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biocore-ntnu / epic

(DEPRECATED) epic: diffuse domain ChIP-Seq caller based on SICER
http://bioepic.readthedocs.io
MIT License
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Epic-effective: TypeError: cannot concatenate 'str' and 'NoneType' objects #91

Open aboyd003 opened 4 years ago

aboyd003 commented 4 years ago

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 commented 4 years ago

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 commented 4 years ago

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 commented 4 years ago

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 epic is no longer maintained :/ I should really archive this repo.

aboyd003 commented 4 years ago

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

endrebak commented 4 years ago

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

On Mon, Dec 30, 2019 at 9:12 PM AMBoyd notifications@github.com wrote:

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

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