Hi, I am trying to run the biobakery workflows tutorial using the biobakery/workflows Docker image. I used the sample output files to run the visualisation workflow but the x-axis of the heatmaps in the final report are all numbers instead of the sample names. I don’t know what’s the issue since all the other graphs are fine.
Any help would be greatly appreciated. Thank you!
Hello, Thank you for the detailed post and sorry for the slow reply. The heatmaps are generated with hclust2. Can you double check your hclust2 version and if needed upgrade to the latest version?
Thank you,
Lauren
Hello Lauren,
Thanks for your reply. The hclust2 version I am using is 1.0.0.
Thank you for the reply. Can you try upgrading your version of the workflows? I think this should resolve the issue with the heatmaps when using the latest hclust2.
Thank you,
Lauren
Hello Lauren,
Thank you for your reply. I have been using the latest version of workflows as well. The problem still persists.
Thank you for the reply. Can you double check the formatting of the input files? If those are okay can you post the workflows version you are using?
Thank you,
Lauren
Hi Lauren,
Thank you for your reply. I realised that I have not been using the latest version of biobakery workflows after all, and the heatmaps problem was solved after I updated to the latest ver (3.0.0.a.7). However, another problem has occurred. When I try to redownload the wmgx databases, I get this error message:
biobakery_workflows_databases --install wmgx
Installing humann utility mapping database
Creating directory to install database: /opt/biobakery_workflows_databases/humann
Creating subdirectory to install database: /opt/biobakery_workflows_databases/humann/utility_mapping
Download URL: http://huttenhower.sph.harvard.edu/humann2_data/full_mapping_v201901.tar.gz
Downloading file of size: 2.55 GB
2.55 GB 100.00 % 6.81 MB/sec 0 min -0 sec
Extracting: /opt/biobakery_workflows_databases/humann/full_mapping_v201901.tar.gz
Database installed: /opt/biobakery_workflows_databases/humann/utility_mapping
HUMAnN configuration file updated: database_folders : utility_mapping = /opt/biobakery_workflows_databases/humann/utility_mapping
Generating strainphlan fasta database
Installing humann nucleotide and protein databases
Creating subdirectory to install database: /opt/biobakery_workflows_databases/humann/chocophlan
Download URL: http://huttenhower.sph.harvard.edu/humann2_data/chocophlan/full_chocophlan.v296_201901.tar.gz
Downloading file of size: 15.30 GB
15.30 GB 100.00 % 3.64 MB/sec 0 min -0 sec
Extracting: /opt/biobakery_workflows_databases/humann/full_chocophlan.v296_201901.tar.gz
Database installed: /opt/biobakery_workflows_databases/humann/chocophlan
HUMAnN configuration file updated: database_folders : nucleotide = /opt/biobakery_workflows_databases/humann/chocophlan
Creating subdirectory to install database: /opt/biobakery_workflows_databases/humann/uniref
Download URL: http://huttenhower.sph.harvard.edu/humann2_data/uniprot/uniref_annotated/uniref90_annotated_v201901.tar.gzDownloading file of size: 19.31 GB
CRITICAL ERROR: Unable to download and extract from URL: http://huttenhower.sph.harvard.edu/humann2_data/uniprot/uniref_annotated/uniref90_annotated_v201901.tar.gz
Unable to install database. Error running command: humann_databases --download uniref uniref90_diamond /opt/biobakery_workflows_databases/humann
I have tried redownloading it many times but the same thing happens. I hope to receive your assistance again, thank you!
Hello - Thank you for the follow up. I am glad to hear the version upgrade resolved the issue. Is it possible you are running out of disk space? If not, you might try again today to see if it was just a temporary issue. Occasionally due to server load large downloads of the databases might be slow.
Thank you,
Lauren
Dear Lauren,
Thank you once again for your help. After clearing up the disk space, I managed to download the databases. However, I’ve run into another error for the visualisation workflow.
Task 0 failed
Name: document
Original error:
Error executing action 0. Original Exception:
Traceback (most recent call last):
File “/usr/local/lib/python3.6/dist-packages/anadama2/runners.py”, line 201, in _run_task_locally
action_func(task)
File “/usr/local/lib/python3.6/dist-packages/anadama2/document.py”, line 290, in create
sh(pandoc_command.format(intermediate_template, temp_report),log_command=True)()
File “/usr/local/lib/python3.6/dist-packages/anadama2/helpers.py”, line 89, in actually_sh
ret = _sh(s, **kwargs)
File “/usr/local/lib/python3.6/dist-packages/anadama2/util/init.py”, line 320, in sh
raise ShellException(proc.returncode, msg.format(cmd, ret[0], ret[1]))
anadama2.util.ShellException: [Errno 43] Command `pandoc /home/N0017/output_vis/tmpw3qtnsoy/wmgx_report.md -o /home/N0017/output_vis/tmpw3qtnsoy/wmgx_report…pdf --variable=linkcolor:Blue --variable=toccolor:Blue --pdf-engine=pdflatex --standalone --toc’ failed.
Out: b’’
Err: b’Error producing PDF.\n! Package inputenc Error: Unicode char \xce\xb2 (U+3B2)\n(inputenc) not set up for use with LaTeX.\n\nSee the inputenc package documentation for explanation.\nType H for immediate help.\n … \n \nl.301 …d, even numbered fatty acid \xce\xb2-oxidation}\n\nTry running pandoc with --pdf-engine=xelatex.\n’
Task 6 failed
Name: archive
Original error:
Task failed because parent task `0’ failed
Traceback (most recent call last):
File “/usr/local/bin/wmgx_vis.py”, line 133, in
workflow.go()
File “/usr/local/lib/python3.6/dist-packages/anadama2/workflow.py”, line 801, in go
self._handle_finished()
File “/usr/local/lib/python3.6/dist-packages/anadama2/workflow.py”, line 833, in _handle_finished
raise RunFailed()
anadama2.workflow.RunFailed
i tried adding --format html and it worked, but i would like to get the pdf version of the report because I managed to get pdfs for other runs that I did. I hope to get some help again, thank you so much.
Hello, I am glad to hear you got the database issue fixed. The latest issue looks like it is coming from your LaTex install. You might try installing LaTex again or try a different package. We use the texlive package for our Ubuntu builds.
Thank you,
Lauren
Dear Lauren,
Thank you for your suggestion. I tried running it with other samples and it is fine, but the one sample that generated the error in the first place is still failing.
I have also encountered another error when running the visualisation workflow:
(Jul 27 04:12:41) [0/2 - 0.00%] **Ready ** Task 0: document
(Jul 27 04:12:41) [0/2 - 0.00%] **Started ** Task 0: document
Exception:
list index out of range
Error messages will be included in output document
Traceback (most recent call last):
File “/usr/local/bin/wmgx_vis.py”, line 133, in
workflow.go()
File “/usr/local/lib/python3.6/dist-packages/anadama2/workflow.py”, line 801, in go
self._handle_finished()
File “/usr/local/lib/python3.6/dist-packages/anadama2/workflow.py”, line 833, in _handle_finished
raise RunFailed()
anadama2.workflow.RunFailed
so far this error has only occurred for samples that do not have 8 input files (eg 3 or 5 sets of paired end reads). do let me know if there’s a solution for this, thank you again!