Epic-effective: TypeError: cannot concatenate 'str' and 'NoneType' objects

[aboyd003]

Hi. I am attempting to use epic effective to estimate the genome size of a custom assembly for a eukaryotic microbe prior to peak calling.
time epic-effective -r 75 /rhome/aboyd003/bigdata/oldGenome/Pinfestans.fa

I receive the following error:
`Traceback (most recent call last):
File "/rhome/aboyd003/.conda/envs/BIOEPIC/bin/epic-effective", line 4, in
import('pkg_resources').run_script('bioepic==0.1.6', 'epic-effective')
File "/rhome/aboyd003/.conda/envs/BIOEPIC/lib/python2.7/site-packages/pkg_resources/init.py", line 666, in run_script
self.require(requires)[0].run_script(script_name, ns)
File "/rhome/aboyd003/.conda/envs/BIOEPIC/lib/python2.7/site-packages/pkg_resources/init.py", line 1462, in run_script
exec(code, namespace, namespace)
File "/rhome/aboyd003/.conda/envs/BIOEPIC/lib/python2.7/site-packages/bioepic-0.1.6-py2.7.egg-info/scripts/epic-effective", line 35, in
effective_genome_size(fasta, read_length, nb_cpu, tmpdir)
File "/rhome/aboyd003/.conda/envs/BIOEPIC/lib/python2.7/site-packages/epic/scripts/effective_genome_size.py", line 22, in effective_genome_size
logging.info("Temporary directory: " + tmpdir)
TypeError: cannot concatenate 'str' and 'NoneType' objects

real 0m0.766s
user 0m0.332s
sys 0m0.079s`

Sample of definition lines from genome file are provided below. The sequences include Ns.

7000000037419696
7000000037419352
7000000037419663
7000000037419515

[endrebak]

Thanks for trying epic-effective and reporting this bug.

Can you please try setting the --tmpdir explicitly?

Like time epic-effective -r 75 /rhome/aboyd003/bigdata/oldGenome/Pinfestans.fa -t /tmp/.

[aboyd003]

Thank you for your reply.

I have followed your suggestion and tried running with the temp directory explicitly declared on the command line time epic-effective -r 75 /rhome/aboyd003/bigdata/oldGenome/Pinfestans.fa -t /rhome/aboyd003/bigdata/oldGenome/tmp/ and declaring it in the function definition effective_genome_size(fasta, read_length, nb_cores, tmpdir="/rhome/aboyd003/bigdata/oldGenome/tmp/". Both methods result in a different error Failed to open input file '/rhome/aboyd003/bigdata/oldGenome/tmp/Pinfestans.fa.jf'
indicating some issue with my usage and line 44 of effective_genome_size.py:
output_file = os.path.join(tmpdir, '{1}.jf'.format(read_length, basename(fasta)))

Do you have any ideas of how to troubleshoot this?

[endrebak]

No, it has been so long since I used/wrote it, unfortunately. epic is no longer maintained :/ I should really archive this repo.

[aboyd003]

No worries. I cannibalized the line for jellyfish and manually did the calculations.

[endrebak]

Wonderful! My PhD money runs out soon, otherwise I'd normally try to help :)

…

On Mon, Dec 30, 2019 at 9:12 PM AMBoyd ***@***.***> wrote: No worries. I cannibalized the line for jellyfish and manually did the calculations. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#91?email_source=notifications&email_token=AEHURUS6LMEXW6GWR6NEGFDQ3JIZDA5CNFSM4J2CX7R2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEH3DIQQ#issuecomment-569783362>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEHURUVKFE64JX7SFSX7ODTQ3JIZDANCNFSM4J2CX7RQ> .