# Could not find "mafft" ("False")

**URL:** <https://forum.biobakery.org/t/could-not-find-mafft-false/3837>\
**Category:** bioBakery workflows\
**Created:** [July 15, 2022, 10:35am UTC](https://forum.biobakery.org/t/could-not-find-mafft-false/3837 "2022-07-15T10:35:25Z")\
**Posts on this page:** 1\
**Page:** 1

<div class="post-metadata">

**Author:** ![imontero](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/imontero/32/3411_2.png) [@imontero](https://forum.biobakery.org/u/imontero)\
**Post date:** [July 15, 2022, 10:35am UTC](https://forum.biobakery.org/t/could-not-find-mafft-false/3837/1 "2022-07-15T10:35:25Z")

</div>

I could not run strainphlan inside biobakery workflows.

2022-07-14 09:16:53,309 LoggerReporter finished ERROR: AnADAMA run finished with errors.  
2022-07-15 12:28:07,641 LoggerReporter started INFO: Beginning AnADAMA run with 79 tasks.  
2022-07-15 12:28:07,651 LoggerReporter started INFO: Workflow description = A workflow for whole metagenome shotgun sequences  
2022-07-15 12:28:07,651 LoggerReporter started INFO: Workflow version = 0.1  
2022-07-15 12:28:07,652 LoggerReporter started INFO: Workflow configuration options  
2022-07-15 12:28:07,652 LoggerReporter started INFO: input\_extension = fastq.gz  
2022-07-15 12:28:07,652 LoggerReporter started INFO: barcode\_file =  
2022-07-15 12:28:07,652 LoggerReporter started INFO: dual\_barcode\_file =  
2022-07-15 12:28:07,652 LoggerReporter started INFO: index\_identifier = \_I1\_001  
2022-07-15 12:28:07,652 LoggerReporter started INFO: min\_pred\_qc\_score = 2  
2022-07-15 12:28:07,652 LoggerReporter started INFO: threads = 2  
2022-07-15 12:28:07,652 LoggerReporter started INFO: pair\_identifier = .R1  
2022-07-15 12:28:07,652 LoggerReporter started INFO: interleaved = False  
2022-07-15 12:28:07,652 LoggerReporter started INFO: bypass\_quality\_control = True  
2022-07-15 12:28:07,652 LoggerReporter started INFO: contaminate\_databases = /home/microviable/biobakery\_workflows\_databases/kneaddata\_db\_human\_genome  
2022-07-15 12:28:07,652 LoggerReporter started INFO: qc\_options =  
2022-07-15 12:28:07,652 LoggerReporter started INFO: functional\_profiling\_options =  
2022-07-15 12:28:07,652 LoggerReporter started INFO: remove\_intermediate\_output = False  
2022-07-15 12:28:07,652 LoggerReporter started INFO: bypass\_functional\_profiling = True  
2022-07-15 12:28:07,652 LoggerReporter started INFO: bypass\_strain\_profiling = False  
2022-07-15 12:28:07,652 LoggerReporter started INFO: run\_strain\_gene\_profiling = False  
2022-07-15 12:28:07,652 LoggerReporter started INFO: bypass\_taxonomic\_profiling = False  
2022-07-15 12:28:07,652 LoggerReporter started INFO: run\_assembly = False  
2022-07-15 12:28:07,652 LoggerReporter started INFO: strain\_profiling\_options =  
2022-07-15 12:28:07,652 LoggerReporter started INFO: taxonomic\_profiling\_options =  
2022-07-15 12:28:07,653 LoggerReporter started INFO: max\_strains = 20  
2022-07-15 12:28:07,653 LoggerReporter started INFO: strain\_list =  
2022-07-15 12:28:07,653 LoggerReporter started INFO: assembly\_options =  
2022-07-15 12:28:07,653 LoggerReporter started INFO: output = /media/microviable/e/Liofilos\_output/metaphlan/rarefied\_paired/  
2022-07-15 12:28:07,653 LoggerReporter started INFO: input = /media/microviable/e/Liofilos\_output/kneaddata/rarefied\_paired  
2022-07-15 12:28:07,653 LoggerReporter started INFO: config = None  
2022-07-15 12:28:07,653 LoggerReporter started INFO: jobs = 1  
2022-07-15 12:28:07,653 LoggerReporter started INFO: grid\_jobs = 0  
2022-07-15 12:28:07,653 LoggerReporter started INFO: grid = None  
2022-07-15 12:28:07,667 LoggerReporter started INFO: grid\_partition =  
2022-07-15 12:28:07,667 LoggerReporter started INFO: grid\_benchmark = off  
2022-07-15 12:28:07,667 LoggerReporter started INFO: grid\_options = None  
2022-07-15 12:28:07,667 LoggerReporter started INFO: grid\_environment = None  
2022-07-15 12:28:07,667 LoggerReporter started INFO: grid\_scratch = None  
2022-07-15 12:28:07,667 LoggerReporter started INFO: dry\_run = False  
2022-07-15 12:28:07,667 LoggerReporter started INFO: skip\_nothing = False  
2022-07-15 12:28:07,667 LoggerReporter started INFO: quit\_early = False  
2022-07-15 12:28:07,668 LoggerReporter started INFO: until\_task = None  
2022-07-15 12:28:07,668 LoggerReporter started INFO: exclude\_task = None  
2022-07-15 12:28:07,668 LoggerReporter started INFO: target = None  
2022-07-15 12:28:07,668 LoggerReporter started INFO: exclude\_target = None  
2022-07-15 12:28:07,668 LoggerReporter started INFO: log\_level = INFO  
2022-07-15 12:28:08,330 LoggerReporter log\_event INFO: task 58, order\_clade\_list : skipped  
2022-07-15 12:28:08,331 LoggerReporter log\_event INFO: task 57, strainphlan\_print\_clades : skipped  
2022-07-15 12:28:08,331 LoggerReporter log\_event INFO: task 39, strainphlan\_sample2markers\_\_\_\_H15\_rarefied : skipped  
2022-07-15 12:28:08,331 LoggerReporter log\_event INFO: task 38, metaphlan\_count\_species : skipped  
2022-07-15 12:28:08,331 LoggerReporter log\_event INFO: task 37, metaphlan\_join\_taxonomic\_profiles : skipped  
2022-07-15 12:28:08,331 LoggerReporter log\_event INFO: task 0, metaphlan\_\_\_\_H15\_rarefied : skipped  
2022-07-15 12:28:08,331 LoggerReporter log\_event INFO: task 56, strainphlan\_sample2markers\_\_\_\_L25\_rarefied : skipped  
2022-07-15 12:28:08,331 LoggerReporter log\_event INFO: task 35, metaphlan\_\_\_\_L25\_rarefied : skipped  
2022-07-15 12:28:08,331 LoggerReporter log\_event INFO: task 55, strainphlan\_sample2markers\_\_\_\_L24\_rarefied : skipped  
2022-07-15 12:28:08,331 LoggerReporter log\_event INFO: task 33, metaphlan\_\_\_\_L24\_rarefied : skipped  
2022-07-15 12:28:08,331 LoggerReporter log\_event INFO: task 54, strainphlan\_sample2markers\_\_\_\_L23\_rarefied : skipped  
2022-07-15 12:28:08,331 LoggerReporter log\_event INFO: task 31, metaphlan\_\_\_\_L23\_rarefied : skipped  
2022-07-15 12:28:08,331 LoggerReporter log\_event INFO: task 53, strainphlan\_sample2markers\_\_\_\_L22\_rarefied : skipped  
2022-07-15 12:28:08,331 LoggerReporter log\_event INFO: task 29, metaphlan\_\_\_\_L22\_rarefied : skipped  
2022-07-15 12:28:08,331 LoggerReporter log\_event INFO: task 52, strainphlan\_sample2markers\_\_\_\_L19\_rarefied : skipped  
2022-07-15 12:28:08,331 LoggerReporter log\_event INFO: task 27, metaphlan\_\_\_\_L19\_rarefied : skipped  
2022-07-15 12:28:08,332 LoggerReporter log\_event INFO: task 51, strainphlan\_sample2markers\_\_\_\_L18\_rarefied : skipped  
2022-07-15 12:28:08,332 LoggerReporter log\_event INFO: task 25, metaphlan\_\_\_\_L18\_rarefied : skipped  
2022-07-15 12:28:08,332 LoggerReporter log\_event INFO: task 50, strainphlan\_sample2markers\_\_\_\_L17\_rarefied : skipped  
2022-07-15 12:28:08,332 LoggerReporter log\_event INFO: task 23, metaphlan\_\_\_\_L17\_rarefied : skipped  
2022-07-15 12:28:08,332 LoggerReporter log\_event INFO: task 49, strainphlan\_sample2markers\_\_\_\_L16\_rarefied : skipped  
2022-07-15 12:28:08,332 LoggerReporter log\_event INFO: task 21, metaphlan\_\_\_\_L16\_rarefied : skipped  
2022-07-15 12:28:08,332 LoggerReporter log\_event INFO: task 48, strainphlan\_sample2markers\_\_\_\_L15\_rarefied : skipped  
2022-07-15 12:28:08,332 LoggerReporter log\_event INFO: task 19, metaphlan\_\_\_\_L15\_rarefied : skipped  
2022-07-15 12:28:08,332 LoggerReporter log\_event INFO: task 47, strainphlan\_sample2markers\_\_\_\_H25\_rarefied : skipped  
2022-07-15 12:28:08,332 LoggerReporter log\_event INFO: task 17, metaphlan\_\_\_\_H25\_rarefied : skipped  
2022-07-15 12:28:08,332 LoggerReporter log\_event INFO: task 46, strainphlan\_sample2markers\_\_\_\_H24\_rarefied : skipped  
2022-07-15 12:28:08,332 LoggerReporter log\_event INFO: task 15, metaphlan\_\_\_\_H24\_rarefied : skipped  
2022-07-15 12:28:08,332 LoggerReporter log\_event INFO: task 45, strainphlan\_sample2markers\_\_\_\_H23\_rarefied : skipped  
2022-07-15 12:28:08,332 LoggerReporter log\_event INFO: task 13, metaphlan\_\_\_\_H23\_rarefied : skipped  
2022-07-15 12:28:08,332 LoggerReporter log\_event INFO: task 44, strainphlan\_sample2markers\_\_\_\_H22\_rarefied : skipped  
2022-07-15 12:28:08,332 LoggerReporter log\_event INFO: task 11, metaphlan\_\_\_\_H22\_rarefied : skipped  
2022-07-15 12:28:08,332 LoggerReporter log\_event INFO: task 43, strainphlan\_sample2markers\_\_\_\_H19\_rarefied : skipped  
2022-07-15 12:28:08,333 LoggerReporter log\_event INFO: task 9, metaphlan\_\_\_\_H19\_rarefied : skipped  
2022-07-15 12:28:08,333 LoggerReporter log\_event INFO: task 42, strainphlan\_sample2markers\_\_\_\_H18\_rarefied : skipped  
2022-07-15 12:28:08,333 LoggerReporter log\_event INFO: task 7, metaphlan\_\_\_\_H18\_rarefied : skipped  
2022-07-15 12:28:08,333 LoggerReporter log\_event INFO: task 41, strainphlan\_sample2markers\_\_\_\_H17\_rarefied : skipped  
2022-07-15 12:28:08,333 LoggerReporter log\_event INFO: task 5, metaphlan\_\_\_\_H17\_rarefied : skipped  
2022-07-15 12:28:08,333 LoggerReporter log\_event INFO: task 40, strainphlan\_sample2markers\_\_\_\_H16\_rarefied : skipped  
2022-07-15 12:28:08,333 LoggerReporter log\_event INFO: task 3, metaphlan\_\_\_\_H16\_rarefied : skipped  
2022-07-15 12:28:08,333 LoggerReporter log\_event INFO: task 59, strainphlan\_clade\_0 : ready and waiting for resources  
2022-07-15 12:28:08,333 LoggerReporter log\_event INFO: task 59, strainphlan\_clade\_0 : starting to run  
2022-07-15 12:28:08,352 anadama2.helpers actually\_sh INFO: Executing with shell: extract\_markers.py --database /home/microviable/workflows/lib/python3.7/site-packages/metaphlan/metaphlan\_databases/mpa\_v30\_CHOCOPhlAn\_201901.pkl --clade s\_\_Ruminococcus\_bromii --output\_dir /media/microviable/e/Liofilos\_output/metaphlan/rarefied\_paired/strainphlan  
2022-07-15 12:29:03,288 anadama2.helpers actually\_sh INFO: Execution complete. Stdout: b’Fri Jul 15 12:28:08 2022: Start extract markers execution\nFri Jul 15 12:28:08 2022: \tGenerating DB markers FASTA…\nFri Jul 15 12:28:49 2022: \tDone.\nFri Jul 15 12:28:49 2022: \tLoading MetaPhlan 3.0 database…\nFri Jul 15 12:28:56 2022: \tDone.\nFri Jul 15 12:28:56 2022: \tNumber of markers for the clade “s\_\_Ruminococcus\_bromii”: 138\nFri Jul 15 12:28:56 2022: \tExporting markers…\nFri Jul 15 12:29:03 2022: \tDone.\nFri Jul 15 12:29:03 2022: Finish extract markers execution (54.85 seconds): Results are stored at “/media/microviable/e/Liofilos\_output/metaphlan/rarefied\_paired/strainphlan/”\n’  
Stderr:  
2022-07-15 12:29:03,298 anadama2.helpers actually\_sh INFO: Executing with shell: strainphlan --samples /media/microviable/e/Liofilos\_output/metaphlan/rarefied\_paired/strainphlan/_/_.pkl --output\_dir /media/microviable/e/Liofilos\_output/metaphlan/rarefied\_paired/strainphlan --clade s\_\_Ruminococcus\_bromii --nprocs 2 --clade\_markers /media/microviable/e/Liofilos\_output/metaphlan/rarefied\_paired/strainphlan/s\_\_Ruminococcus\_bromii.fna \> /media/microviable/e/Liofilos\_output/metaphlan/rarefied\_paired/strainphlan/19\_clade.log && touch /media/microviable/e/Liofilos\_output/metaphlan/rarefied\_paired/strainphlan/19\_clade.tree && if [-f /media/microviable/e/Liofilos\_output/metaphlan/rarefied\_paired/strainphlan/RAxML\_bestTree.s\_\_Ruminococcus\_bromii.tree]; then cp /media/microviable/e/Liofilos\_output/metaphlan/rarefied\_paired/strainphlan/RAxML\_bestTree.s\_\_Ruminococcus\_bromii.tree /media/microviable/e/Liofilos\_output/metaphlan/rarefied\_paired/strainphlan/19\_clade.tree; fi  
2022-07-15 12:29:05,836 LoggerReporter task\_failed ERROR: task 59, strainphlan\_clade\_0 : Failed! Error message : Error executing action 0. Original Exception:  
Traceback (most recent call last):  
File “/home/microviable/workflows/lib/python3.7/site-packages/anadama2/runners.py”, line 201, in \_run\_task\_locally  
action\_func(task)  
File “/home/microviable/workflows/lib/python3.7/site-packages/biobakery\_workflows/tasks/shotgun.py”, line 762, in strainphlan  
args=[os.path.abspath(os.path.join(os.path.dirname(task.depends[0].name),“…”)),os.path.dirname(task.targets[0].name),profile\_clade,threads])  
File “/home/microviable/workflows/lib/python3.7/site-packages/biobakery\_workflows/utilities.py”, line 1049, in run\_task  
return\_code = sh(command)()  
File “/home/microviable/workflows/lib/python3.7/site-packages/anadama2/helpers.py”, line 89, in actually\_sh  
ret = \_sh(s, \*\*kwargs)  
File “/home/microviable/workflows/lib/python3.7/site-packages/anadama2/util/ **init**.py”, line 320, in sh  
raise ShellException(proc.returncode, msg.format(cmd, ret[0], ret[1]))  
anadama2.util.ShellException: [Errno 1] Command `strainphlan --samples /media/microviable/e/Liofilos\_output/metaphlan/rarefied\_paired/strainphlan/_/_.pkl --output\_dir /media/microviable/e/Liofilos\_output/metaphlan/rarefied\_paired/strainphlan --clade s\_\_Ruminococcus\_bromii --nprocs 2 --clade\_markers /media/microviable/e/Liofilos\_output/metaphlan/rarefied\_paired/strainphlan/s\_\_Ruminococcus\_bromii.fna \> /media/microviable/e/Liofilos\_output/metaphlan/rarefied\_paired/strainphlan/19\_clade.log && touch /media/microviable/e/Liofilos\_output/metaphlan/rarefied\_paired/strainphlan/19\_clade.tree && if [-f /media/microviable/e/Liofilos\_output/metaphlan/rarefied\_paired/strainphlan/RAxML\_bestTree.s\_\_Ruminococcus\_bromii.tree]; then cp /media/microviable/e/Liofilos\_output/metaphlan/rarefied\_paired/strainphlan/RAxML\_bestTree.s\_\_Ruminococcus\_bromii.tree /media/microviable/e/Liofilos\_output/metaphlan/rarefied\_paired/strainphlan/19\_clade.tree; fi’ failed.  
Out: b’’  
Err: b’[e] could not find “mafft” (“False”) executable in your PATH environment variable\n\n[e] An error was ocurred executing a external tool, exiting…\nFri Jul 15 12:29:05 2022: Stop StrainPhlAn 3.0 execution.\n’