popoolation2 Activity
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Activity for popoolation2
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Beatriz Cunha Portinha created ticket #49
Script name typo in snp-frequency-diff.pl help
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Tatereal modified a comment on ticket #48
Yes I also created a text file with the same formatting and info of the whole-genome sync file and tried to run using the same command, but it didn't work.
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Yes I also created a text file with the same formatting and info of the whole-genome sync file and tried to run using the same command, but it didn't work.
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Bernadette posted a comment on ticket #11
You will need to install the perl package (Text::NSP::Measures::2D::Fisher::twotailed). This fixed the problem for me. Install cpanminus: sudo apt install cpanminus Install perl package: cpanm Text::NSP::Measures::2D::Fisher::twotailed Link to package: https://metacpan.org/pod/Text::NSP::Measures::2D::Fisher::twotailed
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Mr Schweitzer posted a comment on a wiki page
Hello Mr. Bennardo, I think the two most common ways of adressing multiple testing in GWAS-like data is either using a Bonferroni corrected p-value threshold or by using a False Discovery Rate (FDR) approach. The documentation for the R package "qvalue" is very well written: https://www.bioconductor.org/packages/release/bioc/manuals/qvalue/man/qvalue.pdf
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Lautaro Ezequiel Bennardo posted a comment on a wiki page
Hello everyone, I am using popoolation2 to perform the CMH test between 4 pairs of populations. The issue is that it's giving me very high p-values in general (very low actually), less than 10e-60. Does anyone know how I should choose the p-value cutoff? Or if there's any correction I should apply to these values? Thank you!
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Anonymous posted a comment on a wiki page
Hi everyone, I noticed that when converting an mpileup file to a sync file, positions on a genome are shifted. For example, position 10,923,271 in a reference genome used for mapping was shifted to 10,923,753 in a sync file. Does anyone know how to resolve this error?
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谢思麒 posted a comment on ticket #38
Hello, I have the same problem as you. Have you solved your problem? I wonder if you could teach me！ Thanks， xsq
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Hafiz Muhammad Anas posted a comment on a wiki page
Hello Community Is it possible to annotate snps from snpeff eff tool after getting variants? which file i need to annoate?
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Renan Granado created ticket #48
Fst for specific positions
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Rahia Mashoodh modified a comment on ticket #41
what did you end up concluding? I'm also confused about the output of cmh-test -- the max value I get is 1 and lowest is 5e-09 ... this would suggest no significance differences if this is indeed -log10(pvalue). which is plausible but I just want to make sure I am doing this correctly.
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I'm also confused about the output of cmh-test -- the max value I get is 1 and lowest is 5e-09 ... this would suggest no significance differences. which is plausible but I just want to make sure I am doing this correctly.
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Atikah posted a comment on a wiki page
I just found out that it was rc SNPs not pop SNPs type.
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Hi everyone, I am using Popoolation2 sofware to calculate allele frequency and Fst now. But when I calculate allele difference of my populations, it generates several locus with 1 allele count (only one allele state). Commonly SNPs is a biallele or in some cases it can contain 3 alelles or 4 alleles. And in the minimum coverage, I set it 10 but in the rc file it generates the SNP with coverage less than 10. Do you think there is an error that happening when I use the Popoolation2? I am really appreciate...
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Hello Mr. Kengne, I had the same problem and I managed to get the perl script running by following this solution in the comments here: https://code.google.com/archive/p/popoolation2/issues/19 I hope this helps!
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Maria Cortazar Chinarro posted a comment on ticket #47
Please, does anyone have tried "create-genewise-sync.pl" command in order to do the annotation on a gtf file? Otherwise how do you do the annotation. This is a pity because I cannot finish the pipeline if this is not working properly. I really appreciate if you could help me, Kind regards, Maria//
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Jonas A Kengne posted a comment on ticket #23
Hi Robert, could you please guide me on how to install the Perl Module Text::NSP::Measure.....twotailed.pm. I am a biologist. many thanks in advance
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Hi , I downloaded the online tutorial on popoopulation2 and had some problems in its execution. Could anyone assist pls? problem created mpileup successfully created syn file successfully fisher-test.pl fails (stops on line 9 and 10) Exact message from the terminal: poolseq_test$: perl popoolation2_1201/fisher-test.pl --input p1_p2.sync --output p1_p2.fet --min-count 6 --min-coverage 50 --max-coverage 200 --suppress-noninformative Can't locate Text/NSP/Measures/2D/Fisher/twotailed.pm in @INC (you...
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Hi Erica, I downloaded the online tutorial on popoopulation2 and had some problems in its execution. Could you assist pls? problem created mpileup successfully created syn file successfully fisher-test.pl fails (stops on line 9 and 10) Exact message from the terminal: poolseq_test$: perl popoolation2_1201/fisher-test.pl --input p1_p2.sync --output p1_p2.fet --min-count 6 --min-coverage 50 --max-coverage 200 --suppress-noninformative Can't locate Text/NSP/Measures/2D/Fisher/twotailed.pm in @INC (you...
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Problems with create-genewise-sync.pl
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Hi, I am currently having the same error when I am running the script, the following line is not valid at /sw/apps/bioinfo/popoolation2/1201/rackham/create-genewise-sync.pl line 232, <$ifh> line 360233. Parsing gtf file.. Anyone knows how I can solve the problem?
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Hi, I am currently having the same error when I am running the script, the following line is not valid at /sw/apps/bioinfo/popoolation2/1201/rackham/create-genewise-sync.pl line 232, <$ifh> line 360233. Parsing gtf file.. Anyone knows how I can solve the proble?
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Please, can you upload the igv png images to check whether my results look ok? I cannot acces to thouse pictures: "Voila, the result should look something like this: Note that the result shown above only contain the Fst for a single pairwise comparison (pop1 vs pop2). PoPoolation2 is per default calculating the Fst for all possible pairwise comparisons between populations (when several populations are present in the synchronized file), and these results may just as easily be converted into the .igv...
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Please, can you upload the igv png images to check whether my results looks ok? I cannot acces to thouse pictures: "Voila, the result should look something like this: Note that the result shown above only contain the Fst for a single pairwise comparison (pop1 vs pop2). PoPoolation2 is per default calculating the Fst for all possible pairwise comparisons between populations (when several populations are present in the synchronized file), and these results may just as easily be converted into the .igv...
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Rakan Naboulsi created ticket #46
Discrepancy in Fst values calculated manually and by Popoolation2
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Will Shim posted a comment on ticket #45
Edit: sorry, when I said "This was run in a cluster with 64GB or 512GB of memory", I meant in a node inside the cluster that had those memories. For instance, I run the cmh-test.pl in a node that had 512GB of memory allocated to this script/job only, and was not shared by other jobs. Hope this clears up some misunderstandings. Thanks again! Will
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Segmentation faults when running some PoPoolation2 scripts
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Robert Kofler modified a wiki page
Tutorial
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Omid Jafari posted a comment on a wiki page
Hi dears, Actually I am trying to use your tool to calculate the allele frequency of my Whole genome data. For this porpuse, all steps were being done smoothly but for the step called "Calculate allele frequency differences", the command gets done with giving incomplete out put files. The version of the perl in our server is 5.22 but you have said it should be 5.8 or higher. Do you think is that possible to be effective? Thank you very much in advance. Regards, Omid
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Arijit Ghosh posted a comment on ticket #37
Hi, I guess it wpuld have been solved by now, still just saying, delete that entry manually from the gtf file, and check that region manually.
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I also encountered same problem, I just deleted Fbgn0002781 from the gtf file, will check that region myself manually.
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Thomas Rundell created ticket #44
Error running calculations for genes
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David Rinker posted a comment on a wiki page
Really appreciate having this software availalbe! Currently I'm using it for BSA in fruitfly. In computing Fst I'm confused as to what "pool-size" means. I've seen it mentioned as referring to both individuals and to number of chromosomes (and can see arguments for both). Also, what is the correct syntax for applying it when pools are unequal?--a poster above uses a ":" delimiter so is that correct? And if so am I safe in assuming that "x:y" would apply to the pools in the order in which they were...
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Jernej Bravnicar posted a comment on ticket #43
Hi, try this svn checkout https://svn.code.sf.net/p/popoolation2/code/trunk popoolation2-code all best, Nejc
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prabodh created ticket #43
Unable install popoolation2
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Kyle Turner posted a comment on ticket #42
This may have been a silly mistake in that all it took to fix it was to switch the -fastq-type to sanger.
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Thanks for the quick reply! I started a new ticket to address my problem since it goes past just the sliding window script. It seems that the mpileup2sync did not produce any real results. My mpileup file has data but the produced sync file is only zeros. (the picture attached shows a portion of the sync file. The whole file looks like this though)
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Joanna Griffiths posted a comment on ticket #16
Hi Kyle, This issue was specific to the sliding window script. I managed to fix the issue by changing some of the parameters. I decreased the min-count and min-covered-fraction from the example in the tutorial. These were my final parameters: --min-count 2 --min-coverage 5 --max-coverage 200 --min-covered-fraction 0.2 I think the main issue was that the min-covered-fraction cannot be at 100% (ie 1), so decreasing this should make it work. Rarely will there be sufficient coverage at every single base...
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Thanks for any help! The only thing I can think to do is to try a new alignment protical and see if that gets me anywhere.
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Empty Sync File
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Hello Joanna! So I'm also having this problem of the sync file being completely empty. Looking at my mpilup file there seems to be data there, but none of it is being transfered to the sync file. Any advice on how you got past this problem?
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Arsalan Emami Khoyi created ticket #41
fisher exact test p values !
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Jenni created ticket #40
min covered fraction and contig size...
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Verena Kutschera modified a comment on ticket #39
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<meta charset="UTF-8"> <style type="text/css"><br> p.gdprmyball {<br> font-family: Arial, Helvetica, sans-serif;<br> }</p> <div class="codehilite"><pre><span></span><span class="na">.info</span> <span class="err">{</span> <span class="nl">font-size:</span> <span class="err">17</span><span class="nf">px</span><span class="c">;</span> <span class="err">}</span> </pre></div> <p></style> Unable to display this message Click here to view full message HTML message delayed: GTsd - Date: 09/10/2018 10:44:06...
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Error due to too large insertions when running identify-indel-regions.pl
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Error when run identify-indel-regions.pl
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Balan Ramesh posted a comment on ticket #30
I have the same issue.
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Thanks Joanna, absolutely, it will rarely be the case that there is sufficient coverage at every single base of a sliding window, therefore --min-covered-fraction should be lower than 1.0
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Joanna Griffiths posted a comment on ticket #36
Yes! I managed to fix the issue by changing some of the parameters. I decreased the min-count and min-covered-fraction from the example in the tutorial. These were my final parameters: --min-count 2 --min-coverage 5 --max-coverage 200 --min-covered-fraction 0.2 I think the main issue was that the min-covered-fraction cannot be at 100% (ie 1), so decreasing this should make it work.
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Pablo Deschepper posted a comment on ticket #36
Is this issue already resolved? I am encountering the same problem
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I see that everyting is on the + strand, but 2 exon and 2 CDS sequences are on the - strand. So this might be causing the error. Any suggestions on how to resolve this issue? https://drive.google.com/open?id=1G8eQ-T_YBRavZRY9KIWER5Si7m58XmYo
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https://drive.google.com/open?id=1qczN_WFK3yurzZwbrxXDRuAyqCQ6sPwy
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https://drive.google.com/open?id=1qczN_WFK3yurzZwbrxXDRuAyqCQ6sPwy
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https://drive.google.com/open?id=1qczN_WFK3yurzZwbrxXDRuAyqCQ6sPwy
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Problem creating genewise sync file
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Ok, so I tried making a new .sync file with "sanger" as quality encoding and now my .sync file is perfectly fine! FastQC was telling me that my files were encoded in illumina and I also used the Illumina HiSeq 4000 platform. At least my sync file is ok now without "null" and errors showing up when i calculate Fst.
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Is this already solved? I am having the same issue: "use of uninitalized value". I also have the "null" in my sync file. Additionally, something seemed weird about my sync file when I compare it to my bam files loaded into IGV. (See attached screenshot). As you can see the code in the .sync file does not correspend with the A:T:C:G:N:del seen in the two bam files. I have used samtools 1.7 to make the bam and mpileup files. Then I used the mpileup2sync.pl script with a min-quality of 20 and illumina...
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NAs in sliding window Fst but not in the Fst for each SNP
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James Reeve posted a comment on a wiki page
I'm trying to access the data for the tutorial, however the link appears to be dead. I've tried accessing it with two seperate browsers. How do I access the data?
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Hi Robert, Thanks for your reply. My sync files are composed of all zeros in the columns, but I know this is incorrect. What would cause the sync file to be full of 0? This is what my code for creating the sync file looks like: perl popoolation2_1201/mpileup2sync.pl --fastq-type sanger --min-qual 20 --input all.mpileup --output all_perl.syn
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not sure i get the problem - the sync files in the above example are empty (counts of all alleles are zero) thus the cmh and fst etc will be empty or na (you can not compute allele frequency differences with allele counts zero)
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Hello, Was this problem ever solved? I am receiving the exact same problem. Thanks!
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Melanie Parejo created ticket #35
--min-count for FST and how to filter for biallelic SNPs
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Yann Dorant created ticket #34
FST index precisions
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Hi, It may be caused by your encoding setting choice. See the #13 ticket for more informations
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Mary O'Neill created ticket #33
SYNC ERROR - not all positions converted
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Adam Vorsino posted a comment on ticket #32
Thanks for this Chris! I am in all honestly still not sure whether it worked or not. It is taking forever to run the assessment. I am thinking about trying to break the .sync or .mpileup file into parts and attempting to implement some form of multicore processing on the assessment. Are you finding that it takes a long time to run as well? I am definitly interested to see what you did, if you're willing to share. I will pm you later. Much appreciated, Adam
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Chris Allan posted a comment on ticket #32
Hi Adam, Sorry for the delay. Hopefully your method worked. If you still want me to elaborate on what I did maybe send me an email at cjall6 (at) student.monash.edu and I will get back to you? Regards, Chris
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Hi Chris, Thanks for this... apologies for not getting back sooner. I decided to build the mpileup file in a different way and wanted to respond after the Fst assessment ran. It is taking quite sometime, and I was able to calculate allele frequencies using the mofidifed mpileup... both of those are signs of progress for me. As I am not sure Robert has any more suggestions I thought I would share this. I essentially modifed the mpileup code from: samtools-1.1/samtools mpileup -u --skip-indels -d 250...
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Hi Robert and Adam, Yep, that's right there was 2 samples for my pileup file. I used samtools version 1.3.1 and STAR version 020201 for alignment; I will try another version of samtools to see if that was a problem. In the meantime I adapted a perl script, pileup2base.pl, to derive a sync file I can use with fst-sliding.pl. Regards, Chris
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Hey Robert, Thanks for this. To be safe I tried rerunning everything with Samtools 1.1, apologies for getting back to you so late... it takes some time as I have to essentially re-run Pop1 and then send those outputs through Pop2. It still seems to be giveing the same warning and failure messages: **Use of uninitialized value $rc in uc at /Modules/Synchronized.pm line 31, <$fh> line 206282. **Use of uninitialized value in numeric le (<=) at /Modules/SyncSlider.pm line 84, <$fh> line 206282. **failed...
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for me 1.2 worked or even earlier, please let me know if any of these earlier versions work If this is the problem I will certainly update Pop2... cheers ro
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Hi Robert, Thanks for getting back to me so quickly. I have downloaded samtools version 1.3.1 and used it to replace 1.5 in all aspects of my assessment... sadly I am still getting the same error. Oddly, when samtools 1.5 is used to develop the mpileup with only a single population (in Popoolation 1) it works fine, it's when the populations are combined in Popoolation 2 prior to changing to a sync file that things seem to go awry. Just in case (though I know it is illumina sequencing) I ran the assessment...
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That is absolutely strange, your pileup suggests that you used two bam files as input no? dmel_mitochondrion_genome 19506 A 2 ,$, :E 2 ,$,$ B: Every bam file gets three columns like 2 ,$, :E and than 2 ,$,$ B: but than the next line dmel_mitochondrion_genome 19507 A 1 , < 0 we have bam #1 with 1 , < but the next entry is just 0 (not three columns) Usually empty entries got a star * and three columns. I never saw that before, is this a new behaviour of samtools??? That is really anoying when the output...
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Hi Chris and Robert, I seem to be haveing the same error when I try running the Fst sliding window assessment using sync files developed in both Java and Perl. Each of three populations were alighned to a reference with BWA, trimmed in Trimomatic, and filtered in samtools prior to combining them in an mpileup. I was wondering if you had any breakthroughs, or thoughts on this. Best, Adam
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Hi, So I ran the perl version of mpileup2sync just to see what would happen. It got to a certain point then gave this error: Fucked entry dmel_mitochondrion_genome 19507 A 1 , < 0 at ../popoolation2_1201/Modules/Pileup.pm line 50, <$ifh> line 19507. Here is line 19506-8 of the pileup: dmel_mitochondrion_genome 19506 A 2 ,$, :E 2 ,$,$ B: dmel_mitochondrion_genome 19507 A 1 , < 0 dmel_mitochondrion_genome 19508 T 0 0 Does this mean something is wrong with my pileup? How could I fix it?
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Hi Robert, So, I definitely set my fastq quality encoding to be sanger. Do you have any other suggestions as to why mpileup2sync is printing "null" at so many points of the sync file? I used star for my alignment of rna reads. Is popoolation2 compatible with bwa aligner only? Bwa isn't really splice-aware so that's why I used star. Any help would be really appreciated!
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any other advice? :)
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Hi Robert, Thanks for the advice, but I definitely did use sanger in the mpileup2sync.jar! java -jar /popoolation2_1201/mpileup2sync.jar --fastq-type sanger --min-qual 20 --threads 3 --output myfile.sync --input myfile.mpileup Cheers, Chris
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jup your pileup is sanger
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ahh you probably used the wrong fastq quality encoding. use sanger
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If I run "zcat myfile.mpileup.gz | head -400 > mpileuphead.txt", I get the file attached. Does anything appear wrong with the mpileup file at the 171st base of the reference? Cheers, Chris
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Hi Robert, I finally have some answers! So, the first lines of my sync file appear to be fine: dmel_mitochondrion_genome 1 A 5:0:0:0:0:0 2:0:0:0:0:0 dmel_mitochondrion_genome 2 A 6:0:0:0:0:0 4:0:0:0:0:0 dmel_mitochondrion_genome 3 T 0:7:0:0:0:0 0:6:0:0:0:0 dmel_mitochondrion_genome 4 G 0:0:0:20:0:0 0:0:0:30:0:0 dmel_mitochondrion_genome 5 A 20:0:0:0:0:0 33:0:0:0:0:0 But something goes wrong 170 bases into the reference genome, and the sync file is filled with null entries: dmel_mitochondrion_genome...
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Hi Robert, I got the error for every line, those were just the last lines of the error file which I sent you. So the format is, for every line of my sync file (x), I get this: Use of uninitialized value $rc in uc at /mnt/lustre/projects/tu32/raw_reads/original_data/popoolation2_1201/Modules/Synchronized.pm line 31, <$ifh> line (x). This is what the sync file looked like when I ran mpileup to make 19 samples as opposed to 2 samples. dmel_mitochondrion_genome 1 A 0:0:0:0:0:0 0:0:0:0:0:0 0:0:0:0:0:0...
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it seems you get this error only at the lines 143483-143485...etc of your sync file is this correct? You are not getting it at line 1 etc no? Because than its possible that your sync file is ok at the begining but somehow got corrupted later on. Could you please send me the lines 143483...143493 of your sync file (cat file | head -143493 | tail) cheers ro
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Hi Robert, Sorry to bother you again! Any advice on how to rectify this error? I am still getting the "uninitialized value $rc" error from the Synchronized.pm file. Is the reference character related to the reference genome used? Perhaps I should send you my full .sync file, in case that helps diagnose the problem? I can't attach it here, it is 900MB. Regards, Chris cjall6@student.monash.edu
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Hi Robert, I ran mpileup, mpileup2sync and the sliding-window script again after merging the files properly. This time I only got the first error, as well as a new error for the final line: Use of uninitialized value $rc in uc at /mnt/lustre/projects/tu32/callan/popoolation2_1201/popoolation2_1201/Modules/Synchronized.pm line 31, <$ifh> line 143483. Use of uninitialized value $rc in uc at /mnt/lustre/projects/tu32/callan/popoolation2_1201/popoolation2_1201/Modules/Synchronized.pm line 31, <$ifh>...
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hmm your two files seem perfectly fine. Yes absolutely, you have to merge the files. Pop2 ignores readgroup info. let me know if you still have the same error. cheer sro
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second attachment
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Hi Robert, See attached for the heads of sync and mpileup files. This might be relevant: I just noticed that the sync file appears to have 19 columns for separate samples... This is not what I thought would happen! I thought that it would have been collapsed to 2 columns since the mpileup stage, because although I input 19 bam files to samtools mpileup, it only identified two samples from the read group information (9 for population A, 10 for population B). Perhaps I need to run mpileup again after...
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Hmm, seems something wrong in the sync file $rc is the reference character and this one seems to be missing. could you send me a head of your sync file and the mpileup file you used to generate the sync, cheers ro
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Fst Test error
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Thanks for your reply. I also used Illumina hiseq sequencing but actually set fastq-type option to sanger when running mpileup2sync...strange! I think i'll submit my own ticket! Regards, Chris
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adedayo Adeyanju posted a comment on ticket #30
The error was created from the output of the (Create a synchronized file) java -jar /group/bioinfo/apps/apps/popoolation2_1201/mpileup2sync.jar --input p1_p2.mpileup --output p1_p2_java.sync --fastq-type sanger --min-qual 20 --threads 20 initially, I was using Illumina as my fastq type which is correct but it seems the software did not recognize this I used sanger as my --fastq-type instead of Illumina and that seemed to solve the problem. On Thu, Jul 6, 2017 at 7:25 AM, Chris Allan cjaln200@users.sf.net...
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Hi, I have the same error. Use of uninitialized value $rc in uc at /mnt/lustre/projects/tu32/callan/popoolation2_1201/popoolation2_1201/Modules/Synchronized.pm line 31, <$ifh> line 218. Did you ever find a resolution? Regards, Chris
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Arunkumar Ramesh created ticket #31
subsample-synchronized.pl, dont discard if coverage lower than target coverage
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SNP-frequency-diff.pl output error
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frau ottos sampling-rape
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