total_genome_length is not defined

[yeroslaviz]

Thanks for updating the log and output options so fast. Now I get a different error though. I am using the same command as before

epic --control wt.input.4h.1.reads.bedpe wt.input.4h.2.reads.bedpe --treatment wt.ip.4h.1.reads.bedpe wt.ip.4h.2.reads.bedpe -cpu 10 --genome sacCer3 -egf 0.961651807729 -cs Sc.R64.1.genome -b wt.input.4h.bed -bw wt.input.4h -sbw  wt.input.4h

Iam using a chromsize file, as saccharomyces cerevisiae is not (yet?) defined in your list of genomes, (besides I am using the ensembl annotations and not UCSC)

When running the newest version now (0.2.0), I amgetting the following error

# epic --control wt.input.4h.1.reads.bedpe wt.input.4h.2.reads.bedpe --treatment wt.ip.4h.1.reads.bedpe wt.ip.4h.2.reads.bedpe -cpu 10 --genome sacCer3 -egf 0.961651807729 -cs Sc.R64.1.genome -b wt.input.4h.bed -bw wt.input.4h -sbw wt.input.4h # epic_version: 0.2.0, pandas_version: 0.20.2 (File: epic, Log level: INFO, Time: Thu, 20 Jul 2017 07:53:32 )
Traceback (most recent call last):
  File "/usr/local/bin/epic", line 257, in <module>
    total_genome_length *= sum(args.chromosome_sizes.values())
NameError: name 'total_genome_length' is not defined

Any Ideas, why is this happening? Assa

PS Do I need to use the --genome option at all in this case, if I supply a chromsize file?

[endrebak]

I'm fixing it now.

I'll also write some tests so this does not happen again.

Thanks for reporting. Update 0.2.1 is ready in PyPI will add to bioconda now.

Endre

On Thu, Jul 20, 2017 at 7:59 AM, frymor notifications@github.com wrote:

Thanks for updating the log and output options so fast. Now I get a different error though. I am using the same command as before

epic --control wt.input.4h.1.reads.bedpe wt.input.4h.2.reads.bedpe --treatment wt.ip.4h.1.reads.bedpe wt.ip.4h.2.reads.bedpe -cpu 10 --genome sacCer3 -egf 0.961651807729 -cs Sc.R64.1.genome -b wt.input.4h.bed -bw wt.input.4h -sbw wt.input.4h

Iam using a chromsize file, as saccharomyces cerevisiae is not (yet?) defined in your list of genomes, (besides I am using the ensembl annotations and not UCSC)

When running the newest version now (0.2.0), I amgetting the following error

epic --control wt.input.4h.1.reads.bedpe wt.input.4h.2.reads.bedpe --treatment wt.ip.4h.1.reads.bedpe wt.ip.4h.2.reads.bedpe -cpu 10 --genome sacCer3 -egf 0.961651807729 -cs Sc.R64.1.genome -b wt.input.4h.bed -bw wt.input.4h -sbw wt.input.4h # epic_version: 0.2.0, pandas_version: 0.20.2 (File: epic, Log level: INFO, Time: Thu, 20 Jul 2017 07:53:32 )

Traceback (most recent call last): File "/usr/local/bin/epic", line 257, in total_genome_length *= sum(args.chromosome_sizes.values()) NameError: name 'total_genome_length' is not defined

Any Ideas, why is this happening? Assa

PS Do I need to use the --genome option at all in this case, if I supply a chromsize file?

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