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allind / EukDetect

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Unable to Install eukdetect #35

Closed marynjerey closed 1 year ago

marynjerey commented 1 year ago

(eukdetect) [mchege@crcfe01 tests]$ python test_eukdetect.py .FFF.

FAIL: test_class (main._02_RunRunall)

Traceback (most recent call last): File "test_eukdetect.py", line 26, in test_class self.assertTrue(code==0, msg=stderr) AssertionError: False is not true : b'01/20/2023 14:54:14: Parsing config file ...\nTraceback (most recent call last):\n File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/bin/eukdetect", line 33, in \n sys.exit(load_entry_point(\'EukDetect==1.0.1\', \'console_scripts\', \'eukdetect\')())\n File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/EukDetect-1.0.1-py3.6.egg/eukdetect/runall.py", line 88, in main\nFileNotFoundError: [Errno 2] No such file or directory: \'tests/configfile_for_tests.yml\'\n'

====================================================================== FAIL: test_class (main._03_RunAlnCmd)

Traceback (most recent call last): File "test_eukdetect.py", line 33, in test_class self.assertTrue(code ==0, msg=stderr) AssertionError: False is not true : b'01/20/2023 14:54:14: Parsing config file ...\nTraceback (most recent call last):\n File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/bin/eukdetect", line 33, in \n sys.exit(load_entry_point(\'EukDetect==1.0.1\', \'console_scripts\', \'eukdetect\')())\n File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/EukDetect-1.0.1-py3.6.egg/eukdetect/runall.py", line 88, in main\nFileNotFoundError: [Errno 2] No such file or directory: \'tests/configfile_for_tests.yml\'\n'

====================================================================== FAIL: test_class (main._04_RunAln_and_filter)

Traceback (most recent call last): File "test_eukdetect.py", line 44, in test_class self.assertTrue(alncode==0 and filtercode == 0, msg=alnstderr + filterstderr) AssertionError: False is not true : b'01/20/2023 14:54:14: Parsing config file ...\nTraceback (most recent call last):\n File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/bin/eukdetect", line 33, in \n sys.exit(load_entry_point(\'EukDetect==1.0.1\', \'console_scripts\', \'eukdetect\')())\n File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/EukDetect-1.0.1-py3.6.egg/eukdetect/runall.py", line 88, in main\nFileNotFoundError: [Errno 2] No such file or directory: \'tests/configfile_for_tests.yml\'\n01/20/2023 14:54:14: Parsing config file ...\nTraceback (most recent call last):\n File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/bin/eukdetect", line 33, in \n sys.exit(load_entry_point(\'EukDetect==1.0.1\', \'console_scripts\', \'eukdetect\')())\n File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/EukDetect-1.0.1-py3.6.egg/eukdetect/runall.py", line 88, in main\nFileNotFoundError: [Errno 2] No such file or directory: \'tests/configfile_for_tests.yml\'\n'

Ran 5 tests in 2.852s

FAILED (failures=3) (eukdetect) [mchege@crcfe01 tests]$

allind commented 1 year ago

Thanks for reaching out. The error you're getting is that there isn't a file in the 'tests' directory named 'configfile_for_tests.yml'. This is included in the eukdetect repo so should be present unless you've moved or renamed it. Can you check it's still there (and that you've edited it to add the directory where you've put the database)?

marynjerey commented 1 year ago

Hey Allind, I am still getting an error with my installation: (eukdetect) [mchege@crcfe01 EukDetect]$ ls build dist eukdb EukDetect.egg-info LICENSE rules tests default_configfile.yml environment.yml eukdetect eukdetect_pipeline_schematic.pdf README.md setup.py (eukdetect) [mchege@crcfe01 EukDetect]$ cd tests/ (eukdetect) [mchege@crcfe01 tests]$ nano configfile_for_tests.yml (eukdetect) [mchege@crcfe01 tests]$ cd .. (eukdetect) [mchege@crcfe01 EukDetect]$ python tests/test_eukdetect.py .FFF.

FAIL: test_class (main._02_RunRunall)

Traceback (most recent call last): File "tests/test_eukdetect.py", line 26, in test_class self.assertTrue(code==0, msg=stderr) AssertionError: False is not true : b'01/25/2023 02:42:33: Parsing config file ...\nTraceback (most recent call last):\n File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/bin/eukdetect", line 33, in \n sys.exit(load_entry_point(\'EukDetect==1.0.1\', \'console_scripts\', \'eukdetect\')())\n File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/EukDetect-1.0.1-py3.6.egg/eukdetect/runall.py", line 89, in main\n File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/yaml/init.py", line 114, in load\n return loader.get_single_data()\n File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/yaml/constructor.py", line 49, in get_single_data\n node = self.get_single_node()\n File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/yaml/composer.py", line 39, in get_single_node\n if not self.check_event(StreamEndEvent):\n File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/yaml/parser.py", line 98, in check_event\n self.current_event = self.state()\n File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/yaml/parser.py", line 174, in parse_document_start\n self.peek_token().start_mark)\nyaml.parser.ParserError: expected \'\', but found \'\'\n in "tests/configfile_for_tests.yml", line 6, column 1\n'

====================================================================== FAIL: test_class (main._03_RunAlnCmd)

Traceback (most recent call last): File "tests/test_eukdetect.py", line 33, in test_class self.assertTrue(code ==0, msg=stderr) AssertionError: False is not true : b'01/25/2023 02:42:33: Parsing config file ...\nTraceback (most recent call last):\n File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/bin/eukdetect", line 33, in \n sys.exit(load_entry_point(\'EukDetect==1.0.1\', \'console_scripts\', \'eukdetect\')())\n File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/EukDetect-1.0.1-py3.6.egg/eukdetect/runall.py", line 89, in main\n File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/yaml/init.py", line 114, in load\n return loader.get_single_data()\n File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/yaml/constructor.py", line 49, in get_single_data\n node = self.get_single_node()\n File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/yaml/composer.py", line 39, in get_single_node\n if not self.check_event(StreamEndEvent):\n File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/yaml/parser.py", line 98, in check_event\n self.current_event = self.state()\n File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/yaml/parser.py", line 174, in parse_document_start\n self.peek_token().start_mark)\nyaml.parser.ParserError: expected \'\', but found \'\'\n in "tests/configfile_for_tests.yml", line 6, column 1\n'

====================================================================== FAIL: test_class (main._04_RunAln_and_filter)

Traceback (most recent call last): File "tests/test_eukdetect.py", line 44, in test_class self.assertTrue(alncode==0 and filtercode == 0, msg=alnstderr + filterstderr) AssertionError: False is not true : b'01/25/2023 02:42:34: Parsing config file ...\nTraceback (most recent call last):\n File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/bin/eukdetect", line 33, in \n sys.exit(load_entry_point(\'EukDetect==1.0.1\', \'console_scripts\', \'eukdetect\')())\n File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/EukDetect-1.0.1-py3.6.egg/eukdetect/runall.py", line 89, in main\n File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/yaml/init.py", line 114, in load\n return loader.get_single_data()\n File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/yaml/constructor.py", line 49, in get_single_data\n node = self.get_single_node()\n File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/yaml/composer.py", line 39, in get_single_node\n if not self.check_event(StreamEndEvent):\n File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/yaml/parser.py", line 98, in check_event\n self.current_event = self.state()\n File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/yaml/parser.py", line 174, in parse_document_start\n self.peek_token().start_mark)\nyaml.parser.ParserError: expected \'\', but found \'\'\n in "tests/configfile_for_tests.yml", line 6, column 1\n01/25/2023 02:42:34: Parsing config file ...\nTraceback (most recent call last):\n File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/bin/eukdetect", line 33, in \n sys.exit(load_entry_point(\'EukDetect==1.0.1\', \'console_scripts\', \'eukdetect\')())\n File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/EukDetect-1.0.1-py3.6.egg/eukdetect/runall.py", line 89, in main\n File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/yaml/init.py", line 114, in load\n return loader.get_single_data()\n File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/yaml/constructor.py", line 49, in get_single_data\n node = self.get_single_node()\n File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/yaml/composer.py", line 39, in get_single_node\n if not self.check_event(StreamEndEvent):\n File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/yaml/parser.py", line 98, in check_event\n self.current_event = self.state()\n File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/yaml/parser.py", line 174, in parse_document_start\n self.peek_token().start_mark)\nyaml.parser.ParserError: expected \'\', but found \'\'\n in "tests/configfile_for_tests.yml", line 6, column 1\n'

Ran 5 tests in 1.197s

FAILED (failures=3) (eukdetect) [mchege@crcfe01 EukDetect]$ cd tests/ (eukdetect) [mchege@crcfe01 tests]$ nano configfile_for_tests.yml (eukdetect) [mchege@crcfe01 tests]$ cd .. (eukdetect) [mchege@crcfe01 EukDetect]$ python tests/test_eukdetect.py .FFF.

FAIL: test_class (main._02_RunRunall)

Traceback (most recent call last): File "tests/test_eukdetect.py", line 26, in test_class self.assertTrue(code==0, msg=stderr) AssertionError: False is not true : b'01/25/2023 02:47:21: Parsing config file ...\nTraceback (most recent call last):\n File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/bin/eukdetect", line 33, in \n sys.exit(load_entry_point(\'EukDetect==1.0.1\', \'console_scripts\', \'eukdetect\')())\n File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/EukDetect-1.0.1-py3.6.egg/eukdetect/runall.py", line 89, in main\n File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/yaml/init.py", line 114, in load\n return loader.get_single_data()\n File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/yaml/constructor.py", line 49, in get_single_data\n node = self.get_single_node()\n File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/yaml/composer.py", line 39, in get_single_node\n if not self.check_event(StreamEndEvent):\n File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/yaml/parser.py", line 98, in check_event\n self.current_event = self.state()\n File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/yaml/parser.py", line 174, in parse_document_start\n self.peek_token().start_mark)\nyaml.parser.ParserError: expected \'\', but found \'\'\n in "tests/configfile_for_tests.yml", line 6, column 1\n'

====================================================================== FAIL: test_class (main._03_RunAlnCmd)

Traceback (most recent call last): File "tests/test_eukdetect.py", line 33, in test_class self.assertTrue(code ==0, msg=stderr) AssertionError: False is not true : b'01/25/2023 02:47:21: Parsing config file ...\nTraceback (most recent call last):\n File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/bin/eukdetect", line 33, in \n sys.exit(load_entry_point(\'EukDetect==1.0.1\', \'console_scripts\', \'eukdetect\')())\n File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/EukDetect-1.0.1-py3.6.egg/eukdetect/runall.py", line 89, in main\n File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/yaml/init.py", line 114, in load\n return loader.get_single_data()\n File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/yaml/constructor.py", line 49, in get_single_data\n node = self.get_single_node()\n File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/yaml/composer.py", line 39, in get_single_node\n if not self.check_event(StreamEndEvent):\n File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/yaml/parser.py", line 98, in check_event\n self.current_event = self.state()\n File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/yaml/parser.py", line 174, in parse_document_start\n self.peek_token().start_mark)\nyaml.parser.ParserError: expected \'\', but found \'\'\n in "tests/configfile_for_tests.yml", line 6, column 1\n'

====================================================================== FAIL: test_class (main._04_RunAln_and_filter)

Traceback (most recent call last): File "tests/test_eukdetect.py", line 44, in test_class self.assertTrue(alncode==0 and filtercode == 0, msg=alnstderr + filterstderr) AssertionError: False is not true : b'01/25/2023 02:47:21: Parsing config file ...\nTraceback (most recent call last):\n File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/bin/eukdetect", line 33, in \n sys.exit(load_entry_point(\'EukDetect==1.0.1\', \'console_scripts\', \'eukdetect\')())\n File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/EukDetect-1.0.1-py3.6.egg/eukdetect/runall.py", line 89, in main\n File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/yaml/init.py", line 114, in load\n return loader.get_single_data()\n File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/yaml/constructor.py", line 49, in get_single_data\n node = self.get_single_node()\n File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/yaml/composer.py", line 39, in get_single_node\n if not self.check_event(StreamEndEvent):\n File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/yaml/parser.py", line 98, in check_event\n self.current_event = self.state()\n File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/yaml/parser.py", line 174, in parse_document_start\n self.peek_token().start_mark)\nyaml.parser.ParserError: expected \'\', but found \'\'\n in "tests/configfile_for_tests.yml", line 6, column 1\n01/25/2023 02:47:21: Parsing config file ...\nTraceback (most recent call last):\n File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/bin/eukdetect", line 33, in \n sys.exit(load_entry_point(\'EukDetect==1.0.1\', \'console_scripts\', \'eukdetect\')())\n File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/EukDetect-1.0.1-py3.6.egg/eukdetect/runall.py", line 89, in main\n File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/yaml/init.py", line 114, in load\n return loader.get_single_data()\n File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/yaml/constructor.py", line 49, in get_single_data\n node = self.get_single_node()\n File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/yaml/composer.py", line 39, in get_single_node\n if not self.check_event(StreamEndEvent):\n File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/yaml/parser.py", line 98, in check_event\n self.current_event = self.state()\n File "/afs/crc.nd.edu/user/m/mchege/.conda/envs/eukdetect/lib/python3.6/site-packages/yaml/parser.py", line 174, in parse_document_start\n self.peek_token().start_mark)\nyaml.parser.ParserError: expected \'\', but found \'\'\n in "tests/configfile_for_tests.yml", line 6, column 1\n'

Ran 5 tests in 1.077s

FAILED (failures=3) (eukdetect) [mchege@crcfe01 EukDetect]$ ls build dist eukdb EukDetect.egg-info LICENSE rules tests default_configfile.yml environment.yml eukdetect eukdetect_pipeline_schematic.pdf README.md setup.py (eukdetect) [mchege@crcfe01 EukDetect]$ cd eukdb (eukdetect) [mchege@crcfe01 eukdb]$ ls busco_taxid_link.txt ncbi_eukprot_met_arch_markers.fna.3.bt2 taxa.sqlite marker_genes_per_species.csv ncbi_eukprot_met_arch_markers.fna.4.bt2 taxa.sqlite.traverse.pkl ncbi_eukprot_met_arch_markers.fna ncbi_eukprot_met_arch_markers.fna.rev.1.bt2 taxdump_1_14_2020.tar.gz ncbi_eukprot_met_arch_markers.fna.1.bt2 ncbi_eukprot_met_arch_markers.fna.rev.2.bt2 ncbi_eukprot_met_arch_markers.fna.2.bt2 specific_and_inherited_markers_per_taxid.txt (eukdetect) [mchege@crcfe01 eukdb]$ cd .. (eukdetect) [mchege@crcfe01 EukDetect]$ cd tests/ (eukdetect) [mchege@crcfe01 tests]$ ls configfile_for_tests.yml test_eukdetect.py test_R1.fastq.gz test_R2.fastq.gz (eukdetect) [mchege@crcfe01 tests]$ nano configfile_for_tests.yml (eukdetect) [mchege@crcfe01 tests]$ ls configfile_for_tests.yml test_eukdetect.py test_R1.fastq.gz test_R2.fastq.gz

marynjerey commented 1 year ago

EukDetect_Troubleshoot.txt

marynjerey commented 1 year ago

(base) [mchege@crcfe01 eukdb]$ cd .. (base) [mchege@crcfe01 EukDetect]$ conda activate eukdetect (eukdetect) [mchege@crcfe01 EukDetect]$ ls build dist eukdb EukDetect.egg-info LICENSE rules tests default_configfile.yml environment.yml eukdetect eukdetect_pipeline_schematic.pdf README.md setup.py (eukdetect) [mchege@crcfe01 EukDetect]$ pwd /afs/crc.nd.edu/group/ArchieLab/Mary/EukDetect (eukdetect) [mchege@crcfe01 EukDetect]$ cd tests/ (eukdetect) [mchege@crcfe01 tests]$ ls configfile_for_tests.yml test_eukdetect.py test_R1.fastq.gz test_R2.fastq.gz (eukdetect) [mchege@crcfe01 tests]$ nano configfile_for_tests.yml (eukdetect) [mchege@crcfe01 tests]$ cd .. (eukdetect) [mchege@crcfe01 EukDetect]$ python tests/test_eukdetect.py .....

Ran 5 tests in 61.068s

OK

marynjerey commented 1 year ago

Hey Allind, It has finally worked and onto the next steps !!

marynjerey commented 1 year ago

Hey Allind/Eukdetect,

I am kindly getting this when I run my samples. what could be the problem?

Empty read count file. Likely no aligned reads in the sample. SRR1747042_filtered_hits_eukfrac.txt (END)

Kind regards,

On Wed, Jan 25, 2023 at 12:35 AM Abigail Lind @.***> wrote:

Thanks for reaching out. The error you're getting is that there isn't a file in the 'tests' directory named 'configfile_for_tests.yml'. This is included in the eukdetect repo so should be present unless you've moved or renamed it. Can you check it's still there (and that you've edited it to add the directory where you've put the database)?

— Reply to this email directly, view it on GitHub https://github.com/allind/EukDetect/issues/35#issuecomment-1402717249, or unsubscribe https://github.com/notifications/unsubscribe-auth/AUPGWQBRVNBKJPSMRWDBRJTWUBDI5ANCNFSM6AAAAAAUB56EVI . You are receiving this because you authored the thread.Message ID: @.***>

-- Mary Chege (MSc. Bioinformatics and Molecular biology )

One Health Centre, Institute of Primate Research, Karen, Nairobi.

allind commented 1 year ago

Hi Mary, thanks for your patience. That's not an error message - that means that there were no detected eukaryotic reads in your sequencing.

marynjerey commented 1 year ago

Awesome, thanks!

On Wed, Feb 8, 2023 at 12:58 AM Abigail Lind @.***> wrote:

Hi Mary, thanks for your patience. That's not an error message - that means that there were no detected eukaryotic reads in your sequencing.

— Reply to this email directly, view it on GitHub https://github.com/allind/EukDetect/issues/35#issuecomment-1421514117, or unsubscribe https://github.com/notifications/unsubscribe-auth/AUPGWQD3X65CKYIDVDGV23LWWLAPXANCNFSM6AAAAAAUB56EVI . You are receiving this because you modified the open/close state.Message ID: @.***>

-- Mary Chege (MSc. Bioinformatics and Molecular biology )

One Health Centre, Institute of Primate Research, Karen, Nairobi.

marynjerey commented 1 year ago

Hey Abigail,

I hope that you are well.

I just finished running my samples on the pipeline, out of the 48 samples (about 1.4 billion reads), only 14 samples aligned with about 1 taxon in each sample. The rest of the samples either indicated "No taxa passing filter requirement" and the rest indicated "Empty reads". I couldn't understand these considering it is a high read depth.

I have checked on the pre-filtering intermediate files, and I can see that some samples that ticked for "No taxa passing filter requirement", have a reasonable number of hits, yet they did not pass for alignment.

Kindly advise me on this.

Kind regards,

On Wed, Feb 8, 2023 at 11:01 AM Mary Chege @.***> wrote:

Awesome, thanks!

On Wed, Feb 8, 2023 at 12:58 AM Abigail Lind @.***> wrote:

Hi Mary, thanks for your patience. That's not an error message - that means that there were no detected eukaryotic reads in your sequencing.

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-- Mary Chege (MSc. Bioinformatics and Molecular biology )

One Health Centre, Institute of Primate Research, Karen, Nairobi.

-- Mary Chege (MSc. Bioinformatics and Molecular biology )

One Health Centre, Institute of Primate Research, Karen, Nairobi.

allind commented 1 year ago

Hi Mary,

Would you be open to sharing all of the output from eukdetect with me? I can look through everything and see if there might be something going on. You can compress the folder and email it to me at abigail.lind@gladstone.ucsf.edu.

Best, Abigail