Epic effective for #87
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I would rather recommend that you do not compute epic-effective for hg38, it is included in epic. While the version included is calculated for UCSC, it is not going to make a difference :) Thanks for reporting :) Why do you want to calculate the value? |
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I want to calculate the EFFECTIVE_GENOME_FRACTION for hg38 genome. As it is mentioned in the command -"Use a different effective genome fraction than the one included in epic. The default value depends on the genome and readlength, but is a number between 0 and 1." The value will change based on the read length. So for a particular read length I want to compute the effective genome fraction. |
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I can guarantee you that it will not matter much for epic at least. The
difference between 36 and 100 bp for hg38 is < 10% which does not make a
difference to the statistics. And I cannot help you run it unfortunately.
Do you have a cluster/larger machine to run this on? The problem is that
the another piece of software (jellyfish2) uses too much memory.
…On Fri, Sep 7, 2018 at 2:39 PM parida007 ***@***.***> wrote:
I want to calculate the EFFECTIVE_GENOME_FRACTION for hg38 genome. As it
is mentioned in the command -"Use a different effective genome fraction
than the one included in epic. The default value depends on the genome and
readlength, but is a number between 0 and 1." The value will change based
on the read length. So for a particular read length I want to compute the
effective genome fraction.
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Thanks for your information. No I don't have a large cluster to run it. I have run the command with default parameter setting and getting the enrichment result. Can you please help me to understand what does the following means: |
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It is just output of the software. It says your readlength is 36 and
therefore it chooses a certain egf.
:)
…On Tue, Sep 11, 2018 at 7:39 AM parida007 ***@***.***> wrote:
Thanks for your information. No I don't have a large cluster to run it. I
have run the command with default parameter setting and getting the
enrichment result. Can you please help me to understand what does the
following means:
2553959578.0 effective_genome_fraction (File:
compute_background_probabilites, Log level: DEBUG, Time: Mon, 10 Sep 2018
17:12:44 )
What I have understood is effective genome fraction must be in between 0
and 1. Though initially it shows something like:
Used first 10000 reads of SRR524941.bam.bed to estimate a median read
length of 36.0
Mean readlength: 36.0004, max readlength: 40, min readlength: 32. (File:
find_readlength, Log level: INFO, Time: Mon, 10 Sep 2018 16:54:29 )
Using an effective genome fraction of 0.8269827491300733. (File: genomes,
Log level: INFO, Time: Mon, 10 Sep 2018 16:54:29 )
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That I understood.. but the thing is that can the egf be 2553959578.0 ?? |
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No, that is the effective genome size. Good catch. Should update that :)
…On Tue, Sep 11, 2018 at 10:11 AM parida007 ***@***.***> wrote:
That I understood.. but the thing is that can the egf be 2553959578.0 ??
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So it should be 0.8269827491300733... If I am not wrong.. |
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Yes, but the egs is egf * genome size. The code is correct, the logging
info not.
…On Tue, Sep 11, 2018 at 10:53 AM parida007 ***@***.***> wrote:
So it should be 0.8269827491300733... If I am not wrong..
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epic -t SRR524944.bed SRR524945.bed SRR524946.bed -c ../GSM945859-input/SRR504936.bed ../GSM945859-input/SRR504937.bed --genome hg38 --false-discovery-rate-cutoff 0.01 -o enriched_regions_GSM970218.csv -bw bigwigs -sm matrix.gz # epic_version: 0.2.12, pandas_version: 0.23.4 (File: epic, Log level: INFO, Time: Tue, 11 Sep 2018 15:01:20 )cat: write error: Broken pipe Can you tell me whether this error is having an impact with the final output matrix |
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No, it is not :)
…On Tue, Sep 11, 2018 at 11:29 AM parida007 ***@***.***> wrote:
epic -t SRR524944.bed SRR524945.bed SRR524946.bed -c
../GSM945859-input/SRR504936.bed ../GSM945859-input/SRR504937.bed --genome
hg38 --false-discovery-rate-cutoff 0.01 -o enriched_regions_GSM970218.csv
-bw bigwigs -sm matrix.gz # epic_version: 0.2.12, pandas_version: 0.23.4
(File: epic, Log level: INFO, Time: Tue, 11 Sep 2018 15:01:20 )
cat: write error: Broken pipe
Can you tell me whether this error is having an impact with the final
output matrix
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I want to run the epic-effective for human genome hg38. I am using a 16 gb ram for it but after using the command it is showing memory error.
using the following command:
epic-effective -r 36 GRCh38.p10.genome.fa
getting the following error:
File analyzed: GRCh38.p10.genome.fa (File: effective_genome_size, Log level: INFO, Time: Thu, 06 Sep 2018 17:28:46 )
Genome length: 3236815040 (File: effective_genome_size, Log level: INFO, Time: Thu, 06 Sep 2018 17:28:46 )
File analyzed: GRCh38.p10.genome.fa
Genome length: 3236815040
terminate called after throwing an instance of 'jellyfish::large_hash::array_base<jellyfish::mer_dna_ns::mer_base_static<unsigned long, 0>, unsigned long, atomic::gcc, jellyfish::large_hash::unbounded_array<jellyfish::mer_dna_ns::mer_base_static<unsigned long, 0>, unsigned long, atomic::gcc, allocators::mmap> >::ErrorAllocation'
what(): Failed to allocate 20443042440 bytes of memory
Aborted (core dumped)
Failed to open input file '/tmp/GRCh38.p10.genome.fa.jf'
Traceback (most recent call last):
File "/usr/local/bin/epic-effective", line 38, in
effective_genome_size(fasta, read_length, nb_cpu, tmpdir)
File "/usr/local/lib/python2.7/dist-packages/epic/scripts/effective_genome_size.py", line 56, in effective_genome_size
shell=True)
File "/usr/lib/python2.7/subprocess.py", line 574, in check_output
raise CalledProcessError(retcode, cmd, output=output)
subprocess.CalledProcessError: Command 'jellyfish stats /tmp/GRCh38.p10.genome.fa.jf' returned non-zero exit status 1
rm: cannot remove '/tmp/GRCh38.p10.genome.fa.jf': No such file or directory
But when I use a single chromosome it works fine.
epic-effective -r 36 gencode_chrY.fa
Temporary directory: /tmp/ (File: effective_genome_size, Log level: INFO, Time: Fri, 07 Sep 2018 11:00:26 )
File analyzed: gencode_chrY.fa (File: effective_genome_size, Log level: INFO, Time: Fri, 07 Sep 2018 11:00:26 )
Genome length: 57227415 (File: effective_genome_size, Log level: INFO, Time: Fri, 07 Sep 2018 11:00:26 )
File analyzed: gencode_chrY.fa
Genome length: 57227415
Number unique 36-mers: 21608143 (File: effective_genome_size, Log level: INFO, Time: Fri, 07 Sep 2018 11:00:39 )
Effective genome size: 0.377583768199 (File: effective_genome_size, Log level: INFO, Time: Fri, 07 Sep 2018 11:00:39 )
Number unique 36-mers: 21608143
Effective genome size: 0.377583768199
So how can overcome this issue for effective genome size calculation for entire genome.
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