Closed c-guzman closed 7 years ago
The last time this happened there was a problem with the users files.
Could you please post the output of zcat Control2_treatment.bed.gz | head | cat -et
?
(My guess is that your files are not tab-separated.)
On Thursday, September 8, 2016, Carlos Guzman notifications@github.com wrote:
Command used:
Command executed:
epic --treatment Control2_treatment.bed.gz --control Control2_control.bed.gz --genome hg19 --fragment-size 150 > Control2_epic.bed
Resulting error:
Command error:
epic --treatment Control2_treatment.bed.gz --control Control2_control.bed.gz --genome hg19 --fragment-size 150 (File: epic, Log level: INFO, Time: Thu, 08 Sep 2016 11:56:47 )
gzip: stdout: Broken pipe Used first 10000 reads of Control2_treatment.bed.gz to estimate a median read length of 34.0 Mean readlength: 33.3074, max readlength: 37, min readlength: 20. (File: find_readlength, Log level: INFO, Time: Thu, 08 Sep 2016 11:56:47 ) Using an effective genome fraction of 0.810858412293. (File: genomes, Log level: INFO, Time: Thu, 08 Sep 2016 11:56:47 ) Binning Control2_treatment.bed.gz (File: run_epic, Log level: INFO, Time: Thu, 08 Sep 2016 11:56:47 ) Binning chromosomes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, M, X, Y (File: count_reads_in_windows, Log level: INFO, Time: Thu, 08 Sep 2016 11:56:47 ) Merging the bins on both strands per chromosome. (File: count_reads_in_windows, Log level: INFO, Time: Thu, 08 Sep 2016 12:00:12 ) Binning Control2_control.bed.gz (File: run_epic, Log level: INFO, Time: Thu, 08 Sep 2016 12:00:13 ) Binning chromosomes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, M, X, Y (File: count_reads_in_windows, Log level: INFO, Time: Thu, 08 Sep 2016 12:00:13 ) Merging the bins on both strands per chromosome. (File: count_reads_in_windows, Log level: INFO, Time: Thu, 08 Sep 2016 12:03:40 ) Merging ChIP and Input data. (File: helper_functions, Log level: INFO, Time: Thu, 08 Sep 2016 12:03:40 ) 2510169508.0 effective_genome_length (File: compute_background_probabilites, Log level: DEBUG, Time: Thu, 08 Sep 2016 12:03:40 ) 200 window size (File: compute_background_probabilites, Log level: DEBUG, Time: Thu, 08 Sep 2016 12:03:40 ) 0 total chip count (File: compute_background_probabilites, Log level: DEBUG, Time: Thu, 08 Sep 2016 12:03:40 ) 0.0 average_window_readcount (File: compute_background_probabilites, Log level: DEBUG, Time: Thu, 08 Sep 2016 12:03:40 ) 1 island_enriched_threshold (File: compute_background_probabilites, Log level: DEBUG, Time: Thu, 08 Sep 2016 12:03:40 ) 4.0 gap_contribution (File: compute_background_probabilites, Log level: DEBUG, Time: Thu, 08 Sep 2016 12:03:40 ) 1.0 boundary_contribution (File: compute_background_probabilites, Log level: DEBUG, Time: Thu, 08 Sep 2016 12:03:40 ) Traceback (most recent call last): File "/usr/local/anaconda2/bin/epic", line 4, in
import('pkg_resources').run_script('bioepic==0.1.6', 'epic') File "/usr/local/anaconda2/lib/python2.7/site-packages/pkg_resources.py", line 461, in run_script self.require(requires)[0].run_script(script_name, ns) File "/usr/local/anaconda2/lib/python2.7/site-packages/pkg_resources.py", line 1194, in run_script execfile(script_filename, namespace, namespace) File "/usr/local/anaconda2/lib/python2.7/site-packages/bioepic-0.1.6-py2.7.egg-info/scripts/epic", line 165, in run_epic(args) File "/usr/local/anaconda2/lib/python2.7/site-packages/epic/run/run_epic.py", line 45, in run_epic compute_background_probabilities(nb_chip_reads, args) File "/usr/local/anaconda2/lib/python2.7/site-packages/epic/statistics/compute_background_probabilites.py", line 49, in compute_background_probabilities boundary_contribution, genome_length_in_bins) File "/usr/local/anaconda2/lib/python2.7/site-packages/epic/statistics/compute_score_threshold.py", line 24, in compute_score_threshold current_scaled_score = int(round(score / BIN_SIZE)) OverflowError: cannot convert float infinity to integer Any ideas?
— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/endrebak/epic/issues/38, or mute the thread https://github.com/notifications/unsubscribe-auth/AQ9I0v4qV0KRQOWrbWeG0em76JWACekEks5qoE_dgaJpZM4J4SS- .
And if this is not it, I will probably be able to find the bug right away if you could send me the files privately through dropbox or something.
Head of treatment bed:
10^I60560^I60594^IHWI-EAS306_8184_FC309UE_CR_3_72_357_713^I1^I+$
10^I61167^I61200^IHWI-EAS306_8184_FC309UE_CR_2_78_553_1598^I1^I-$
10^I62038^I62073^IHWI-EAS306_8184_FC309UE_CR_2_78_539_852^I1^I-$
10^I62082^I62116^IHWI-EAS306_8184_FC309UE_CR_3_72_1521_1020^I1^I-$
10^I62305^I62340^IHWI-EAS306_8184_FC309UE_CR_2_55_774_35^I1^I-$
10^I62578^I62611^IHWI-EAS306_8184_FC309UE_CR_2_26_1576_1213^I1^I-$
10^I62588^I62621^IHWI-EAS306_8184_FC309UE_CR_2_79_1251_742^I1^I-$
10^I62742^I62775^IHWI-EAS306_8184_FC309UE_CR_3_13_999_509^I1^I+$
10^I63075^I63105^IHWI-EAS306_8184_FC309UE_CR_3_44_859_1033^I1^I-$
10^I63765^I63799^IHWI-EAS306_8184_FC309UE_CR_3_24_1570_486^I1^I+$
Head of Input bed:
10^I60560^I60594^IHWI-EAS306_8184_FC309UE_CR_3_72_357_713^I1^I+$
10^I61167^I61200^IHWI-EAS306_8184_FC309UE_CR_2_78_553_1598^I1^I-$
10^I62038^I62073^IHWI-EAS306_8184_FC309UE_CR_2_78_539_852^I1^I-$
10^I62082^I62116^IHWI-EAS306_8184_FC309UE_CR_3_72_1521_1020^I1^I-$
10^I62305^I62340^IHWI-EAS306_8184_FC309UE_CR_2_55_774_35^I1^I-$
10^I62578^I62611^IHWI-EAS306_8184_FC309UE_CR_2_26_1576_1213^I1^I-$
10^I62588^I62621^IHWI-EAS306_8184_FC309UE_CR_2_79_1251_742^I1^I-$
10^I62742^I62775^IHWI-EAS306_8184_FC309UE_CR_3_13_999_509^I1^I+$
10^I63075^I63105^IHWI-EAS306_8184_FC309UE_CR_3_44_859_1033^I1^I-$
10^I63765^I63799^IHWI-EAS306_8184_FC309UE_CR_3_24_1570_486^I1^I+$
I can send the files to you via dropbox if you still need them. They're encode files. Specifically ENCSR000DLY and it's associated control.
I used bamtobed from bedtools to generate these bed files so i'm not entirely sure why they wouldn't be tab separated to begin with.
I was able to reproduce this; it happens when there is no "chr" in the chromosome names. For now you can solve it by running
sed "s/^/chr/" treatment.bed > ucsc_treatment.bed sed "s/^/chr/" input.bed > ucsc_input.bed
Thanks for reporting. I will support encode style chromo names soon, but do not have time to fix it right now.
On Fri, Sep 9, 2016 at 4:55 PM, Carlos Guzman notifications@github.com wrote:
Head of treatment bed:
10^I60560^I60594^IHWI-EAS306_8184_FC309UE_CR_3_72_357_713^I1^I+$ 10^I61167^I61200^IHWI-EAS306_8184_FC309UE_CR_2_78_553_1598^I1^I-$ 10^I62038^I62073^IHWI-EAS306_8184_FC309UE_CR_2_78_539_852^I1^I-$ 10^I62082^I62116^IHWI-EAS306_8184_FC309UE_CR_3_72_1521_1020^I1^I-$ 10^I62305^I62340^IHWI-EAS306_8184_FC309UE_CR_2_55_774_35^I1^I-$ 10^I62578^I62611^IHWI-EAS306_8184_FC309UE_CR_2_26_1576_1213^I1^I-$ 10^I62588^I62621^IHWI-EAS306_8184_FC309UE_CR_2_79_1251_742^I1^I-$ 10^I62742^I62775^IHWI-EAS306_8184_FC309UE_CR_3_13_999_509^I1^I+$ 10^I63075^I63105^IHWI-EAS306_8184_FC309UE_CR_3_44_859_1033^I1^I-$ 10^I63765^I63799^IHWI-EAS306_8184_FC309UE_CR_3_24_1570_486^I1^I+$
Head of Input bed:
10^I60560^I60594^IHWI-EAS306_8184_FC309UE_CR_3_72_357_713^I1^I+$ 10^I61167^I61200^IHWI-EAS306_8184_FC309UE_CR_2_78_553_1598^I1^I-$ 10^I62038^I62073^IHWI-EAS306_8184_FC309UE_CR_2_78_539_852^I1^I-$ 10^I62082^I62116^IHWI-EAS306_8184_FC309UE_CR_3_72_1521_1020^I1^I-$ 10^I62305^I62340^IHWI-EAS306_8184_FC309UE_CR_2_55_774_35^I1^I-$ 10^I62578^I62611^IHWI-EAS306_8184_FC309UE_CR_2_26_1576_1213^I1^I-$ 10^I62588^I62621^IHWI-EAS306_8184_FC309UE_CR_2_79_1251_742^I1^I-$ 10^I62742^I62775^IHWI-EAS306_8184_FC309UE_CR_3_13_999_509^I1^I+$ 10^I63075^I63105^IHWI-EAS306_8184_FC309UE_CR_3_44_859_1033^I1^I-$ 10^I63765^I63799^IHWI-EAS306_8184_FC309UE_CR_3_24_1570_486^I1^I+$
I can send the files to you via dropbox if you still need them. They're encode files. Specifically ENCSR000DLY and it's associated control.
— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/endrebak/epic/issues/38#issuecomment-245937519, or mute the thread https://github.com/notifications/unsubscribe-auth/AQ9I0vvVW6pY5nzQ-Sb69-z5GZJ0RLFUks5qoXNWgaJpZM4J4SS- .
Great! Thank you!
All of zebrafish genome contigs are not called ~ "^chr". IMHO chromosome names should be assumed to be any arbitrary strings without white characters.
Thanks for the feedback!
I agree that epic should handle gencode genome names, but I do not see how to handle arbitrary strings.
The problem is that I have a lookup table for each supported genome:
# example dm3
chr2L 23011544
chr2LHet 368872
chr2R 21146708
chr2RHet 3288761
chr3L 24543557
chr3LHet 2555491
chr3R 27905053
chr3RHet 2517507
chr4 1351857
chrU 10049037
chrUextra 29004656
chrX 22422827
chrXHet 204112
chrYHet 347038
chrM 19517
I need to match the chromosome names in the user's bed files to the chromosome names in the lookup table. If the names are arbitrary strings I do not see how to do it.
Also, contigs (are those non-canonical chromosome parts?) are not supported because they would mess with mappability and total genome length. Of course if the contig length is <<< genome length, this should not matter much.
Edit: I think the only problem with arbitrary names for chromosomes is that I cannot remove reads that are shifted outside of the chromosome boundaries, which is a minor issue. I'll think about whether I should add a --non-canonical-chromosomes
flag (suggestions for better names accepted).
Edit2: Also, the built-in chromosome names are there to save time; without them, I would need another pass through the data to fetch the chromosome names. This is because to make each core work with one chromosome, I need to know which chromosomes are in the data. Of course cut -f 1 | sort -u
would fetch all the chromo names for me and take very little time...
Edit3: With non-canonical genome names, the bigwigs created by epic won't be viewable in the UCSC genome browser.
@balwierz In 0.1.21
I have added the flag --chromsizes/-cs
so that arbitrary genomes, assemblies or simulated data can be used.
Command used:
Resulting error:
Any ideas?