Funannotate compare - ValueError: invalid literal for int() with base 10:

[mikaeldahl]

I upgraded to 0.7.1 today and received a new error I didn't get with 0.6.2.
When it start parsing the genomes it ends and gives the following error message

##########################
funannotate compare -i Saico_2 Neo_irre2 --cpus 24 [10:51]

[10:51:47 AM]: OS: linux2, 24 cores, ~ 49 GB RAM. Python: 2.7.13
[10:51:47 AM]: Running funannotate v0.7.1
[10:51:47 AM]: Now parsing 2 genomes
[10:51:50 AM]: working on Saitoella complicata NRRL Y-17804 genome
Traceback (most recent call last):
File "/home/mikael/.linuxbrew/Cellar/funannotate/0.7.1/libexec/bin/funannotate-compare.py", line 160, in
if int(genomeStats[9]) == 0:
ValueError: invalid literal for int() with base 10: '7,211'

########################3

[nextgenusfs]

Should be fixed ea9c34a

[nextgenusfs]

brew upgrade funannotate should get you past this, sorry about the bug.

[mikaeldahl]

Yes I got pass that but unfortuntely I run into a new error.
#################################
mikael@mikael-HP-Z600-Workstation[compare_genomes] funannotate compare -i Saico_2 Neo_irre2 --cpus 24 [ 7:57]

[07:59:00 PM]: OS: linux2, 24 cores, ~ 49 GB RAM. Python: 2.7.13
[07:59:00 PM]: Running funannotate v0.7.2
[07:59:00 PM]: Now parsing 2 genomes
[07:59:03 PM]: working on Saitoella complicata NRRL Y-17804 genome
Traceback (most recent call last):
File "/home/mikael/.linuxbrew/Cellar/funannotate/0.7.2/libexec/bin/funannotate-compare.py", line 165, in
functional = lib.getGBKannotation(GBK)
File "/home/mikael/.linuxbrew/Cellar/funannotate/0.7.2/libexec/lib/library.py", line 2046, in getGBKannotation
meropsDict = MEROPS2dict(os.path.join(parentdir, 'DB', 'merops_formatted.fa'))
File "/home/mikael/.linuxbrew/Cellar/funannotate/0.7.2/libexec/lib/library.py", line 1917, in MEROPS2dict
with open(input, 'rU') as fasta:
IOError: [Errno 2] No such file or directory: '/home/mikael/.linuxbrew/Cellar/funannotate/0.7.2/libexec/DB/merops_formatted.fa'
###################################################

[nextgenusfs]

You need to run funannotate setup again when you upgrade versions.

…

On Jul 21, 2017, at 1:03 PM, mikaeldahl ***@***.***> wrote: Yes I got pass that but unfortuntely I run into a new error. ################################# ***@***.***[compare_genomes] funannotate compare -i Saico_2 Neo_irre2 --cpus 24 [ 7:57] [07:59:00 PM]: OS: linux2, 24 cores, ~ 49 GB RAM. Python: 2.7.13 [07:59:00 PM]: Running funannotate v0.7.2 [07:59:00 PM]: Now parsing 2 genomes [07:59:03 PM]: working on Saitoella complicata NRRL Y-17804 genome Traceback (most recent call last): File "/home/mikael/.linuxbrew/Cellar/funannotate/0.7.2/libexec/bin/funannotate-compare.py", line 165, in functional = lib.getGBKannotation(GBK) File "/home/mikael/.linuxbrew/Cellar/funannotate/0.7.2/libexec/lib/library.py", line 2046, in getGBKannotation meropsDict = MEROPS2dict(os.path.join(parentdir, 'DB', 'merops_formatted.fa')) File "/home/mikael/.linuxbrew/Cellar/funannotate/0.7.2/libexec/lib/library.py", line 1917, in MEROPS2dict with open(input, 'rU') as fasta: IOError: [Errno 2] No such file or directory: '/home/mikael/.linuxbrew/Cellar/funannotate/0.7.2/libexec/DB/merops_formatted.fa' ################################################### — You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub, or mute the thread.

[mikaeldahl]

Which file or files are parsed for the compare? Skickat från min iPhone

…

21 juli 2017 kl. 23:30 skrev Jon Palmer ***@***.***>: You need to run funannotate setup again when you upgrade versions. > On Jul 21, 2017, at 1:03 PM, mikaeldahl ***@***.***> wrote: > > Yes I got pass that but unfortuntely I run into a new error. > ################################# > ***@***.***[compare_genomes] funannotate compare -i Saico_2 Neo_irre2 --cpus 24 [ 7:57] > > [07:59:00 PM]: OS: linux2, 24 cores, ~ 49 GB RAM. Python: 2.7.13 > [07:59:00 PM]: Running funannotate v0.7.2 > [07:59:00 PM]: Now parsing 2 genomes > [07:59:03 PM]: working on Saitoella complicata NRRL Y-17804 genome > Traceback (most recent call last): > File "/home/mikael/.linuxbrew/Cellar/funannotate/0.7.2/libexec/bin/funannotate-compare.py", line 165, in > functional = lib.getGBKannotation(GBK) > File "/home/mikael/.linuxbrew/Cellar/funannotate/0.7.2/libexec/lib/library.py", line 2046, in getGBKannotation > meropsDict = MEROPS2dict(os.path.join(parentdir, 'DB', 'merops_formatted.fa')) > File "/home/mikael/.linuxbrew/Cellar/funannotate/0.7.2/libexec/lib/library.py", line 1917, in MEROPS2dict > with open(input, 'rU') as fasta: > IOError: [Errno 2] No such file or directory: '/home/mikael/.linuxbrew/Cellar/funannotate/0.7.2/libexec/DB/merops_formatted.fa' > ################################################### > > — > You are receiving this because you modified the open/close state. > Reply to this email directly, view it on GitHub, or mute the thread. > — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.

[nextgenusfs]

The script can't find the merops database fasta file, which needs to be in the DB directory. The DB directory is symlinked (usually), so you can run:

funannotate setup -m all -d /path/to/funannotate/DB/folder

Which should properly setup the symlink. If you still get errors, try to remove the symlink first and then re-run, i.e.

rm -r /home/mikael/.linuxbrew/Cellar/funannotate/0.7.2/libexec/DB

[mikaeldahl]

Thanks again, when I removed the symlink it worked fine =) 2017-07-24 18:31 GMT+02:00 Jon Palmer <notifications@github.com>:

…

The script can't find the merops database fasta file, which needs to be in the DB directory. The DB directory is symlinked (usually), so you can run: funannotate setup -m all -d /path/to/funannotate/DB/folder Which should properly setup the symlink. If you still get errors, try to remove the symlink first and then re-run, i.e. rm -r /home/mikael/.linuxbrew/Cellar/funannotate/0.7.2/libexec/DB — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#98 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AHUnsE_l71o0M5hRRDpU1sK45n98VJYSks5sRMbkgaJpZM4OfJb4> .

-- [image: cid:image001.png@01D15E60.83EE02E0] *Mikael Dahl, Ph.D. * Forskare | Researcher in the research program Evolutionary Biology Uppsala universitet *| * Uppsala University Institutionen för ekologi och genetik *| *Dept. of Ecology and Genetics Address: Evolutionsbiologiskt centrum, Norbyvägen 18D, 752 36 Uppsala Phone: +46 (0)70-3217371 <dahl.mikael@gmail.com> dahl.mikael@gmail.com

[nextgenusfs]

Great. I tried to make the home-brew upgrade automatically recognize the softlink and link it for you, but it is kind of clunky and doesn't always work.