bammds_intersect dying with correct bam and mike files

[morenomayar]

bammds_intersect dies when trying with data for the simulations:

When I try this on eos:

bammds_intersect --debug /home/jmoreno/data/my_kelvin_data/MDSTests/HGDPdata/HGDP_hg19.one_allele.txt /home/jmoreno/data/my_kelvin_data/MDSTests/DownSampling/DownSampled_3e+06_HGDP00927.flt.sort.rmdup.realign.md.bam -m 30 -n 20

I get (from the merge part): Use of uninitialized value in join or string at /home/jmoreno/data/my_kelvin_data/MDSTests/contamination/bammds_merge line 115, <> line 4.

From the fillout part: Can't call method "new" on an undefined value at (eval 1) line 82.

And of course the plotting part dies: Error in read.table(file = file, header = header, sep = sep, quote = quote, : no lines available in input Calls: all -> read_data_files -> read.csv -> read.table Execution halted

These files work for populationmdsplot_victor

[ole-tange]

Cause by triallelic site. The site is now in testinputfiles/chr1pos99610153.*.

[ole-tange]

Seems fixed now.

I have been able to run this twice:

./bammds --debug test/DownSampled_3e+06_HGDP00927.flt.sort.rmdup.realign.md.bam test/HGDP_hg19.one_allele.txt

[morenomayar]

I tried again on eos, and it keeps dying. =( I ran: bammds --debug /home/jmoreno/data/my_kelvin_data/MDSTests/DownSampling/DownSampled_3e+06_HGDP00927.flt.sort.rmdup.realign.md.bam /home/jmoreno/data/my_kelvin_data/MDSTests/HGDPdata/HGDP_hg19.one_allele.txt

And got:

Use of uninitialized value in join or string at /home/jmoreno/data/my_kelvin_data/MDSTests/contamination/bammds_merge line 115, <> line 4. Use of uninitialized value in join or string at /home/jmoreno/data/my_kelvin_data/MDSTests/contamination/bammds_merge line 115, <> line 4. Use of uninitialized value in join or string at /home/jmoreno/data/my_kelvin_data/MDSTests/contamination/bammds_merge line 115, <> line 8. Use of uninitialized value in join or string at /home/jmoreno/data/my_kelvin_data/MDSTests/contamination/bammds_merge line 115, <> line 9. Use of uninitialized value in join or string at /home/jmoreno/data/my_kelvin_data/MDSTests/contamination/bammds_merge line 115, <> line 3. Use of uninitialized value in join or string at /home/jmoreno/data/my_kelvin_data/MDSTests/contamination/bammds_merge line 115, <> line 3. Use of uninitialized value in join or string at /home/jmoreno/data/my_kelvin_data/MDSTests/contamination/bammds_merge line 115, <> line 4. Use of uninitialized value in join or string at /home/jmoreno/data/my_kelvin_data/MDSTests/contamination/bammds_merge line 115, <> line 5. Use of uninitialized value in join or string at /home/jmoreno/data/my_kelvin_data/MDSTests/contamination/bammds_merge line 115, <> line 3. bammds_fillout tmp/DownSampled_3e+06_HGDP00927.flt.sort.rmdup.realign.md,HGDP_hg19.one_allele.legend.csv > tmp/DownSampled_3e+06_HGDP00927.flt.sort.rmdup.realign.md,HGDP_hg19.one_allele.legend.filled.csv Attempting to create directory /home/jmoreno/perl5 bammds_plot.r tmp/DownSampled_3e+06_HGDP00927.flt.sort.rmdup.realign.md,HGDP_hg19.one_allele.asd.gz tmp/DownSampled_3e+06_HGDP00927.flt.sort.rmdup.realign.md,HGDP_hg19.one_allele.legend.filled.csv DownSampled_3e+06_HGDP00927.flt.sort.rmdup.realign.md,HGDP_hg19.one_allele.pdf 1 2 Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : line 939 did not have 323936 elements Calls: all -> read_data_files -> read.table -> scan Execution halted

Do you have any ideas?

[ole-tange]

I have re-tested. It works for me on eos. Did you forget to run 'svn up'?

[ole-tange]

Believe fixed in [231].

[morenomayar]

Works now! It was caused by id of triallelic sites. Probably we should output the total number/proportion of total triallelic sites somewhere.

[sapfo]

yes it would be nice to have that in the summary somehow although some people might be confused about it....

On Wed, Oct 30, 2013 at 7:22 PM, morenomayar notifications@github.comwrote:

Works now! It was caused by id of triallelic sites. Probably we should output the total number/proportion of total triallelic sites somewhere.

— Reply to this email directly or view it on GitHubhttps://github.com/ole-tange/barmaids/issues/50#issuecomment-27423109 .

[ole-tange]

Can you make a minimal test set that reproduces the problem?

What kind of output would you like?

/Ole

On Fri, Nov 1, 2013 at 12:53 AM, sapfo notifications@github.com wrote:

yes it would be nice to have that in the summary somehow although some people might be confused about it....

On Wed, Oct 30, 2013 at 7:22 PM, morenomayar notifications@github.comwrote:

Works now! It was caused by id of triallelic sites. Probably we should output the total number/proportion of total triallelic sites somewhere.

— Reply to this email directly or view it on GitHub< https://github.com/ole-tange/barmaids/issues/50#issuecomment-27423109> .

— Reply to this email directly or view it on GitHubhttps://github.com/ole-tange/barmaids/issues/50#issuecomment-27538850 .

[morenomayar]

Probably just have an extra option --triSummary or something. If true, send the output that we already have to a file: The base counts per triallelic site and total counts and proportions per processor. It shouldn't be very very sophisticated, I think.

[sapfo]

--debug standard error to somewhere. will be solved in issue #76.