Certainly! I just ran the humann_test --run-functional-tests-end-to-end command to see if I could run end-to-end tests.
I encountered some errors during my first attempt, beginning with:
ERROR: The MetaPhlAn taxonomic profile provided does not contain the database version vOct22_CHOCOPhlAnSGB_202403 in any of its header lines.
ERROR
After doing some research, I returned to MetaPhlAn’s mapping arguments:
$ metaphlan --help
usage: metaphlan --input_type {fastq,fasta,bowtie2out,sam} [--force] [--bowtie2db METAPHLAN_BOWTIE2_DB] [-x INDEX] [--bt2_ps BowTie2 presets] [--bowtie2_exe BOWTIE2_EXE] [--bowtie2_build BOWTIE2_BUILD]
[--bowtie2out FILE_NAME] [--min_mapq_val MIN_MAPQ_VAL] [--no_map] [--tmp_dir] [--tax_lev TAXONOMIC_LEVEL] [--min_cu_len] [--min_alignment_len] [--add_viruses] [--ignore_eukaryotes]
[--ignore_bacteria] [--ignore_archaea] [--ignore_ksgbs] [--ignore_usgbs] [--stat_q] [--perc_nonzero] [--ignore_markers IGNORE_MARKERS] [--avoid_disqm] [--stat] [-t ANALYSIS TYPE]
[--nreads NUMBER_OF_READS] [--pres_th PRESENCE_THRESHOLD] [--clade] [--min_ab] [--profile_vsc] [--vsc_out VSC_OUT] [--vsc_breadth VSC_BREADTH] [-o output file] [--sample_id_key name]
[--use_group_representative] [--sample_id value] [-s sam_output_file] [--legacy-output] [--CAMI_format_output] [--unclassified_estimation] [--mpa3] [--biom biom_output] [--mdelim mdelim]
[--nproc N] [--subsampling SUBSAMPLING] [--subsampling_output SUBSAMPLING_OUTPUT] [--subsampling_paired SUBSAMPLING_PAIRED] [-1 FORWARD_READS] [-2 REVERSE_READS] [--mapping_subsampling]
[--subsampling_seed SUBSAMPLING_SEED] [--install] [--offline] [--force_download] [--read_min_len READ_MIN_LEN] [-v] [-h]
[INPUT_FILE] [OUTPUT_FILE]
[...]
Mapping arguments:
[...]
--bowtie2db METAPHLAN_BOWTIE2_DB
Folder containing the MetaPhlAn database. You can specify the location by exporting the DEFAULT_DB_FOLDER variable in the shell.[default *****/.pixi/envs/default/lib/python3.12/site-packages/metaphlan/metaphlan_databases]
I defined the DEFAULT_DB_FOLDER environment variable to point to that data/databases/metaphlan/vOct22_CHOCOPhlAnSGB_202403/ location (I use its absolute path instead of the relative path shown here).
However, that didn’t fix the errors:
$ DEFAULT_DB_FOLDER=<ABSOLUTE_PATH>/data/databases/metaphlan/vOct22_CHOCOPhlAnSGB_202403/ ; humann_test --run-functional-tests-end-to-end
Please note running functional end to end tests requires all dependencies of HUMAnN.
test_calculate_percent_identity (basic_tests_nucleotide_search.TestBasicHumannNucleotideSearchFunctions.test_calculate_percent_identity)
Test the calculate percent identity function ... ok
[... output omitted for brevity ...]
test_humann_fasta (functional_tests_humann.TestFunctionalHumannEndtoEnd.test_humann_fasta)
Test the standard humann flow on a fasta input file ...
Testing command:
humann --input *****/envs/default/lib/python3.12/site-packages/humann/tests/data/demo.fasta --output /tmp/humann_test_gdwdsxho_fasta --nucleotide-database *****/envs/default/lib/python3.12/site-packages/humann/tests/../data/chocophlan_DEMO --protein-database *****/envs/default/lib/python3.12/site-packages/humann/tests/../data/uniref_DEMO
Output files will be written to: /tmp/humann_test_gdwdsxho_fasta
Running metaphlan ........
ERROR: The MetaPhlAn taxonomic profile provided does not contain the database version vOct22_CHOCOPhlAnSGB_202403 in any of its header lines.
ERROR
[... output omitted for brevity ...]
test_humann_fasta_bypass_translated_search (functional_tests_humann.TestFunctionalHumannEndtoEnd.test_humann_fasta_bypass_translated_search)
Test the standard humann flow on a fasta input file ...
Testing command:
humann --input *****/envs/default/lib/python3.12/site-packages/humann/tests/data/demo.fasta --output /tmp/humann_test_l4uz9dj1_fasta_bypass_translated_search --bypass-translated-search --nucleotide-database *****/envs/default/lib/python3.12/site-packages/humann/tests/../data/chocophlan_DEMO --protein-database *****/envs/default/lib/python3.12/site-packages/humann/tests/../data/uniref_DEMO
Output files will be written to: /tmp/humann_test_l4uz9dj1_fasta_bypass_translated_search
Running metaphlan ........
ERROR: The MetaPhlAn taxonomic profile provided does not contain the database version vOct22_CHOCOPhlAnSGB_202403 in any of its header lines.
ERROR
test_humann_fastq (functional_tests_humann.TestFunctionalHumannEndtoEnd.test_humann_fastq)
Test the standard humann flow on a fastq input file ...
Testing command:
humann --input *****/envs/default/lib/python3.12/site-packages/humann/tests/data/demo.fastq --output /tmp/humann_test_9pjawlwt_fastq --nucleotide-database *****/envs/default/lib/python3.12/site-packages/humann/tests/../data/chocophlan_DEMO --protein-database *****/envs/default/lib/python3.12/site-packages/humann/tests/../data/uniref_DEMO
Output files will be written to: /tmp/humann_test_9pjawlwt_fastq
Running metaphlan ........
ERROR: The MetaPhlAn taxonomic profile provided does not contain the database version vOct22_CHOCOPhlAnSGB_202403 in any of its header lines.
ERROR
[... output omitted for brevity ...]
test_humann_fastq_bypass_translated_search (functional_tests_humann.TestFunctionalHumannEndtoEnd.test_humann_fastq_bypass_translated_search)
Test the standard humann flow on a fastq input file ...
Testing command:
humann --input *****/envs/default/lib/python3.12/site-packages/humann/tests/data/demo.fastq --output /tmp/humann_test_t121b3t3_fastq_bypass_translated_search --bypass-translated-search --nucleotide-database *****/envs/default/lib/python3.12/site-packages/humann/tests/../data/chocophlan_DEMO --protein-database *****/envs/default/lib/python3.12/site-packages/humann/tests/../data/uniref_DEMO
Output files will be written to: /tmp/humann_test_t121b3t3_fastq_bypass_translated_search
Running metaphlan ........
ERROR: The MetaPhlAn taxonomic profile provided does not contain the database version vOct22_CHOCOPhlAnSGB_202403 in any of its header lines.
ERROR
test_humann_fastq_custom_taxonomic_profile (functional_tests_humann.TestFunctionalHumannEndtoEnd.test_humann_fastq_custom_taxonomic_profile)
Test the standard humann flow on a fastq input file ...
Testing command:
humann --input *****/envs/default/lib/python3.12/site-packages/humann/tests/data/demo.fastq --output /tmp/humann_test_cciaavqf_fastq_custom_taxonomic_profile --taxonomic-profile *****/envs/default/lib/python3.12/site-packages/humann/tests/data/demo_metaphlan_bugs_list.tsv --nucleotide-database *****/envs/default/lib/python3.12/site-packages/humann/tests/../data/chocophlan_DEMO --protein-database *****/envs/default/lib/python3.12/site-packages/humann/tests/../data/uniref_DEMO
Output files will be written to: /tmp/humann_test_cciaavqf_fastq_custom_taxonomic_profile
ERROR: The MetaPhlAn taxonomic profile provided does not contain the database version vOct22_CHOCOPhlAnSGB_202403 in any of its header lines.
ERROR
[... output omitted for brevity ...]
test_humann_fastq_biom_output (functional_tests_biom_humann.TestFunctionalHumannEndtoEndBiom.test_humann_fastq_biom_output)
Test the standard humann flow on a fastq input file ...
Testing command:
humann --input *****/envs/default/lib/python3.12/site-packages/humann/tests/data/demo.fastq --output /tmp/humann_test_6zf3z75c_fastq --output-format biom --nucleotide-database *****/envs/default/lib/python3.12/site-packages/humann/tests/../data/chocophlan_DEMO --protein-database *****/envs/default/lib/python3.12/site-packages/humann/tests/../data/uniref_DEMO
Output files will be written to: /tmp/humann_test_6zf3z75c_fastq
Running metaphlan ........
ERROR: The MetaPhlAn taxonomic profile provided does not contain the database version vOct22_CHOCOPhlAnSGB_202403 in any of its header lines.
ERROR
[... output omitted for brevity ...]
======================================================================
ERROR: test_humann_fasta (functional_tests_humann.TestFunctionalHumannEndtoEnd.test_humann_fasta)
Test the standard humann flow on a fasta input file
----------------------------------------------------------------------
Traceback (most recent call last):
File "*****/envs/default/lib/python3.12/site-packages/humann/tests/utils.py", line 59, in run_command
subprocess.check_call(command)
File "*****/envs/default/lib/python3.12/subprocess.py", line 413, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['humann', '--input', '*****/envs/default/lib/python3.12/site-packages/humann/tests/data/demo.fasta', '--output', '/tmp/humann_test_gdwdsxho_fasta', '--nucleotide-database', '*****/envs/default/lib/python3.12/site-packages/humann/tests/../data/chocophlan_DEMO', '--protein-database', '*****/envs/default/lib/python3.12/site-packages/humann/tests/../data/uniref_DEMO']' returned non-zero exit status 1.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "*****/envs/default/lib/python3.12/site-packages/humann/tests/functional_tests_humann.py", line 45, in test_humann_fasta
utils.run_humann(command)
File "*****/envs/default/lib/python3.12/site-packages/humann/tests/utils.py", line 50, in run_humann
run_command(command)
File "*****/envs/default/lib/python3.12/site-packages/humann/tests/utils.py", line 61, in run_command
raise EnvironmentError("Warning: Unable to execute command in test.\n"+" ".join(command))
OSError: Warning: Unable to execute command in test.
humann --input *****/envs/default/lib/python3.12/site-packages/humann/tests/data/demo.fasta --output /tmp/humann_test_gdwdsxho_fasta --nucleotide-database *****/envs/default/lib/python3.12/site-packages/humann/tests/../data/chocophlan_DEMO --protein-database *****/envs/default/lib/python3.12/site-packages/humann/tests/../data/uniref_DEMO
======================================================================
ERROR: test_humann_fasta_bypass_translated_search (functional_tests_humann.TestFunctionalHumannEndtoEnd.test_humann_fasta_bypass_translated_search)
Test the standard humann flow on a fasta input file
----------------------------------------------------------------------
Traceback (most recent call last):
File "*****/envs/default/lib/python3.12/site-packages/humann/tests/utils.py", line 59, in run_command
subprocess.check_call(command)
File "*****/envs/default/lib/python3.12/subprocess.py", line 413, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['humann', '--input', '*****/envs/default/lib/python3.12/site-packages/humann/tests/data/demo.fasta', '--output', '/tmp/humann_test_l4uz9dj1_fasta_bypass_translated_search', '--bypass-translated-search', '--nucleotide-database', '*****/envs/default/lib/python3.12/site-packages/humann/tests/../data/chocophlan_DEMO', '--protein-database', '*****/envs/default/lib/python3.12/site-packages/humann/tests/../data/uniref_DEMO']' returned non-zero exit status 1.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "*****/envs/default/lib/python3.12/site-packages/humann/tests/functional_tests_humann.py", line 182, in test_humann_fasta_bypass_translated_search
utils.run_humann(command)
File "*****/envs/default/lib/python3.12/site-packages/humann/tests/utils.py", line 50, in run_humann
run_command(command)
File "*****/envs/default/lib/python3.12/site-packages/humann/tests/utils.py", line 61, in run_command
raise EnvironmentError("Warning: Unable to execute command in test.\n"+" ".join(command))
OSError: Warning: Unable to execute command in test.
humann --input *****/envs/default/lib/python3.12/site-packages/humann/tests/data/demo.fasta --output /tmp/humann_test_l4uz9dj1_fasta_bypass_translated_search --bypass-translated-search --nucleotide-database *****/envs/default/lib/python3.12/site-packages/humann/tests/../data/chocophlan_DEMO --protein-database *****/envs/default/lib/python3.12/site-packages/humann/tests/../data/uniref_DEMO
======================================================================
ERROR: test_humann_fastq (functional_tests_humann.TestFunctionalHumannEndtoEnd.test_humann_fastq)
Test the standard humann flow on a fastq input file
----------------------------------------------------------------------
Traceback (most recent call last):
File "*****/envs/default/lib/python3.12/site-packages/humann/tests/utils.py", line 59, in run_command
subprocess.check_call(command)
File "*****/envs/default/lib/python3.12/subprocess.py", line 413, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['humann', '--input', '*****/envs/default/lib/python3.12/site-packages/humann/tests/data/demo.fastq', '--output', '/tmp/humann_test_9pjawlwt_fastq', '--nucleotide-database', '*****/envs/default/lib/python3.12/site-packages/humann/tests/../data/chocophlan_DEMO', '--protein-database', '*****/envs/default/lib/python3.12/site-packages/humann/tests/../data/uniref_DEMO']' returned non-zero exit status 1.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "*****/envs/default/lib/python3.12/site-packages/humann/tests/functional_tests_humann.py", line 26, in test_humann_fastq
utils.run_humann(command)
File "*****/envs/default/lib/python3.12/site-packages/humann/tests/utils.py", line 50, in run_humann
run_command(command)
File "*****/envs/default/lib/python3.12/site-packages/humann/tests/utils.py", line 61, in run_command
raise EnvironmentError("Warning: Unable to execute command in test.\n"+" ".join(command))
OSError: Warning: Unable to execute command in test.
humann --input *****/envs/default/lib/python3.12/site-packages/humann/tests/data/demo.fastq --output /tmp/humann_test_9pjawlwt_fastq --nucleotide-database *****/envs/default/lib/python3.12/site-packages/humann/tests/../data/chocophlan_DEMO --protein-database *****/envs/default/lib/python3.12/site-packages/humann/tests/../data/uniref_DEMO
======================================================================
ERROR: test_humann_fastq_bypass_translated_search (functional_tests_humann.TestFunctionalHumannEndtoEnd.test_humann_fastq_bypass_translated_search)
Test the standard humann flow on a fastq input file
----------------------------------------------------------------------
Traceback (most recent call last):
File "*****/envs/default/lib/python3.12/site-packages/humann/tests/utils.py", line 59, in run_command
subprocess.check_call(command)
File "*****/envs/default/lib/python3.12/subprocess.py", line 413, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['humann', '--input', '*****/envs/default/lib/python3.12/site-packages/humann/tests/data/demo.fastq', '--output', '/tmp/humann_test_t121b3t3_fastq_bypass_translated_search', '--bypass-translated-search', '--nucleotide-database', '*****/envs/default/lib/python3.12/site-packages/humann/tests/../data/chocophlan_DEMO', '--protein-database', '*****/envs/default/lib/python3.12/site-packages/humann/tests/../data/uniref_DEMO']' returned non-zero exit status 1.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "*****/envs/default/lib/python3.12/site-packages/humann/tests/functional_tests_humann.py", line 162, in test_humann_fastq_bypass_translated_search
utils.run_humann(command)
File "*****/envs/default/lib/python3.12/site-packages/humann/tests/utils.py", line 50, in run_humann
run_command(command)
File "*****/envs/default/lib/python3.12/site-packages/humann/tests/utils.py", line 61, in run_command
raise EnvironmentError("Warning: Unable to execute command in test.\n"+" ".join(command))
OSError: Warning: Unable to execute command in test.
humann --input *****/envs/default/lib/python3.12/site-packages/humann/tests/data/demo.fastq --output /tmp/humann_test_t121b3t3_fastq_bypass_translated_search --bypass-translated-search --nucleotide-database *****/envs/default/lib/python3.12/site-packages/humann/tests/../data/chocophlan_DEMO --protein-database *****/envs/default/lib/python3.12/site-packages/humann/tests/../data/uniref_DEMO
======================================================================
ERROR: test_humann_fastq_custom_taxonomic_profile (functional_tests_humann.TestFunctionalHumannEndtoEnd.test_humann_fastq_custom_taxonomic_profile)
Test the standard humann flow on a fastq input file
----------------------------------------------------------------------
Traceback (most recent call last):
File "*****/envs/default/lib/python3.12/site-packages/humann/tests/utils.py", line 59, in run_command
subprocess.check_call(command)
File "*****/envs/default/lib/python3.12/subprocess.py", line 413, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['humann', '--input', '*****/envs/default/lib/python3.12/site-packages/humann/tests/data/demo.fastq', '--output', '/tmp/humann_test_cciaavqf_fastq_custom_taxonomic_profile', '--taxonomic-profile', '*****/envs/default/lib/python3.12/site-packages/humann/tests/data/demo_metaphlan_bugs_list.tsv', '--nucleotide-database', '*****/envs/default/lib/python3.12/site-packages/humann/tests/../data/chocophlan_DEMO', '--protein-database', '*****/envs/default/lib/python3.12/site-packages/humann/tests/../data/uniref_DEMO']' returned non-zero exit status 1.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "*****/envs/default/lib/python3.12/site-packages/humann/tests/functional_tests_humann.py", line 243, in test_humann_fastq_custom_taxonomic_profile
utils.run_humann(command)
File "*****/envs/default/lib/python3.12/site-packages/humann/tests/utils.py", line 50, in run_humann
run_command(command)
File "*****/envs/default/lib/python3.12/site-packages/humann/tests/utils.py", line 61, in run_command
raise EnvironmentError("Warning: Unable to execute command in test.\n"+" ".join(command))
OSError: Warning: Unable to execute command in test.
humann --input *****/envs/default/lib/python3.12/site-packages/humann/tests/data/demo.fastq --output /tmp/humann_test_cciaavqf_fastq_custom_taxonomic_profile --taxonomic-profile *****/envs/default/lib/python3.12/site-packages/humann/tests/data/demo_metaphlan_bugs_list.tsv --nucleotide-database *****/envs/default/lib/python3.12/site-packages/humann/tests/../data/chocophlan_DEMO --protein-database *****/envs/default/lib/python3.12/site-packages/humann/tests/../data/uniref_DEMO
======================================================================
ERROR: test_humann_fastq_biom_output (functional_tests_biom_humann.TestFunctionalHumannEndtoEndBiom.test_humann_fastq_biom_output)
Test the standard humann flow on a fastq input file
----------------------------------------------------------------------
Traceback (most recent call last):
File "*****/envs/default/lib/python3.12/site-packages/humann/tests/utils.py", line 59, in run_command
subprocess.check_call(command)
File "*****/envs/default/lib/python3.12/subprocess.py", line 413, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['humann', '--input', '*****/envs/default/lib/python3.12/site-packages/humann/tests/data/demo.fastq', '--output', '/tmp/humann_test_6zf3z75c_fastq', '--output-format', 'biom', '--nucleotide-database', '*****/envs/default/lib/python3.12/site-packages/humann/tests/../data/chocophlan_DEMO', '--protein-database', '*****/envs/default/lib/python3.12/site-packages/humann/tests/../data/uniref_DEMO']' returned non-zero exit status 1.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "*****/envs/default/lib/python3.12/site-packages/humann/tests/functional_tests_biom_humann.py", line 28, in test_humann_fastq_biom_output
utils.run_humann(command)
File "*****/envs/default/lib/python3.12/site-packages/humann/tests/utils.py", line 50, in run_humann
run_command(command)
File "*****/envs/default/lib/python3.12/site-packages/humann/tests/utils.py", line 61, in run_command
raise EnvironmentError("Warning: Unable to execute command in test.\n"+" ".join(command))
OSError: Warning: Unable to execute command in test.
humann --input *****/envs/default/lib/python3.12/site-packages/humann/tests/data/demo.fastq --output /tmp/humann_test_6zf3z75c_fastq --output-format biom --nucleotide-database *****/envs/default/lib/python3.12/site-packages/humann/tests/../data/chocophlan_DEMO --protein-database *****/envs/default/lib/python3.12/site-packages/humann/tests/../data/uniref_DEMO
----------------------------------------------------------------------
Ran 189 tests in 2413.340s
FAILED (errors=6)
Note that I have been successfully running HUMAnN 4 for the last several months.
I’m glad you managed to solve all the issues, @Faeze_Darbaniyan. Happy profiling! 