qiime itsxpress trim-pair-output-unmerged error

Hi,

I am getting error while running qiime itsxpress, should I also need to load BBmerge separately?

qiime itsxpress trim-pair-output-unmerged --i-per-sample-sequences /users/3052771/sharedscratch/Amplicon_data_july_2018/ITS_analysis/GCTU_PN0057_ITS_data/PN0057_ITS_fastq_files/ITS_REPEAT_WHOLE_ANALYSIS/sequences.qza --p-region ITS1 --p-taxa F --o-trimmed eaxct.qza
Plugin error from itsxpress:

name ‘Error’ is not defined

Debug info has been saved to /tmp/qiime2-q2cli-err-zkvoxbz7.log
[[email protected] [kelvin2] ITS_REPEAT_WHOLE_ANALYSIS]$ vi /tmp/qiime2-q2cli-err-zkvoxbz7.log

ERROR:root:BBmerge was not found, make sure BBmerge is executable
Traceback (most recent call last):
File “/opt/gridware/depots/54e7fb3c/el7/pkg/apps/qiime2/2019.1.0/bin/lib/python3.6/site-packages/q2cli/commands.py”, line 274, in call
results = action(**arguments)
File “</opt/gridware/depots/54e7fb3c/el7/pkg/apps/qiime2/2019.1.0/bin/lib/python3.6/site-packages/decorator.py:decorator-gen-268>”, line 2, in trim_pair_output_unmerged
File “/opt/gridware/depots/54e7fb3c/el7/pkg/apps/qiime2/2019.1.0/bin/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 231, in bound_callable
output_types, provenance)
File “/opt/gridware/depots/54e7fb3c/el7/pkg/apps/qiime2/2019.1.0/bin/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 365, in callable_executor
output_views = self._callable(**view_args)
File “/opt/gridware/depots/54e7fb3c/el7/pkg/apps/qiime2/2019.1.0/bin/lib/python3.6/site-packages/q2_itsxpress/_itsxpress.py”, line 242, in trim_pair_output_unmerged
cluster_id=cluster_id)
File “/opt/gridware/depots/54e7fb3c/el7/pkg/apps/qiime2/2019.1.0/bin/lib/python3.6/site-packages/q2_itsxpress/_itsxpress.py”, line 344, in main
raise Error(“Sample {} could not be processed, continuing with the next sample.”.format(sequence_id))
NameError: name ‘Error’ is not defined

Thanks
Yogesh

Hey @Yogesh_Gupta,

Looks like there are maybe two things misbehaving here:

  1. Error is probably meant to be Exception, but that’s a code problem and doesn’t actually change the situation (and not something you can fix).

  2. Your install seems to be missing some tools. Could you describe what steps you took to install the plugin? As well as what version of qiime you are running (qiime info)?

Thanks!

cc @Adam_Rivers

It looks like BBtools was not found. This most likely happened because itsxpress was not installed or it wasn’t installed with conda (Which automatically installs bbtools).

You currently have to install itsxpress with conda and q2-itsxpress (the accompanying qiime plugin) with pip. This will be simplified in future versions.

1 Like

Thanks, It was installed by admin on HPC, I need to ask them I did they installed it.

Thanks
Yogesh

thanks, installation issue is fixed but now getting other error: do I need to remove some of the samples?

ERROR:root:Could not perform read merging with BBmerge. Error from BBmerge was:
java -ea -Xmx1000m -Xms1000m -Djava.library.path=/opt/gridware/depots/54e7fb3c/el7/pkg/apps/qiime2/2019.4.0/bin/opt/bbmap-38.56-0/jni/ -cp /opt/gridware/depots/54e7fb3c/el7/pkg/apps/qiime2/2019.4.0/bin/opt/bbmap-38.56-0/current/ jgi.BBMerge in=/tmp/qiime2-archive-67lzi528/8ba6909f-a1b2-4398-885c-107e85161adf/data/Root-10_S55_L001_108_L001_R1_001.fastq.gz in2=/tmp/qiime2-archive-67lzi528/8ba6909f-a1b2-4398-885c-107e85161adf/data/Root-10_S55_L001_109_L001_R2_001.fastq.gz out=/tmp/itsxpress_8xh55ays/seq.fq.gz t=1
Error: could not find libjava.so
Error: Could not find Java SE Runtime Environment.
Traceback (most recent call last):
File “/opt/gridware/depots/54e7fb3c/el7/pkg/apps/qiime2/2019.4.0/bin/lib/python3.6/site-packages/itsxpress/main.py”, line 657, in _merge_reads
p1.check_returncode()
File “/opt/gridware/depots/54e7fb3c/el7/pkg/apps/qiime2/2019.4.0/bin/lib/python3.6/subprocess.py”, line 369, in check_returncode
self.stderr)
subprocess.CalledProcessError: Command ‘[‘bbmerge.sh’, ‘in=/tmp/qiime2-archive-67lzi528/8ba6909f-a1b2-4398-885c-107e85161adf/data/Root-10_S55_L001_108_L001_R1_001.fastq.gz’, ‘in2=/tmp/qiime2-archive-67lzi528/8ba6909f-a1b2-4398-885c-107e85161adf/data/Root-10_S55_L001_109_L001_R2_001.fastq.gz’, ‘out=/tmp/itsxpress_8xh55ays/seq.fq.gz’, ‘t=1’]’ returned non-zero exit status 2.
Traceback (most recent call last):

Hi @Yogesh_Gupta,

It looks like your system administrator is not using conda to install these. You should indicate to your sysadmin that you need a JRE where QIIME 2 is installed (openJDK should be fine) and to double check that these dependencies work as indicated by the conda recipe:

If it’s possible, you might also ask for a user-controllable install of conda, then you could manage the installation (which is very straight-forward as long as it stays in conda). Then you should be able to avoid these situations.

Hi,

error in ITSxpress run:

ERROR:root:Could not perform read merging with BBmerge. Error from BBmerge was:
  java -ea -Xmx1000m -Xms1000m -Djava.library.path=/opt/gridware/depots/54e7fb3c/el7/pkg/apps/qiime2/2019.4.0/bin/opt/bbmap-38.56-0/jni/ -cp /opt/gridware/depots/54e7fb3c/el7/pkg/apps/qiime2/2019.4.0/bin/opt/bbmap-38.56-0/current/ jgi.BBMerge in=/tmp/qiime2-archive-xb0m72nj/24dec6f1-c541-42b1-ace6-2743697e2031/data/Root-11_S65_L001_108_L001_R1_001.fastq.gz in2=/tmp/qiime2-archive-xb0m72nj/24dec6f1-c541-42b1-ace6-2743697e2031/data/Root-11_S65_L001_109_L001_R2_001.fastq.gz out=/tmp/itsxpress_5y41d1m8/seq.fq.gz t=1
Error: could not find libjava.so
Error: Could not find Java SE Runtime Environment.
Traceback (most recent call last):
  File "/opt/gridware/depots/54e7fb3c/el7/pkg/apps/qiime2/2019.4.0/bin/lib/python3.6/site-packages/itsxpress/main.py", line 657, in _merge_reads
    p1.check_returncode()
  File "/opt/gridware/depots/54e7fb3c/el7/pkg/apps/qiime2/2019.4.0/bin/lib/python3.6/subprocess.py", line 369, in check_returncode
    self.stderr)
subprocess.CalledProcessError: Command '['bbmerge.sh', 'in=/tmp/qiime2-archive-xb0m72nj/24dec6f1-c541-42b1-ace6-2743697e2031/data/Root-11_S65_L001_108_L001_R1_001.fastq.gz', 'in2=/tmp/qiime2-archive-xb0m72nj/24dec6f1-c541-42b1-ace6-2743697e2031/data/Root-11_S65_L001_109_L001_R2_001.fastq.gz', 'out=/tmp/itsxpress_5y41d1m8/seq.fq.gz', 't=1']' returned non-zero exit status 2.
Traceback (most recent call last):

qiime info

qiime info

System versions

Python version: 3.6.7

QIIME 2 release: 2019.4

QIIME 2 version: 2019.4.0

q2cli version: 2019.4.0

Installed plugins

alignment: 2019.4.0

composition: 2019.4.0

cutadapt: 2019.4.0

dada2: 2019.4.0

deblur: 2019.4.0

demux: 2019.4.1

diversity: 2019.4.0

emperor: 2019.4.0

feature-classifier: 2019.4.0

feature-table: 2019.4.0

fragment-insertion: 2019.4.0

gneiss: 2019.4.0

itsxpress: 1.7.4

longitudinal: 2019.4.0

metadata: 2019.4.0

phylogeny: 2019.4.0

quality-control: 2019.4.0

quality-filter: 2019.4.0

sample-classifier: 2019.4.0

taxa: 2019.4.0

types: 2019.4.1

vsearch: 2019.4.0

Application config directory

/users/3052771/.config/q2cli

Thanks
Yogesh

Hello Yogesh,

Looks like this is the same error. Show this to your system administrator and have them install Java.

Colin

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