LookupError: unknown encoding: utf8

[s4351982]

I got an error at the last step when I ran one of my samples using graftM, while the other samples were fine. Can anyone advise me about the issue? Thanks

05/17/2018 04:10:32 PM INFO: Working on SB8205_S33_R1_001
05/17/2018 04:10:32 PM INFO: Working on forward reads
05/17/2018 04:20:05 PM INFO: 37320 read(s) detected
05/17/2018 04:20:06 PM INFO: aligning reads to reference package database
05/17/2018 04:23:45 PM INFO: Filtered 10568 short sequences from the alignment
05/17/2018 04:23:45 PM INFO: 26752 sequences remaining
05/17/2018 04:23:49 PM INFO: Working on reverse reads
05/17/2018 04:33:23 PM INFO: 37203 read(s) detected
05/17/2018 04:33:23 PM INFO: aligning reads to reference package database
05/17/2018 04:36:56 PM INFO: Filtered 10525 short sequences from the alignment
05/17/2018 04:36:56 PM INFO: 26678 sequences remaining
05/17/2018 04:36:58 PM INFO: Placing reads into phylogenetic tree
05/18/2018 11:12:17 AM INFO: Placements finished
05/18/2018 11:12:28 AM INFO: Reading classifications
05/18/2018 11:12:30 AM INFO: Reads classified
05/18/2018 11:13:06 AM INFO: 18647 reads found that crossover in SB8205_S33_R1_001_forward_clustered.fa
05/18/2018 11:20:50 AM INFO: Writing summary table
05/18/2018 11:20:50 AM INFO: Writing biom file
Traceback (most recent call last):
File "/usr/local/bin/graftM", line 345, in
Run(args).main()
File "/usr/local/lib/python2.7/dist-packages/graftm/run.py", line 526, in main
self.graft()
File "/usr/local/lib/python2.7/dist-packages/graftm/run.py", line 445, in graft
hit_read_count_list)
File "/usr/local/lib/python2.7/dist-packages/graftm/run.py", line 123, in summarise
biom_successful = self.s.write_biom(base_list, placements_list, f)
File "/usr/local/lib/python2.7/dist-packages/graftm/summarise.py", line 138, in write_biom
table.to_hdf5(biom_file_io, 'GraftM graft')
File "/usr/local/lib/python2.7/dist-packages/biom/table.py", line 3605, in to_hdf5
self.group_metadata(axis='observation'), 'csr', compression)
File "/usr/local/lib/python2.7/dist-packages/biom/table.py", line 3557, in axis_dump
data=[i.encode('utf8') for i in ids],
LookupError: unknown encoding: utf8

[wwood]

Hi,
I've not seen this error before, but searching on the internet suggests there might be something amiss with your Python installation, and that potentially re-installation may help? This doesn't seem to be an issue related to graftm, specifically.

[s4351982]

Hi Ben, Thanks for your reply. The weird thing was when I opened a new server window and ran it again, the error did not appear. Regards, Guangli From: Ben J Woodcroft <notifications@github.com> Sent: Friday, 18 May 2018 7:19 PM To: geronimp/graftM <graftM@noreply.github.com> Cc: Guangli Feng <guangli.feng@uq.net.au>; Author <author@noreply.github.com> Subject: Re: [geronimp/graftM] LookupError: unknown encoding: utf8 (#252) Hi, I've not seen this error before, but searching on the internet suggests there might be something amiss with your Python installation, and that potentially re-installation may help? This doesn't seem to be an issue related to graftm, specifically. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<#252 (comment)>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AlRNeGA9jtcQVmDl3GhQ8KdFiz8auCOxks5tzpH6gaJpZM4UEUJS>.

[wwood]

Alrighty, good to hear. I'm closing this issue for now, but feel free to reopen it if there is anything further.
Thanks, ben