OBITools3 issueshttps://git.metabarcoding.org/obitools/obitools3/-/issues2019-01-07T10:14:30Zhttps://git.metabarcoding.org/obitools/obitools3/-/issues/2The path in the Doxygen configuration file must be relative2019-01-07T10:14:30ZEric CoissacThe path in the Doxygen configuration file must be relativeIn the doxyfile you must indicate the path as relative to the doc directory and I think move the Doxyfile to the doc directory. Then yo will be able to run doxygen from the Makefile of the doc directory for building the XML doxygen file. In the doxyfile you must indicate the path as relative to the doc directory and I think move the Doxyfile to the doc directory. Then yo will be able to run doxygen from the Makefile of the doc directory for building the XML doxygen file. SpecificationsEric CoissacEric Coissachttps://git.metabarcoding.org/obitools/obitools3/-/issues/9openat function problem2018-08-17T01:28:21ZCeline Mercieropenat function problemWhen I compile, I get warnings:
```
_env/include -I/Library/Frameworks/Python.framework/Versions/3.4/include/python3.4m -c src/obidmscolumn.c -o build/temp.macosx-10.6-intel-3.4/src/obidmscolumn.o -msse2 -Wno-unused-function
src/obidmscolumn.c:172:14: warning: implicit declaration of function 'openat' is invalid in C99 [-Wimplicit-function-declaration]
versionfd = openat(directoryfd, versionfile, O_RDWR);
^
1 warning generated.
src/obidmscolumn.c:172:14: warning: implicit declaration of function 'openat' is invalid in C99 [-Wimplicit-function-declaration]
versionfd = openat(directoryfd, versionfile, O_RDWR);
^
1 warning generated.
```
And when I try to import the class in ipython I get an error:
```
In [1]: from obitools3.obidms.obidmscolumn.capidmscolumn import OBIDMS_column
---------------------------------------------------------------------------
ImportError Traceback (most recent call last)
<ipython-input-1-2ec07f270a2d> in <module>()
----> 1 from obitools3.obidms.obidmscolumn.capidmscolumn import OBIDMS_column
ImportError: dlopen(/Users/celinemercier/Documents/workspace/OBITools3/obitools3_env/lib/python3.4/site-packages/obitools3/obidms/obidmscolumn/capidmscolumn.so, 2): Symbol not found: _openat
Referenced from: /Users/celinemercier/Documents/workspace/OBITools3/obitools3_env/lib/python3.4/site-packages/obitools3/obidms/obidmscolumn/capidmscolumn.so
Expected in: flat namespace
in /Users/celinemercier/Documents/workspace/OBITools3/obitools3_env/lib/python3.4/site-packages/obitools3/obidms/obidmscolumn/capidmscolumn.so
```When I compile, I get warnings:
```
_env/include -I/Library/Frameworks/Python.framework/Versions/3.4/include/python3.4m -c src/obidmscolumn.c -o build/temp.macosx-10.6-intel-3.4/src/obidmscolumn.o -msse2 -Wno-unused-function
src/obidmscolumn.c:172:14: warning: implicit declaration of function 'openat' is invalid in C99 [-Wimplicit-function-declaration]
versionfd = openat(directoryfd, versionfile, O_RDWR);
^
1 warning generated.
src/obidmscolumn.c:172:14: warning: implicit declaration of function 'openat' is invalid in C99 [-Wimplicit-function-declaration]
versionfd = openat(directoryfd, versionfile, O_RDWR);
^
1 warning generated.
```
And when I try to import the class in ipython I get an error:
```
In [1]: from obitools3.obidms.obidmscolumn.capidmscolumn import OBIDMS_column
---------------------------------------------------------------------------
ImportError Traceback (most recent call last)
<ipython-input-1-2ec07f270a2d> in <module>()
----> 1 from obitools3.obidms.obidmscolumn.capidmscolumn import OBIDMS_column
ImportError: dlopen(/Users/celinemercier/Documents/workspace/OBITools3/obitools3_env/lib/python3.4/site-packages/obitools3/obidms/obidmscolumn/capidmscolumn.so, 2): Symbol not found: _openat
Referenced from: /Users/celinemercier/Documents/workspace/OBITools3/obitools3_env/lib/python3.4/site-packages/obitools3/obidms/obidmscolumn/capidmscolumn.so
Expected in: flat namespace
in /Users/celinemercier/Documents/workspace/OBITools3/obitools3_env/lib/python3.4/site-packages/obitools3/obidms/obidmscolumn/capidmscolumn.so
```https://git.metabarcoding.org/obitools/obitools3/-/issues/11distutils2018-08-17T01:28:21ZCeline MercierdistutilsThe new distutils don't work for me, I get the error:
```
Look for CPU architecture... [('LITTLE_END', None)]
error: [Errno 2] No such file or directory: 'doc/sphinx/build_dir.txt'
```The new distutils don't work for me, I get the error:
```
Look for CPU architecture... [('LITTLE_END', None)]
error: [Errno 2] No such file or directory: 'doc/sphinx/build_dir.txt'
```Eric CoissacEric Coissachttps://git.metabarcoding.org/obitools/obitools3/-/issues/40Installation problems on linux systems2019-04-10T15:32:54ZCeline MercierInstallation problems on linux systems**On leca-34**:
Running into this error at compilation:
```
build/temp.linux-x86_64-3.4/pyrex/obitools3/apps/progress.c: In function ‘__pyx_pf_9obitools3_4apps_8progress_11ProgressBar_2__call__’:
build/temp.linux-x86_64-3.4/pyrex/obitools3/apps/progress.c:1727:9: error: format not a string literal and no format arguments [-Werror=format-security]
((void)fprintf(stderr, __pyx_k__5));
^
cc1: some warnings being treated as errors
error: command 'x86_64-linux-gnu-gcc' failed with exit status 1
```
**On luke21** (ALL RESOLVED NOW but writing here to keep track):
1. The inline functions were not read properly and had to turn them into macros.
2. Then, when trying to run an obi command, ran into this error:
```
obi import --fastq -d 'tdms' -v 'Import big fastq' '150529_SND405_A_L004_GWM-656.filtered.fastq'
Traceback (most recent call last):
File "/scratch_r730/home/cmercier/devel/obitools3/OBITools3-0.00.0/bin/obi", line 29, in <module>
from obitools3.apps.config import getConfiguration # @UnresolvedImport
File "python/obitools3/apps/config.pyx", line 16, in init obitools3.apps.config (build/temp.linux-x86_64-3.5/pyrex/obitools3/apps/config.c:2477)
from _curses import version
ImportError: libncurses.so.5: cannot open shared object file: No such file or directory
```
Fixed with this import:
`module load ncurses/5.9_gcc-4.6.2`
3. Then had to add all C files in all *.cfiles Cython files.**On leca-34**:
Running into this error at compilation:
```
build/temp.linux-x86_64-3.4/pyrex/obitools3/apps/progress.c: In function ‘__pyx_pf_9obitools3_4apps_8progress_11ProgressBar_2__call__’:
build/temp.linux-x86_64-3.4/pyrex/obitools3/apps/progress.c:1727:9: error: format not a string literal and no format arguments [-Werror=format-security]
((void)fprintf(stderr, __pyx_k__5));
^
cc1: some warnings being treated as errors
error: command 'x86_64-linux-gnu-gcc' failed with exit status 1
```
**On luke21** (ALL RESOLVED NOW but writing here to keep track):
1. The inline functions were not read properly and had to turn them into macros.
2. Then, when trying to run an obi command, ran into this error:
```
obi import --fastq -d 'tdms' -v 'Import big fastq' '150529_SND405_A_L004_GWM-656.filtered.fastq'
Traceback (most recent call last):
File "/scratch_r730/home/cmercier/devel/obitools3/OBITools3-0.00.0/bin/obi", line 29, in <module>
from obitools3.apps.config import getConfiguration # @UnresolvedImport
File "python/obitools3/apps/config.pyx", line 16, in init obitools3.apps.config (build/temp.linux-x86_64-3.5/pyrex/obitools3/apps/config.c:2477)
from _curses import version
ImportError: libncurses.so.5: cannot open shared object file: No such file or directory
```
Fixed with this import:
`module load ncurses/5.9_gcc-4.6.2`
3. Then had to add all C files in all *.cfiles Cython files.https://git.metabarcoding.org/obitools/obitools3/-/issues/47Handling of view name uniqueness2017-11-03T03:14:45ZCeline MercierHandling of view name uniquenessWhen creating a view, the uniqueness of the view name is checked by going through the views stored in the view file of the DMS, but if a view with the same name has been created but not written in the view file yet, it is not detected. How do we handle this?When creating a view, the uniqueness of the view name is checked by going through the views stored in the view file of the DMS, but if a view with the same name has been created but not written in the view file yet, it is not detected. How do we handle this?https://git.metabarcoding.org/obitools/obitools3/-/issues/49Bug during a second import2017-11-03T03:14:45ZEric CoissacBug during a second importI wanted to try the new obitools and started with obi import using the two fastq files from the wolf tutorial.
The first trial :
```{shell}
obi import -d wolf -v forward --fastq wolf_F.fastq
```
was ok but the second one
```{shell}
obi import -d wolf -v reverse --fastq wolf_R.fastq
```
produced this nice error :
```{shell}
DEBUG src/obiavl.c:2196:obi_avl_group_add, obi_errno = 20, errno = 0 :
Trying to add a value in an AVL group that is read-only.
Traceback (most recent call last):
File "/Users/coissac/git/obitools3/OBITools3-0.00.0/bin/obi", line 47, in <module>
config[root_config_name]['module'].run(config)
File "python/obitools3/commands/import.pyx", line 120, in obitools3.commands.import.run (build/temp.macosx-10.6-intel-3.5/pyrex/obitools3/commands/import.c:2050)
File "python/obitools3/obidms/_obiseq.pyx", line 50, in obitools3.obidms._obiseq.OBI_Nuc_Seq_Stored.set_id (build/temp.macosx-10.6-intel-3.5/pyrex/obitools3/obidms/_obiseq.c:2367)
File "python/obitools3/obidms/_obiseq.pyx", line 51, in obitools3.obidms._obiseq.OBI_Nuc_Seq_Stored.set_id (build/temp.macosx-10.6-intel-3.5/pyrex/obitools3/obidms/_obiseq.c:2309)
File "python/obitools3/obidms/_obidms.pyx", line 567, in obitools3.obidms._obidms.OBIView_line.__setitem__ (build/temp.macosx-10.6-intel-3.5/pyrex/obitools3/obidms/_obidms.c:10386)
File "python/obitools3/obidms/_obidmscolumn_str.pyx", line 30, in obitools3.obidms._obidmscolumn_str.OBIDMS_column_str.set_line (build/temp.macosx-10.6-intel-3.5/pyrex/obitools3/obidms/_obidmscolumn_str.c:1599)
File "python/obitools3/obidms/_obidmscolumn_str.pyx", line 37, in obitools3.obidms._obidmscolumn_str.OBIDMS_column_str.set_line (build/temp.macosx-10.6-intel-3.5/pyrex/obitools3/obidms/_obidmscolumn_str.c:1491)
Exception: Problem setting a value in a column
```I wanted to try the new obitools and started with obi import using the two fastq files from the wolf tutorial.
The first trial :
```{shell}
obi import -d wolf -v forward --fastq wolf_F.fastq
```
was ok but the second one
```{shell}
obi import -d wolf -v reverse --fastq wolf_R.fastq
```
produced this nice error :
```{shell}
DEBUG src/obiavl.c:2196:obi_avl_group_add, obi_errno = 20, errno = 0 :
Trying to add a value in an AVL group that is read-only.
Traceback (most recent call last):
File "/Users/coissac/git/obitools3/OBITools3-0.00.0/bin/obi", line 47, in <module>
config[root_config_name]['module'].run(config)
File "python/obitools3/commands/import.pyx", line 120, in obitools3.commands.import.run (build/temp.macosx-10.6-intel-3.5/pyrex/obitools3/commands/import.c:2050)
File "python/obitools3/obidms/_obiseq.pyx", line 50, in obitools3.obidms._obiseq.OBI_Nuc_Seq_Stored.set_id (build/temp.macosx-10.6-intel-3.5/pyrex/obitools3/obidms/_obiseq.c:2367)
File "python/obitools3/obidms/_obiseq.pyx", line 51, in obitools3.obidms._obiseq.OBI_Nuc_Seq_Stored.set_id (build/temp.macosx-10.6-intel-3.5/pyrex/obitools3/obidms/_obiseq.c:2309)
File "python/obitools3/obidms/_obidms.pyx", line 567, in obitools3.obidms._obidms.OBIView_line.__setitem__ (build/temp.macosx-10.6-intel-3.5/pyrex/obitools3/obidms/_obidms.c:10386)
File "python/obitools3/obidms/_obidmscolumn_str.pyx", line 30, in obitools3.obidms._obidmscolumn_str.OBIDMS_column_str.set_line (build/temp.macosx-10.6-intel-3.5/pyrex/obitools3/obidms/_obidmscolumn_str.c:1599)
File "python/obitools3/obidms/_obidmscolumn_str.pyx", line 37, in obitools3.obidms._obidmscolumn_str.OBIDMS_column_str.set_line (build/temp.macosx-10.6-intel-3.5/pyrex/obitools3/obidms/_obidmscolumn_str.c:1491)
Exception: Problem setting a value in a column
```https://git.metabarcoding.org/obitools/obitools3/-/issues/52Obi import bug: last sequence of fasta files2017-11-03T03:14:45ZCeline MercierObi import bug: last sequence of fasta filesThe last sequence of fasta files is ignored and not imported with the obi import command (fastq works fine).The last sequence of fasta files is ignored and not imported with the obi import command (fastq works fine).https://git.metabarcoding.org/obitools/obitools3/-/issues/54Bug when opening an uncompressed file2017-11-03T03:14:45ZEric CoissacBug when opening an uncompressed fileThe four first characters are lostThe four first characters are losthttps://git.metabarcoding.org/obitools/obitools3/-/issues/56Bug ProgressBar2017-11-03T03:14:45ZCeline MercierBug ProgressBar```
Traceback (most recent call last):
File "/Users/celinemercier/Documents/workspace/OBITools3/OBITools3-0.00.0/bin/obi", line 49, in <module>
config[root_config_name]['module'].run(config)
File "python/obitools3/commands/import.pyx", line 93, in obitools3.commands.import.run (build/temp.macosx-10.6-intel-3.5/pyrex/obitools3/commands/import.c:1761)
pb = ProgressBar(35000000, config, seconde=5)
File "python/obitools3/apps/progress.pyx", line 48, in obitools3.apps.progress.ProgressBar.__init__ (build/temp.macosx-10.6-intel-3.5/pyrex/obitools3/apps/progress.c:1214)
self._head = str2bytes(head)
AttributeError: 'obitools3.apps.progress.ProgressBar' object has no attribute '_head'
``````
Traceback (most recent call last):
File "/Users/celinemercier/Documents/workspace/OBITools3/OBITools3-0.00.0/bin/obi", line 49, in <module>
config[root_config_name]['module'].run(config)
File "python/obitools3/commands/import.pyx", line 93, in obitools3.commands.import.run (build/temp.macosx-10.6-intel-3.5/pyrex/obitools3/commands/import.c:1761)
pb = ProgressBar(35000000, config, seconde=5)
File "python/obitools3/apps/progress.pyx", line 48, in obitools3.apps.progress.ProgressBar.__init__ (build/temp.macosx-10.6-intel-3.5/pyrex/obitools3/apps/progress.c:1214)
self._head = str2bytes(head)
AttributeError: 'obitools3.apps.progress.ProgressBar' object has no attribute '_head'
```Eric CoissacEric Coissachttps://git.metabarcoding.org/obitools/obitools3/-/issues/63DMS compatibility between OSX and Ubuntu (Linux?)2019-09-25T12:57:46ZCeline MercierDMS compatibility between OSX and Ubuntu (Linux?)There is an error when reading a DMS imported from an OSX system on Ubuntu. Needs further testing.There is an error when reading a DMS imported from an OSX system on Ubuntu. Needs further testing.Celine MercierCeline Mercierhttps://git.metabarcoding.org/obitools/obitools3/-/issues/66obi uniq re-merge merged informations2019-08-27T18:27:21ZCeline Mercierobi uniq re-merge merged informationsThere is a known issue in the OBItools 1 when using obiuniq on sequences already containing merged tags. Since I re-used a lot of the code, make sure everything works as intended.There is a known issue in the OBItools 1 when using obiuniq on sequences already containing merged tags. Since I re-used a lot of the code, make sure everything works as intended.Celine MercierCeline Mercierhttps://git.metabarcoding.org/obitools/obitools3/-/issues/77Memory bug2020-05-30T14:55:40ZCeline MercierMemory bugThere is a memory bug... somewhere. It's hard to trigger, so if you run into it I'm interested.There is a memory bug... somewhere. It's hard to trigger, so if you run into it I'm interested.Celine MercierCeline Mercierhttps://git.metabarcoding.org/obitools/obitools3/-/issues/88Crash in obi less2021-02-10T04:29:28ZEric CoissacCrash in obi lessDoing the wolf tutorial, I tried to do an `obi less` on the ngsfilter table.
It crashes nicely ;-)
```bash
obi less wolf/ngsfile
Traceback (most recent call last):
File "/usr/local/bin/obi", line 4, in <module>
__import__('pkg_resources').run_script('OBITools3==3.0.0b39', 'obi')
File "/Users/coissac/src/obitools3-hpc/obi3-env/lib/python3.9/site-packages/pkg_resources/__init__.py", line 665, in run_script
self.require(requires)[0].run_script(script_name, ns)
File "/Users/coissac/src/obitools3-hpc/obi3-env/lib/python3.9/site-packages/pkg_resources/__init__.py", line 1463, in run_script
exec(code, namespace, namespace)
File "/Users/coissac/src/obitools3-hpc/obi3-env/lib/python3.9/site-packages/OBITools3-3.0.0b39-py3.9-macosx-10.9-x86_64.egg/EGG-INFO/scripts/obi", line 62, in <module>
config[root_config_name]['module'].run(config)
File "python/obitools3/commands/less.pyx", line 39, in obitools3.commands.less.run
MacBook-Pro-2:Tromso-2021 coissac$ Traceback (most recent call last):
File "/usr/local/bin/obi", line 4, in <module>
__import__('pkg_resources').run_script('OBITools3==3.0.0b39', 'obi')
File "/Users/coissac/src/obitools3-hpc/obi3-env/lib/python3.9/site-packages/pkg_resources/__init__.py", line 665, in run_script
self.require(requires)[0].run_script(script_name, ns)
File "/Users/coissac/src/obitools3-hpc/obi3-env/lib/python3.9/site-packages/pkg_resources/__init__.py", line 1463, in run_script
```Doing the wolf tutorial, I tried to do an `obi less` on the ngsfilter table.
It crashes nicely ;-)
```bash
obi less wolf/ngsfile
Traceback (most recent call last):
File "/usr/local/bin/obi", line 4, in <module>
__import__('pkg_resources').run_script('OBITools3==3.0.0b39', 'obi')
File "/Users/coissac/src/obitools3-hpc/obi3-env/lib/python3.9/site-packages/pkg_resources/__init__.py", line 665, in run_script
self.require(requires)[0].run_script(script_name, ns)
File "/Users/coissac/src/obitools3-hpc/obi3-env/lib/python3.9/site-packages/pkg_resources/__init__.py", line 1463, in run_script
exec(code, namespace, namespace)
File "/Users/coissac/src/obitools3-hpc/obi3-env/lib/python3.9/site-packages/OBITools3-3.0.0b39-py3.9-macosx-10.9-x86_64.egg/EGG-INFO/scripts/obi", line 62, in <module>
config[root_config_name]['module'].run(config)
File "python/obitools3/commands/less.pyx", line 39, in obitools3.commands.less.run
MacBook-Pro-2:Tromso-2021 coissac$ Traceback (most recent call last):
File "/usr/local/bin/obi", line 4, in <module>
__import__('pkg_resources').run_script('OBITools3==3.0.0b39', 'obi')
File "/Users/coissac/src/obitools3-hpc/obi3-env/lib/python3.9/site-packages/pkg_resources/__init__.py", line 665, in run_script
self.require(requires)[0].run_script(script_name, ns)
File "/Users/coissac/src/obitools3-hpc/obi3-env/lib/python3.9/site-packages/pkg_resources/__init__.py", line 1463, in run_script
```https://git.metabarcoding.org/obitools/obitools3/-/issues/89Crash when path includes non-ascii letters...2021-12-07T13:51:16ZEric CoissacCrash when path includes non-ascii letters...If you import a sequence file into the DMS and the absolute path of that file includes a non ascii character, then the import crash at the end (after the actual sequence import).If you import a sequence file into the DMS and the absolute path of that file includes a non ascii character, then the import crash at the end (after the actual sequence import).https://git.metabarcoding.org/obitools/obitools3/-/issues/91Problem of quoting quotes when reporting obi commands including quotes in the...2021-02-11T10:59:08ZEric CoissacProblem of quoting quotes when reporting obi commands including quotes in the historyWhen you run a command like that one that includes quotes and double quotes
```bash
obi grep -p "len(sequence)>=80 and sequence['COUNT']>=10" \
wolf/cleaned_metadata_sequences \
wolf/denoised_sequences
```
The history is reporting it like that :
```bash
obi grep -p len(sequence)>=80 and sequence['COUNT']>=10 wolf/cleaned_metadata_sequences wolf/denoised_sequences
```
The previous command is not following a correct Unix syntax because the double quotes have been lost.
It induces also error in the generated dot file if you use the -d option of the obi history command.When you run a command like that one that includes quotes and double quotes
```bash
obi grep -p "len(sequence)>=80 and sequence['COUNT']>=10" \
wolf/cleaned_metadata_sequences \
wolf/denoised_sequences
```
The history is reporting it like that :
```bash
obi grep -p len(sequence)>=80 and sequence['COUNT']>=10 wolf/cleaned_metadata_sequences wolf/denoised_sequences
```
The previous command is not following a correct Unix syntax because the double quotes have been lost.
It induces also error in the generated dot file if you use the -d option of the obi history command.https://git.metabarcoding.org/obitools/obitools3/-/issues/101escape character in option value2021-04-06T22:54:56ZCeline Mercierescape character in option valueWhen parsing e.g. `--sep '\t'`, the option manager reads the option value as two characters '\'+'t' instead of as the tab character '\t'.
I implemented a dirty workaround that only works for '\t', so I would like to find a real solution for all characters with a backslash/escape character.When parsing e.g. `--sep '\t'`, the option manager reads the option value as two characters '\'+'t' instead of as the tab character '\t'.
I implemented a dirty workaround that only works for '\t', so I would like to find a real solution for all characters with a backslash/escape character.https://git.metabarcoding.org/obitools/obitools3/-/issues/105Error when a folder has the same path and name as a DMS2021-04-15T20:17:57ZCeline MercierError when a folder has the same path and name as a DMSIf a folder has the same path and name as a DMS (root name of the DMS), the URI is not properly decoded because the program tries to follow the path inside the folder.
The URI decoding algorithm should be able to recognize that a DMS also matches, and go with what works best (opening of a view, or of a DMS).If a folder has the same path and name as a DMS (root name of the DMS), the URI is not properly decoded because the program tries to follow the path inside the folder.
The URI decoding algorithm should be able to recognize that a DMS also matches, and go with what works best (opening of a view, or of a DMS).Celine MercierCeline Mercierhttps://git.metabarcoding.org/obitools/obitools3/-/issues/114obi ls not managing properly views with complicated names2021-09-07T22:55:40ZFrédéric Boyerobi ls not managing properly views with complicated namesSee the following sequences of two commands:
```
$obi grep -p 'sequence["error"]=="No reverse primer match"' WCH-80.3tag2/NOTFILTERED WCH-80.3tag2/NOTFILTERED.NOREVERSEPRIMERMATCH
2021-08-04 10:26:57,551 [grep : INFO ] obi grep
100.0 % |##################################################|] remain : 00:00:00
2021-08-04 10:27:07,277 [grep : INFO ] Grepped 1297012 entries
2021-08-04 10:27:29,126 [grep : INFO ] Done.
$ obi ls WCH-80.3tag2
2021-08-04 10:27:40,664 [ls : INFO ] obi ls
# DMS name: WCH-80.3tag2
# Views:
# AMPLICON: Date created: Tue Jul 20 02:06:02 2021 ; Line count: 6230849
# FILTERED: Date created: Tue Jul 20 02:25:53 2021 ; Line count: 1695966
# FORWARD: Date created: Tue Jul 20 01:45:54 2021 ; Line count: 6230849
# NGSFILTER: Date created: Tue Jul 20 02:25:52 2021 ; Line count: 38400
# NOTFILTERED: Date created: Tue Jul 20 02:25:53 2021 ; Line count: 4534883
# NOTFILTERED: Date created: Tue Jul 20 02:25:53 2021 ; Line count: 4534883
# REVERSE: Date created: Tue Jul 20 01:56:00 2021 ; Line count: 6230849
# Taxonomies:
```
the View `NOTFILTERED` is listed twice whereas the view `NOTFILTERED.NOREVERSEPRIMERMATCH` is not listed.
Nevertheless, the view `NOTFILTERED.NOREVERSEPRIMERMATCH` can be individually checked with `obi ls`
```
$obi ls WCH-80.3tag2/NOTFILTERED.NOREVERSEPRIMERMATCH
2021-08-04 10:31:42,608 [ls : INFO ] obi ls
# View name:
NOTFILTERED.NOREVERSEPRIMERMATCH
# Date created:
Wed Aug 4 10:27:07 2021
# Line count:
1297012
# Columns:
NUC_SEQ, data type: OBI_SEQ
ID, data type: OBI_STR
DEFINITION, data type: OBI_STR
QUALITY, data type: OBI_QUAL
seq_length, data type: OBI_INT
overlap_length, data type: OBI_INT
score_norm, data type: OBI_FLOAT
shift, data type: OBI_INT
ali_direction, data type: OBI_STR
score, data type: OBI_FLOAT
mode, data type: OBI_STR
COUNT, data type: OBI_INT
avg_quality, data type: OBI_FLOAT
head_quality, data type: OBI_FLOAT
mid_quality, data type: OBI_FLOAT
tail_quality, data type: OBI_FLOAT
seq_length_ori, data type: OBI_INT
direction, data type: OBI_STR
reverse_errors, data type: OBI_INT
reverse_primer, data type: OBI_SEQ
reverse_match, data type: OBI_SEQ
error, data type: OBI_STR
forward_errors, data type: OBI_INT
forward_primer, data type: OBI_SEQ
forward_match, data type: OBI_SEQ
status, data type: OBI_STR
forward_tag, data type: OBI_SEQ
reverse_tag, data type: OBI_SEQ
reversed, data type: OBI_BOOL
pairedend_limit, data type: OBI_INT
```
See the following sequences of two commands:
```
$obi grep -p 'sequence["error"]=="No reverse primer match"' WCH-80.3tag2/NOTFILTERED WCH-80.3tag2/NOTFILTERED.NOREVERSEPRIMERMATCH
2021-08-04 10:26:57,551 [grep : INFO ] obi grep
100.0 % |##################################################|] remain : 00:00:00
2021-08-04 10:27:07,277 [grep : INFO ] Grepped 1297012 entries
2021-08-04 10:27:29,126 [grep : INFO ] Done.
$ obi ls WCH-80.3tag2
2021-08-04 10:27:40,664 [ls : INFO ] obi ls
# DMS name: WCH-80.3tag2
# Views:
# AMPLICON: Date created: Tue Jul 20 02:06:02 2021 ; Line count: 6230849
# FILTERED: Date created: Tue Jul 20 02:25:53 2021 ; Line count: 1695966
# FORWARD: Date created: Tue Jul 20 01:45:54 2021 ; Line count: 6230849
# NGSFILTER: Date created: Tue Jul 20 02:25:52 2021 ; Line count: 38400
# NOTFILTERED: Date created: Tue Jul 20 02:25:53 2021 ; Line count: 4534883
# NOTFILTERED: Date created: Tue Jul 20 02:25:53 2021 ; Line count: 4534883
# REVERSE: Date created: Tue Jul 20 01:56:00 2021 ; Line count: 6230849
# Taxonomies:
```
the View `NOTFILTERED` is listed twice whereas the view `NOTFILTERED.NOREVERSEPRIMERMATCH` is not listed.
Nevertheless, the view `NOTFILTERED.NOREVERSEPRIMERMATCH` can be individually checked with `obi ls`
```
$obi ls WCH-80.3tag2/NOTFILTERED.NOREVERSEPRIMERMATCH
2021-08-04 10:31:42,608 [ls : INFO ] obi ls
# View name:
NOTFILTERED.NOREVERSEPRIMERMATCH
# Date created:
Wed Aug 4 10:27:07 2021
# Line count:
1297012
# Columns:
NUC_SEQ, data type: OBI_SEQ
ID, data type: OBI_STR
DEFINITION, data type: OBI_STR
QUALITY, data type: OBI_QUAL
seq_length, data type: OBI_INT
overlap_length, data type: OBI_INT
score_norm, data type: OBI_FLOAT
shift, data type: OBI_INT
ali_direction, data type: OBI_STR
score, data type: OBI_FLOAT
mode, data type: OBI_STR
COUNT, data type: OBI_INT
avg_quality, data type: OBI_FLOAT
head_quality, data type: OBI_FLOAT
mid_quality, data type: OBI_FLOAT
tail_quality, data type: OBI_FLOAT
seq_length_ori, data type: OBI_INT
direction, data type: OBI_STR
reverse_errors, data type: OBI_INT
reverse_primer, data type: OBI_SEQ
reverse_match, data type: OBI_SEQ
error, data type: OBI_STR
forward_errors, data type: OBI_INT
forward_primer, data type: OBI_SEQ
forward_match, data type: OBI_SEQ
status, data type: OBI_STR
forward_tag, data type: OBI_SEQ
reverse_tag, data type: OBI_SEQ
reversed, data type: OBI_BOOL
pairedend_limit, data type: OBI_INT
```