samtools-1.6 and 1.9: plot-bamstats generates broken gnuplot script #1065

mmokrejs · 2019-06-11T09:55:54Z

Hi Peter,
I am getting errors when gnuplot is executed on the script generated by plot-bamstats on Linux.

$ plot-bamstats -p ./html/sample2/plot ./html/sample2/plot.stat

end
^
"./html/sample2/plot-quals-hm.gp" line 128: invalid command

The command exited with non-zero status 256:
	gnuplot ./html/sample2/plot-quals-hm.gp

 at /apps/all/SAMtools/1.9-intel-2017a/bin/plot-bamstats line 51.
	main::error('The command exited with non-zero status 256:\x{a}\x{9}gnuplot ./html/...') called at /apps/all/SAMtools/1.9-intel-2017a/bin/plot-bamstats line 317
	main::plot('./html/sample2/plot-quals-hm.gp') called at /apps/all/SAMtools/1.9-intel-2017a/bin/plot-bamstats line 818
	main::plot_qualities('HASH(0x1b69420)') called at /apps/all/SAMtools/1.9-intel-2017a/bin/plot-bamstats line 33

I tried also samtools-1.6 but it breaks on the same error (extraneous end commands in two places). It seems they are printed by the perl code due to some missing checks somewhere for some sections.

I see in issue #183 that there is (or used to be) some develop branch, I will test it later.

plot-quals-hm.gp.txt

The text was updated successfully, but these errors were encountered:

valeriuo · 2019-06-17T12:07:29Z

I successfully ran gnuplot (5.2) on your file and got the attached image. What version of gnuplot/OS are you using?

mmokrejs · 2019-06-17T12:36:32Z

$ gnuplot -version

	G N U P L O T
	Version 5.2 patchlevel 7    last modified 2019-05-29

I am on Centos7 Linux.

pd3 · 2019-06-18T15:36:20Z

Looks like this behavior is specific to the most recent versions of gnuplot. @mmokrejs can you try if the script works after removing the extra end? If so, that will be easy to fix :-)

mmokrejs · 2019-06-19T23:18:23Z

@pd3 Sorry, I forgot to mention that explicitly, I did that already on the two places and it helped. That is actually why I wrote that supposedly the perl code does not output the if part due to failing condition but just always outputs the end. I do not remember what I saw in the figure, but the crash was gone for sure.

pd3 · 2019-06-24T13:27:33Z

Thanks. You don't happen to have the source file that was used to generate the stats by any chance? I failed to reproduce the problem with gnuplot 5.2 patchlevel 6.

mmokrejs · 2019-06-24T15:19:57Z

Right, I do:
plot.stat.txt

pd3 · 2019-06-25T09:09:51Z

I can confirm this is a problem with 5.2.7 but not with 5.2.6.

Unfortunately, versions prior to 5.2.7 require the two end statements to finish the matrix data section whereas 5.2.7 requires one end.

daviesrob · 2019-06-26T10:26:13Z

This is probably related to this fix in 5.2.7 (from the release notes) :

FIX prevent extra read past the end of a datablock holding matrix data

In 5.2.2 I can get it to work by putting a blank line between the end of the matrix and a single end, like this:

	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1	0	0	0	1	1	0	4	2	0	4	0	0	10	10	22	10	4	0	0	0

end
                set origin 0,0.03
                ...

Does that work in 5.2.7 as well?

mmokrejs · 2019-06-26T10:54:20Z

You mean this?

$ diff -u ./html/sample2/plot-quals-hm.gp.ori ./html/sample2/plot-quals-hm.gp
--- ./html/sample2/plot-quals-hm.gp.ori	2019-06-26 11:37:59.546303314 +0200
+++ ./html/sample2/plot-quals-hm.gp	2019-06-26 12:49:54.233036830 +0200
@@ -124,7 +124,7 @@
 	0	0	14	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	3	1	2	0	46	13	6	22	12	44	16	20	6	0
 	0	0	24	0	0	1	0	0	3	0	0	0	2	0	1	1	0	6	1	3	3	3	0	2	10	1	7	0	0	16	5	14	5	29	19	21	4	0	0
 	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1	0	0	0	1	1	0	4	2	0	40	0	10	10	22	10	4	0	0	0
-end
+
 end
 
                 set origin 0,0.03
$ gnuplot ./html/sample2/plot-quals-hm.gp

end
^
"./html/sample2/plot-quals-hm.gp" line 244: invalid command

$ gnuplot -V
gnuplot 5.2 patchlevel 7
$

daviesrob · 2019-06-26T11:04:12Z

Try doing the same thing for the second matrix.

mmokrejs · 2019-06-26T12:57:05Z

Right.

$ diff -u ./html/sample2/plot-quals-hm.gp.ori ./html/sample2/plot-quals-hm.gp
--- ./html/sample2/plot-quals-hm.gp.ori	2019-06-26 11:37:59.546303314 +0200
+++ ./html/sample2/plot-quals-hm.gp	2019-06-26 14:54:10.004372915 +0200
@@ -124,7 +124,7 @@
 	0	0	14	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	3	1	2	0	46	13	6	22	12	44	16	20	6	0
 	0	0	24	0	0	1	0	0	3	0	0	0	2	0	1	1	0	6	1	3	3	3	0	2	10	1	7	0	0	16	5	14	5	29	19	21	4	0	0
 	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1	0	0	0	1	1	0	4	2	0	40	0	10	10	22	10	4	0	0	0
-end
+
 end
 
                 set origin 0,0.03
@@ -240,5 +240,5 @@
 	0	0	28	0	0	0	0	0	0	0	0	1	1	0	1	0	0	0	2	0	0	0	0	0	3	0	0	4	1	36	2	7	12	12	32	5	13	0	0
 	0	0	34	0	0	0	2	0	0	0	5	2	0	0	1	6	0	0	2	1	0	6	4	0	2	0	0	2	2	36	0	2	18	7	16	8	4	0	0
 	0	0	5	0	0	0	0	0	0	0	0	0	0	1	0	0	2	0	1	0	1	0	0	1	1	0	0	1	0	32	1	1	2	10	5	1	0	0	0
-end
+
 end
$

Actually that is why I mentioned initially extraneous (or out-of-order) end statements.

daviesrob · 2019-06-27T16:18:33Z

@mmokrejs Could you confirm that #1068 fixes this, please?

pd3 · 2019-06-28T09:27:27Z

It works in 5.0.0 and 5.2.7, thanks!

daviesrob mentioned this issue Jun 27, 2019

Fix plot-bamstats quality heatmap on newer gnuplot #1068

Merged

valeriuo closed this as completed in ed9713e Jul 1, 2019

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samtools-1.6 and 1.9: plot-bamstats generates broken gnuplot script #1065

samtools-1.6 and 1.9: plot-bamstats generates broken gnuplot script #1065

mmokrejs commented Jun 11, 2019 •

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daviesrob commented Jun 27, 2019

pd3 commented Jun 28, 2019

samtools-1.6 and 1.9: plot-bamstats generates broken gnuplot script #1065

samtools-1.6 and 1.9: plot-bamstats generates broken gnuplot script #1065

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