line 654, in _merge_reads
raise e
File “/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/itsxpress/main.py”, line 650, in _merge_reads
p1.check_returncode()
File “/miniconda3/envs/qiime2-2020.6/lib/python3.6/subprocess.py”, line 389, in check_returncode
self.stderr)
subprocess.CalledProcessError: Command ‘[‘bbmerge.sh’, ‘in=/tmp/qiime2-archive-j59v3jb4/cd8af088-d77f-4da7-bb0e-f36452a4546a/data/S1_0_L001_R1_001.fastq.gz’, ‘in2=/tmp/qiime2-archive-j59v3jb4/cd8af088-d77f-4da7-bb0e-f36452a4546a/data/S1_1_L001_R2_001.fastq.gz’, ‘out=/tmp/itsxpress_chq9fald/seq.fq.gz’, ‘t=1’, ‘maxmismatches=40’, ‘maxratio=0.3’]’ returned non-zero exit status 1.

Plugin error from itsxpress:

Command ‘[‘bbmerge.sh’, ‘in=/tmp/qiime2-archive-j59v3jb4/cd8af088-d77f-4da7-bb0e-f36452a4546a/data/S1_0_L001_R1_001.fastq.gz’, ‘in2=/tmp/qiime2-archive-j59v3jb4/cd8af088-d77f-4da7-bb0e-f36452a4546a/data/S1_1_L001_R2_001.fastq.gz’, ‘out=/tmp/itsxpress_chq9fald/seq.fq.gz’, ‘t=1’, ‘maxmismatches=40’, ‘maxratio=0.3’]’ returned non-zero exit status 1.

Hi @Tori,
Thanks for your patience… I am not the developer of q2-itsxpress so cannot debug, but let’s see if @Adam_Rivers (the developer) has some advice for you.

:mushroom:

Sorry, just saw this. you need to upgrade bbtools to a newer version in the conda environment you are running. Anything <=38.23 should work.

2 Likes

Hi Adam_Rivers, I have the same problem that Tori and I can’t figure out how to upgrade bbtools in the conda environment. I downloaded the 38.86 version of bbmap and then I installed it, but the plugin seems to only try to work with the older version… Some clue??

Thanks in advance,

David

I would guess that itsxpress and q2-itsxpress are not installed in the same conda environment as qiime2. If you are in the qiime2 environment and conda doesn’t find the executable there it will look for it other places and those other places may have access to a different version of bbtools. Running conda list from within the qiime2 environment` may help you see what is available.

Thanks for getting back to me! My version of bbmap is 38.18. I tried using the command “conda update bbmap”, and it only updated to 38.22, which still did not work for itsxpress. Do you have any suggestions for installing the most recent version? (Also I ran the “conda list” command, and both itsxpress and q2-itsxpress are installed correctly for me).

Same as the last Tori’s comment.

I guess that the problem could be solved (but I do not know how to do it) if the q2-itsxpress plugin would access to an updated repository than bioconda/noarch::bbmap-38.18-0. Am I right?