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tools for working with genome variation graphs
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vg call fails: Address not mapped to object #1459

Open ChriKub opened 6 years ago

ChriKub commented 6 years ago

Hi,

I tried to call variants from a short read mapping to a 2 genome variation graph but vg call fails. This happens on two independent graphs with different input sequences and sequencing data sets.

vg call -v -p -t 20 -r Chr1 -r Chr2 -r Chr3 -r Chr4 -r Chr5 -z augment.translation -s augment.support -b graph.vg graph.augmented > variant.vcf 2> variant.out

Mininimum binned average coverage: 0,0 (bin 3 / 107902) Maxinimum binned average coverage: 662.38,695.52 (bin 9888 / 107902) Stack trace (most recent call last):

31 | Source "impl/stCactusGraphs.c", line 1160, in stSnarl_makeRecursiveSnarl

  Source "impl/stCactusGraphs.c", line 1151, in stSnarl_makeRecursiveSnarl [0xdc2094]

30 | Source "impl/stCactusGraphs.c", line 1179, in stSnarl_makeRecursiveSnarl

  Source "impl/stCactusGraphs.c", line 1195, in stSnarl_makeRecursiveSnarl [0xdc203d]

29 | Source "impl/stCactusGraphs.c", line 1160, in stSnarl_makeRecursiveSnarl

  Source "impl/stCactusGraphs.c", line 1151, in stSnarl_makeRecursiveSnarl [0xdc2094]

28 | Source "impl/stCactusGraphs.c", line 1179, in stSnarl_makeRecursiveSnarl

  Source "impl/stCactusGraphs.c", line 1195, in stSnarl_makeRecursiveSnarl [0xdc203d]

27 | Source "impl/stCactusGraphs.c", line 1160, in stSnarl_makeRecursiveSnarl

  Source "impl/stCactusGraphs.c", line 1151, in stSnarl_makeRecursiveSnarl [0xdc2094]

26 | Source "impl/stCactusGraphs.c", line 1160, in stSnarl_makeRecursiveSnarl

  Source "impl/stCactusGraphs.c", line 1151, in stSnarl_makeRecursiveSnarl [0xdc2094]

25 | Source "impl/stCactusGraphs.c", line 1179, in stSnarl_makeRecursiveSnarl

  Source "impl/stCactusGraphs.c", line 1195, in stSnarl_makeRecursiveSnarl [0xdc203d]

24 | Source "impl/stCactusGraphs.c", line 1160, in stSnarl_makeRecursiveSnarl

  Source "impl/stCactusGraphs.c", line 1151, in stSnarl_makeRecursiveSnarl [0xdc2094]

23 | Source "impl/stCactusGraphs.c", line 1179, in stSnarl_makeRecursiveSnarl

  Source "impl/stCactusGraphs.c", line 1195, in stSnarl_makeRecursiveSnarl [0xdc203d]

22 | Source "impl/stCactusGraphs.c", line 1160, in stSnarl_makeRecursiveSnarl

  Source "impl/stCactusGraphs.c", line 1151, in stSnarl_makeRecursiveSnarl [0xdc2094]

21 | Source "impl/stCactusGraphs.c", line 1179, in stSnarl_makeRecursiveSnarl

  Source "impl/stCactusGraphs.c", line 1195, in stSnarl_makeRecursiveSnarl [0xdc203d]

20 | Source "impl/stCactusGraphs.c", line 1160, in stSnarl_makeRecursiveSnarl

  Source "impl/stCactusGraphs.c", line 1151, in stSnarl_makeRecursiveSnarl [0xdc2094]

19 | Source "impl/stCactusGraphs.c", line 1160, in stSnarl_makeRecursiveSnarl

  Source "impl/stCactusGraphs.c", line 1151, in stSnarl_makeRecursiveSnarl [0xdc2094]

18 | Source "impl/stCactusGraphs.c", line 1179, in stSnarl_makeRecursiveSnarl

  Source "impl/stCactusGraphs.c", line 1195, in stSnarl_makeRecursiveSnarl [0xdc203d]

17 | Source "impl/stCactusGraphs.c", line 1160, in stSnarl_makeRecursiveSnarl

  Source "impl/stCactusGraphs.c", line 1151, in stSnarl_makeRecursiveSnarl [0xdc2094]

16 | Source "impl/stCactusGraphs.c", line 1179, in stSnarl_makeRecursiveSnarl

  Source "impl/stCactusGraphs.c", line 1195, in stSnarl_makeRecursiveSnarl [0xdc203d]

15 | Source "impl/stCactusGraphs.c", line 1160, in stSnarl_makeRecursiveSnarl

  Source "impl/stCactusGraphs.c", line 1151, in stSnarl_makeRecursiveSnarl [0xdc2094]

14 | Source "impl/stCactusGraphs.c", line 1160, in stSnarl_makeRecursiveSnarl

  Source "impl/stCactusGraphs.c", line 1151, in stSnarl_makeRecursiveSnarl [0xdc2094]

13 | Source "impl/stCactusGraphs.c", line 1179, in stSnarl_makeRecursiveSnarl

  Source "impl/stCactusGraphs.c", line 1195, in stSnarl_makeRecursiveSnarl [0xdc203d]

12 | Source "impl/stCactusGraphs.c", line 1160, in stSnarl_makeRecursiveSnarl

  Source "impl/stCactusGraphs.c", line 1151, in stSnarl_makeRecursiveSnarl [0xdc2094]

11 | Source "impl/stCactusGraphs.c", line 1179, in stSnarl_makeRecursiveSnarl

  Source "impl/stCactusGraphs.c", line 1195, in stSnarl_makeRecursiveSnarl [0xdc203d]

10 | Source "impl/stCactusGraphs.c", line 1160, in stSnarl_makeRecursiveSnarl

  Source "impl/stCactusGraphs.c", line 1151, in stSnarl_makeRecursiveSnarl [0xdc2094]

9 | Source "impl/stCactusGraphs.c", line 1179, in stSnarl_makeRecursiveSnarl

  Source "impl/stCactusGraphs.c", line 1195, in stSnarl_makeRecursiveSnarl [0xdc203d]

8 | Source "impl/stCactusGraphs.c", line 1160, in stSnarl_makeRecursiveSnarl

  Source "impl/stCactusGraphs.c", line 1151, in stSnarl_makeRecursiveSnarl [0xdc2094]

7 | Source "impl/stCactusGraphs.c", line 1160, in stSnarl_makeRecursiveSnarl

  Source "impl/stCactusGraphs.c", line 1151, in stSnarl_makeRecursiveSnarl [0xdc2094]

6 | Source "impl/stCactusGraphs.c", line 1179, in stSnarl_makeRecursiveSnarl

  Source "impl/stCactusGraphs.c", line 1195, in stSnarl_makeRecursiveSnarl [0xdc203d]

5 | Source "impl/stCactusGraphs.c", line 1160, in stSnarl_makeRecursiveSnarl

  Source "impl/stCactusGraphs.c", line 1151, in stSnarl_makeRecursiveSnarl [0xdc2094]

4 | Source "impl/stCactusGraphs.c", line 1179, in stSnarl_makeRecursiveSnarl

  Source "impl/stCactusGraphs.c", line 1195, in stSnarl_makeRecursiveSnarl [0xdc203d]

3 | Source "impl/stCactusGraphs.c", line 1146, in stSnarl_constructEmptySnarl

  Source "impl/stCactusGraphs.c", line 1079, in stSnarl_makeRecursiveSnarl [0xdc1f24]

2 Source "impl/sonLibList.c", line 39, in stList_construct3 [0xdcbf4b]

1 Source "impl/sonLibCommon.c", line 42, in st_calloc [0xdcaea0]

0 | Source "src/tcmalloc.cc", line 1645, in do_calloc

| Source "src/tcmalloc.cc", line 1234, in memset
  Source "/usr/include/x86_64-linux-gnu/bits/string3.h", line 90, in tc_calloc [0x1165e8e]
     87:       return __dest;
     88:     }
     89: #endif
  >  90:   return __builtin___memset_chk (__dest, __ch, __len, __bos0 (__dest));
     91: }
     92:
     93: #ifdef __USE_MISC

Segmentation fault (Address not mapped to object [0x7ffd8aeeeff8])

adamnovak commented 6 years ago

Address not mapped to object is just a message from the stack trace code. I suspect what you are having here is a stack overflow, caused by very deeply nested snarl structure in the graph (see the long chain of recursive calls to stSnarl_makeRecursiveSnarl).

We don't currently support graphs with long dangling pieces; they get parsed into nested unary snarls, but if the tree gets too deep we can't recurse over it and we explode.

The right solution is to rewrite all our recursive algorithms as iterative algorithms. The short-term solution is to convince vg call to use a different primary path to structure the snarl traversal, or make the graph more linear-shaped.

What shapes are the graphs you are working on? Do they include, for example, edges between different chromosomes? Or multiple alternative telomeres?

ChriKub commented 6 years ago

Thanks for your reply. It is probably a long dangling piece/telomere. The graph was constructed using reveal, thus it is linear and does not contain any edges between chromosomes, or repeats. I will try to introduce a single node at the end of each chromosome to anchor the telomeres. That should fix the problem for now, right? Do you intend to rewrite the algorithm to be able to cope with this at any point, as this problem should be fairly common when working with whole genome alignments.

adamnovak commented 6 years ago

Hello,

Yes, clamping each connected component down to a single head and a single tail should resolve this. Let me know if it doesn't.

We have vague plans to rewrite the algorithm to handle these cases, but it's unfortunately not critical path for handling any of the graphs the core development team is working on. This might be a good project for someone who does want to work on graphs with that structure and wants to submit a PR. Failing that, I think it's on our "eventually" list.

What I really want to do is to rework unary snarls at the conceptual level; what right now is a very deep nested structure of unary snarls IMHO ought to be a chain of normal snarls ending in a single unary terminal snarl. But I think our team has even less free time to hash that out.

On Tue, Feb 27, 2018 at 1:16 AM, ChriKub notifications@github.com wrote:

Thanks for your reply. It is probably a long dangling piece/telomere. The graph was constructed using reveal, thus it is linear and does not contain any edges between chromosomes, or repeats. I will try to introduce a single node at the end of each chromosome to anchor the telomeres. That should fix the problem for now, right? Do you intend to rewrite the algorithm to be able to cope with this at any point, as this problem should be fairly common when working with whole genome alignments.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/vgteam/vg/issues/1459#issuecomment-368802392, or mute the thread https://github.com/notifications/unsubscribe-auth/AE0_X8c9YsWvVM5-GE6aBWAFJwcERO3eks5tY8gJgaJpZM4SKoEB .

ChriKub commented 6 years ago

Hi Adam, I tried clamping down the ends, but it still throws an error. I'm not sure if it is the same, although stSnarl_makeRecursiveSnarl is still called.

Reading input graph Calling variants with support caller Primary path AT6909_Chr1 average/off-path assumed coverage: 20.8359,20.9331 Mininimum binned average coverage: 0,0 (bin 1 / 121089) Maxinimum binned average coverage: 1522.12,1510.03 (bin 15804 / 121089) Primary path AT6909_Chr2 average/off-path assumed coverage: 23.2543,23.2987 Mininimum binned average coverage: 0,0 (bin 19 / 80086) Maxinimum binned average coverage: 1141.86,1172.46 (bin 13936 / 80086) Primary path AT6909_Chr3 average/off-path assumed coverage: 21.3937,21.4521 Mininimum binned average coverage: 0,0 (bin 1 / 93697) Maxinimum binned average coverage: 814.596,1477.78 (bin 31430 / 93697) Primary path AT6909_Chr4 average/off-path assumed coverage: 21.1099,21.1626 Mininimum binned average coverage: 0,0 (bin 2 / 74903) Maxinimum binned average coverage: 1128.95,1159.84 (bin 27777 / 74903) Primary path AT6909_Chr5 average/off-path assumed coverage: 20.7084,20.7151 Mininimum binned average coverage: 0,0 (bin 1 / 109331) Maxinimum binned average coverage: 662.38,695.52 (bin 9905 / 109331) Stack trace (most recent call last):

31 | Source "impl/stCactusGraphs.c", line 1160, in stSnarl_makeRecursiveSnarl

  Source "impl/stCactusGraphs.c", line 1151, in stSnarl_makeRecursiveSnarl [0xdc2094]

30 | Source "impl/stCactusGraphs.c", line 1160, in stSnarl_makeRecursiveSnarl

  Source "impl/stCactusGraphs.c", line 1151, in stSnarl_makeRecursiveSnarl [0xdc2094]

29 | Source "impl/stCactusGraphs.c", line 1160, in stSnarl_makeRecursiveSnarl

  Source "impl/stCactusGraphs.c", line 1151, in stSnarl_makeRecursiveSnarl [0xdc2094]

28 | Source "impl/stCactusGraphs.c", line 1179, in stSnarl_makeRecursiveSnarl

  Source "impl/stCactusGraphs.c", line 1195, in stSnarl_makeRecursiveSnarl [0xdc203d]

27 | Source "impl/stCactusGraphs.c", line 1160, in stSnarl_makeRecursiveSnarl

  Source "impl/stCactusGraphs.c", line 1151, in stSnarl_makeRecursiveSnarl [0xdc2094]

26 | Source "impl/stCactusGraphs.c", line 1179, in stSnarl_makeRecursiveSnarl

  Source "impl/stCactusGraphs.c", line 1195, in stSnarl_makeRecursiveSnarl [0xdc203d]

25 | Source "impl/stCactusGraphs.c", line 1160, in stSnarl_makeRecursiveSnarl

  Source "impl/stCactusGraphs.c", line 1151, in stSnarl_makeRecursiveSnarl [0xdc2094]

24 | Source "impl/stCactusGraphs.c", line 1160, in stSnarl_makeRecursiveSnarl

  Source "impl/stCactusGraphs.c", line 1151, in stSnarl_makeRecursiveSnarl [0xdc2094]

23 | Source "impl/stCactusGraphs.c", line 1179, in stSnarl_makeRecursiveSnarl

  Source "impl/stCactusGraphs.c", line 1195, in stSnarl_makeRecursiveSnarl [0xdc203d]

22 | Source "impl/stCactusGraphs.c", line 1160, in stSnarl_makeRecursiveSnarl

  Source "impl/stCactusGraphs.c", line 1151, in stSnarl_makeRecursiveSnarl [0xdc2094]

21 | Source "impl/stCactusGraphs.c", line 1179, in stSnarl_makeRecursiveSnarl

  Source "impl/stCactusGraphs.c", line 1195, in stSnarl_makeRecursiveSnarl [0xdc203d]

20 | Source "impl/stCactusGraphs.c", line 1160, in stSnarl_makeRecursiveSnarl

  Source "impl/stCactusGraphs.c", line 1151, in stSnarl_makeRecursiveSnarl [0xdc2094]

19 | Source "impl/stCactusGraphs.c", line 1160, in stSnarl_makeRecursiveSnarl

  Source "impl/stCactusGraphs.c", line 1151, in stSnarl_makeRecursiveSnarl [0xdc2094]

18 | Source "impl/stCactusGraphs.c", line 1179, in stSnarl_makeRecursiveSnarl

  Source "impl/stCactusGraphs.c", line 1195, in stSnarl_makeRecursiveSnarl [0xdc203d]

17 | Source "impl/stCactusGraphs.c", line 1160, in stSnarl_makeRecursiveSnarl

  Source "impl/stCactusGraphs.c", line 1151, in stSnarl_makeRecursiveSnarl [0xdc2094]

16 | Source "impl/stCactusGraphs.c", line 1179, in stSnarl_makeRecursiveSnarl

  Source "impl/stCactusGraphs.c", line 1195, in stSnarl_makeRecursiveSnarl [0xdc203d]

15 | Source "impl/stCactusGraphs.c", line 1160, in stSnarl_makeRecursiveSnarl

  Source "impl/stCactusGraphs.c", line 1151, in stSnarl_makeRecursiveSnarl [0xdc2094]

14 | Source "impl/stCactusGraphs.c", line 1179, in stSnarl_makeRecursiveSnarl

  Source "impl/stCactusGraphs.c", line 1195, in stSnarl_makeRecursiveSnarl [0xdc203d]

13 | Source "impl/stCactusGraphs.c", line 1160, in stSnarl_makeRecursiveSnarl

  Source "impl/stCactusGraphs.c", line 1151, in stSnarl_makeRecursiveSnarl [0xdc2094]

12 | Source "impl/stCactusGraphs.c", line 1179, in stSnarl_makeRecursiveSnarl

  Source "impl/stCactusGraphs.c", line 1195, in stSnarl_makeRecursiveSnarl [0xdc203d]

11 | Source "impl/stCactusGraphs.c", line 1160, in stSnarl_makeRecursiveSnarl

  Source "impl/stCactusGraphs.c", line 1151, in stSnarl_makeRecursiveSnarl [0xdc2094]

10 | Source "impl/stCactusGraphs.c", line 1179, in stSnarl_makeRecursiveSnarl

  Source "impl/stCactusGraphs.c", line 1195, in stSnarl_makeRecursiveSnarl [0xdc203d]

9 | Source "impl/stCactusGraphs.c", line 1160, in stSnarl_makeRecursiveSnarl

  Source "impl/stCactusGraphs.c", line 1151, in stSnarl_makeRecursiveSnarl [0xdc2094]

8 | Source "impl/stCactusGraphs.c", line 1179, in stSnarl_makeRecursiveSnarl

  Source "impl/stCactusGraphs.c", line 1195, in stSnarl_makeRecursiveSnarl [0xdc203d]

7 | Source "impl/stCactusGraphs.c", line 1160, in stSnarl_makeRecursiveSnarl

  Source "impl/stCactusGraphs.c", line 1151, in stSnarl_makeRecursiveSnarl [0xdc2094]

6 | Source "impl/stCactusGraphs.c", line 1179, in stSnarl_makeRecursiveSnarl

  Source "impl/stCactusGraphs.c", line 1195, in stSnarl_makeRecursiveSnarl [0xdc203d]

5 | Source "impl/stCactusGraphs.c", line 1160, in stSnarl_makeRecursiveSnarl

  Source "impl/stCactusGraphs.c", line 1151, in stSnarl_makeRecursiveSnarl [0xdc2094]

4 | Source "impl/stCactusGraphs.c", line 1179, in stSnarl_makeRecursiveSnarl

  Source "impl/stCactusGraphs.c", line 1195, in stSnarl_makeRecursiveSnarl [0xdc203d]

3 | Source "impl/stCactusGraphs.c", line 1160, in stSnarl_makeRecursiveSnarl

  Source "impl/stCactusGraphs.c", line 1151, in stSnarl_makeRecursiveSnarl [0xdc2094]

2 | Source "impl/stCactusGraphs.c", line 1146, in stSnarl_constructEmptySnarl

  Source "impl/stCactusGraphs.c", line 1075, in stSnarl_makeRecursiveSnarl [0xdc1f09]

1 Source "impl/sonLibCommon.c", line 42, in st_calloc [0xdcaea0]

0 Source "src/tcmalloc.cc", line 1641, in tc_calloc [0x1165e02]

Segmentation fault (Address not mapped to object [0x7ffefc36eff8])

adamnovak commented 6 years ago

Hm.

It could be that the reads are introducing long dangling tails somehow. Can vg snarls graph.vg >/dev/null run through on the graph reference you are using? If so, the problem is the graph augmentation with the reads. If not, there's still something complex in the snarl structure of the base graph.

On Wed, Mar 7, 2018 at 1:38 AM, ChriKub notifications@github.com wrote:

Hi Adam, I tried clamping down the ends, but it still throws an error. I'm not sure if it is the same, although stSnarl_makeRecursiveSnarl is still called.

Reading input graph Calling variants with support caller Primary path AT6909_Chr1 average/off-path assumed coverage: 20.8359,20.9331 Mininimum binned average coverage: 0,0 (bin 1 / 121089) Maxinimum binned average coverage: 1522.12,1510.03 (bin 15804 / 121089) Primary path AT6909_Chr2 average/off-path assumed coverage: 23.2543,23.2987 Mininimum binned average coverage: 0,0 (bin 19 / 80086) Maxinimum binned average coverage: 1141.86,1172.46 (bin 13936 / 80086) Primary path AT6909_Chr3 average/off-path assumed coverage: 21.3937,21.4521 Mininimum binned average coverage: 0,0 (bin 1 / 93697) Maxinimum binned average coverage: 814.596,1477.78 (bin 31430 / 93697) Primary path AT6909_Chr4 average/off-path assumed coverage: 21.1099,21.1626 Mininimum binned average coverage: 0,0 (bin 2 / 74903) Maxinimum binned average coverage: 1128.95,1159.84 (bin 27777 / 74903) Primary path AT6909_Chr5 average/off-path assumed coverage: 20.7084,20.7151 Mininimum binned average coverage: 0,0 (bin 1 / 109331) Maxinimum binned average coverage: 662.38,695.52 (bin 9905 / 109331) Stack trace (most recent call last):

31 https://github.com/vgteam/vg/issues/31 | Source

"impl/stCactusGraphs.c", line 1160, in stSnarl_makeRecursiveSnarl Source "impl/stCactusGraphs.c", line 1151, in stSnarl_makeRecursiveSnarl [0xdc2094]

30 https://github.com/vgteam/vg/issues/30 | Source

"impl/stCactusGraphs.c", line 1160, in stSnarl_makeRecursiveSnarl Source "impl/stCactusGraphs.c", line 1151, in stSnarl_makeRecursiveSnarl [0xdc2094]

29 https://github.com/vgteam/vg/issues/29 | Source

"impl/stCactusGraphs.c", line 1160, in stSnarl_makeRecursiveSnarl Source "impl/stCactusGraphs.c", line 1151, in stSnarl_makeRecursiveSnarl [0xdc2094]

28 https://github.com/vgteam/vg/issues/28 | Source

"impl/stCactusGraphs.c", line 1179, in stSnarl_makeRecursiveSnarl Source "impl/stCactusGraphs.c", line 1195, in stSnarl_makeRecursiveSnarl [0xdc203d]

27 https://github.com/vgteam/vg/issues/27 | Source

"impl/stCactusGraphs.c", line 1160, in stSnarl_makeRecursiveSnarl Source "impl/stCactusGraphs.c", line 1151, in stSnarl_makeRecursiveSnarl [0xdc2094]

26 https://github.com/vgteam/vg/issues/26 | Source

"impl/stCactusGraphs.c", line 1179, in stSnarl_makeRecursiveSnarl Source "impl/stCactusGraphs.c", line 1195, in stSnarl_makeRecursiveSnarl [0xdc203d]

25 https://github.com/vgteam/vg/issues/25 | Source

"impl/stCactusGraphs.c", line 1160, in stSnarl_makeRecursiveSnarl Source "impl/stCactusGraphs.c", line 1151, in stSnarl_makeRecursiveSnarl [0xdc2094]

24 https://github.com/vgteam/vg/pull/24 | Source

"impl/stCactusGraphs.c", line 1160, in stSnarl_makeRecursiveSnarl Source "impl/stCactusGraphs.c", line 1151, in stSnarl_makeRecursiveSnarl [0xdc2094]

23 https://github.com/vgteam/vg/issues/23 | Source

"impl/stCactusGraphs.c", line 1179, in stSnarl_makeRecursiveSnarl Source "impl/stCactusGraphs.c", line 1195, in stSnarl_makeRecursiveSnarl [0xdc203d]

22 https://github.com/vgteam/vg/issues/22 | Source

"impl/stCactusGraphs.c", line 1160, in stSnarl_makeRecursiveSnarl Source "impl/stCactusGraphs.c", line 1151, in stSnarl_makeRecursiveSnarl [0xdc2094]

21 https://github.com/vgteam/vg/issues/21 | Source

"impl/stCactusGraphs.c", line 1179, in stSnarl_makeRecursiveSnarl Source "impl/stCactusGraphs.c", line 1195, in stSnarl_makeRecursiveSnarl [0xdc203d]

20 https://github.com/vgteam/vg/issues/20 | Source

"impl/stCactusGraphs.c", line 1160, in stSnarl_makeRecursiveSnarl Source "impl/stCactusGraphs.c", line 1151, in stSnarl_makeRecursiveSnarl [0xdc2094]

19 https://github.com/vgteam/vg/issues/19 | Source

"impl/stCactusGraphs.c", line 1160, in stSnarl_makeRecursiveSnarl Source "impl/stCactusGraphs.c", line 1151, in stSnarl_makeRecursiveSnarl [0xdc2094]

18 https://github.com/vgteam/vg/issues/18 | Source

"impl/stCactusGraphs.c", line 1179, in stSnarl_makeRecursiveSnarl Source "impl/stCactusGraphs.c", line 1195, in stSnarl_makeRecursiveSnarl [0xdc203d]

17 https://github.com/vgteam/vg/issues/17 | Source

"impl/stCactusGraphs.c", line 1160, in stSnarl_makeRecursiveSnarl Source "impl/stCactusGraphs.c", line 1151, in stSnarl_makeRecursiveSnarl [0xdc2094]

16 https://github.com/vgteam/vg/issues/16 | Source

"impl/stCactusGraphs.c", line 1179, in stSnarl_makeRecursiveSnarl Source "impl/stCactusGraphs.c", line 1195, in stSnarl_makeRecursiveSnarl [0xdc203d]

15 https://github.com/vgteam/vg/issues/15 | Source

"impl/stCactusGraphs.c", line 1160, in stSnarl_makeRecursiveSnarl Source "impl/stCactusGraphs.c", line 1151, in stSnarl_makeRecursiveSnarl [0xdc2094]

14 https://github.com/vgteam/vg/issues/14 | Source

"impl/stCactusGraphs.c", line 1179, in stSnarl_makeRecursiveSnarl Source "impl/stCactusGraphs.c", line 1195, in stSnarl_makeRecursiveSnarl [0xdc203d]

13 https://github.com/vgteam/vg/issues/13 | Source

"impl/stCactusGraphs.c", line 1160, in stSnarl_makeRecursiveSnarl Source "impl/stCactusGraphs.c", line 1151, in stSnarl_makeRecursiveSnarl [0xdc2094]

12 https://github.com/vgteam/vg/issues/12 | Source

"impl/stCactusGraphs.c", line 1179, in stSnarl_makeRecursiveSnarl Source "impl/stCactusGraphs.c", line 1195, in stSnarl_makeRecursiveSnarl [0xdc203d]

11 https://github.com/vgteam/vg/issues/11 | Source

"impl/stCactusGraphs.c", line 1160, in stSnarl_makeRecursiveSnarl Source "impl/stCactusGraphs.c", line 1151, in stSnarl_makeRecursiveSnarl [0xdc2094]

10 https://github.com/vgteam/vg/issues/10 | Source

"impl/stCactusGraphs.c", line 1179, in stSnarl_makeRecursiveSnarl Source "impl/stCactusGraphs.c", line 1195, in stSnarl_makeRecursiveSnarl [0xdc203d]

9 https://github.com/vgteam/vg/issues/9 | Source

"impl/stCactusGraphs.c", line 1160, in stSnarl_makeRecursiveSnarl Source "impl/stCactusGraphs.c", line 1151, in stSnarl_makeRecursiveSnarl [0xdc2094]

8 https://github.com/vgteam/vg/issues/8 | Source

"impl/stCactusGraphs.c", line 1179, in stSnarl_makeRecursiveSnarl Source "impl/stCactusGraphs.c", line 1195, in stSnarl_makeRecursiveSnarl [0xdc203d]

7 https://github.com/vgteam/vg/issues/7 | Source

"impl/stCactusGraphs.c", line 1160, in stSnarl_makeRecursiveSnarl Source "impl/stCactusGraphs.c", line 1151, in stSnarl_makeRecursiveSnarl [0xdc2094]

6 https://github.com/vgteam/vg/issues/6 | Source

"impl/stCactusGraphs.c", line 1179, in stSnarl_makeRecursiveSnarl Source "impl/stCactusGraphs.c", line 1195, in stSnarl_makeRecursiveSnarl [0xdc203d]

5 https://github.com/vgteam/vg/issues/5 | Source

"impl/stCactusGraphs.c", line 1160, in stSnarl_makeRecursiveSnarl Source "impl/stCactusGraphs.c", line 1151, in stSnarl_makeRecursiveSnarl [0xdc2094]

4 https://github.com/vgteam/vg/pull/4 | Source

"impl/stCactusGraphs.c", line 1179, in stSnarl_makeRecursiveSnarl Source "impl/stCactusGraphs.c", line 1195, in stSnarl_makeRecursiveSnarl [0xdc203d]

3 https://github.com/vgteam/vg/issues/3 | Source

"impl/stCactusGraphs.c", line 1160, in stSnarl_makeRecursiveSnarl Source "impl/stCactusGraphs.c", line 1151, in stSnarl_makeRecursiveSnarl [0xdc2094]

2 https://github.com/vgteam/vg/issues/2 | Source

"impl/stCactusGraphs.c", line 1146, in stSnarl_constructEmptySnarl Source "impl/stCactusGraphs.c", line 1075, in stSnarl_makeRecursiveSnarl [0xdc1f09]

1 https://github.com/vgteam/vg/issues/1 Source "impl/sonLibCommon.c",

line 42, in st_calloc [0xdcaea0]

0 Source "src/tcmalloc.cc", line 1641, in tc_calloc [0x1165e02]

Segmentation fault (Address not mapped to object [0x7ffefc36eff8])

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ChriKub commented 6 years ago

It doesn't run through. So I will need to have a closer look into the graph. Is there any way of identifying the snarl that kills it with vg snarls?

Stack trace (most recent call last):

31 Source "src/snarls.cpp", line 180, in recursively_emit_snarls [0x94e5fe]

30 Source "src/snarls.cpp", line 180, in recursively_emit_snarls [0x94e5fe]

29 Source "src/snarls.cpp", line 180, in recursively_emit_snarls [0x94e5fe]

28 Source "src/snarls.cpp", line 180, in recursively_emit_snarls [0x94e5fe]

27 Source "src/snarls.cpp", line 180, in recursively_emit_snarls [0x94e5fe]

26 Source "src/snarls.cpp", line 180, in recursively_emit_snarls [0x94e5fe]

25 Source "src/snarls.cpp", line 145, in recursively_emit_snarls [0x94e53d]

24 Source "src/snarls.cpp", line 180, in recursively_emit_snarls [0x94e5fe]

23 Source "src/snarls.cpp", line 145, in recursively_emit_snarls [0x94e53d]

22 Source "src/snarls.cpp", line 180, in recursively_emit_snarls [0x94e5fe]

21 Source "src/snarls.cpp", line 145, in recursively_emit_snarls [0x94e53d]

20 Source "src/snarls.cpp", line 180, in recursively_emit_snarls [0x94e5fe]

19 Source "src/snarls.cpp", line 145, in recursively_emit_snarls [0x94e53d]

18 Source "src/snarls.cpp", line 180, in recursively_emit_snarls [0x94e5fe]

17 Source "src/snarls.cpp", line 145, in recursively_emit_snarls [0x94e53d]

16 Source "src/snarls.cpp", line 180, in recursively_emit_snarls [0x94e5fe]

15 Source "src/snarls.cpp", line 145, in recursively_emit_snarls [0x94e53d]

14 Source "src/snarls.cpp", line 180, in recursively_emit_snarls [0x94e5fe]

13 Source "src/snarls.cpp", line 145, in recursively_emit_snarls [0x94e53d]

12 Source "src/snarls.cpp", line 180, in recursively_emit_snarls [0x94e5fe]

11 Source "src/snarls.cpp", line 145, in recursively_emit_snarls [0x94e53d]

10 Source "src/snarls.cpp", line 180, in recursively_emit_snarls [0x94e5fe]

9 Source "src/snarls.cpp", line 145, in recursively_emit_snarls [0x94e53d]

8 Source "src/snarls.cpp", line 180, in recursively_emit_snarls [0x94e5fe]

7 Source "src/snarls.cpp", line 145, in recursively_emit_snarls [0x94e53d]

6 Source "src/snarls.cpp", line 180, in recursively_emit_snarls [0x94e5fe]

5 Source "src/snarls.cpp", line 180, in recursively_emit_snarls [0x94e5fe]

4 Source "src/snarls.cpp", line 145, in recursively_emit_snarls [0x94e53d]

3 Source "src/snarls.cpp", line 180, in recursively_emit_snarls [0x94e5fe]

2 Source "src/snarls.cpp", line 145, in recursively_emit_snarls [0x94e53d]

1 Source "src/snarls.cpp", line 180, in recursively_emit_snarls [0x94e5fe]

0 Source "src/snarls.cpp", line 73, in recursively_emit_snarls [0x94e331]

Segmentation fault (Address not mapped to object [0x7ffeb3d39f18])

adamnovak commented 6 years ago

You could hook up a debugger and see what some of the node IDs involved are by inspecting the arguments to those recursively_emit_snarls calls, I suppose. Or you could add some extra code to make it dump the snarls it is working on. There's not really a way to dump the problematic snarls right now.

On Wed, Mar 7, 2018 at 3:56 PM, ChriKub notifications@github.com wrote:

It doesn't run through. So I will need to have a closer look into the graph. Is there any way of identifying the snarl that kills it with vg snarls?

Stack trace (most recent call last):

31 https://github.com/vgteam/vg/issues/31 Source "src/snarls.cpp",

line 180, in recursively_emit_snarls [0x94e5fe]

30 https://github.com/vgteam/vg/issues/30 Source "src/snarls.cpp",

line 180, in recursively_emit_snarls [0x94e5fe]

29 https://github.com/vgteam/vg/issues/29 Source "src/snarls.cpp",

line 180, in recursively_emit_snarls [0x94e5fe]

28 https://github.com/vgteam/vg/issues/28 Source "src/snarls.cpp",

line 180, in recursively_emit_snarls [0x94e5fe]

27 https://github.com/vgteam/vg/issues/27 Source "src/snarls.cpp",

line 180, in recursively_emit_snarls [0x94e5fe]

26 https://github.com/vgteam/vg/issues/26 Source "src/snarls.cpp",

line 180, in recursively_emit_snarls [0x94e5fe]

25 https://github.com/vgteam/vg/issues/25 Source "src/snarls.cpp",

line 145, in recursively_emit_snarls [0x94e53d]

24 https://github.com/vgteam/vg/pull/24 Source "src/snarls.cpp", line

180, in recursively_emit_snarls [0x94e5fe]

23 https://github.com/vgteam/vg/issues/23 Source "src/snarls.cpp",

line 145, in recursively_emit_snarls [0x94e53d]

22 https://github.com/vgteam/vg/issues/22 Source "src/snarls.cpp",

line 180, in recursively_emit_snarls [0x94e5fe]

21 https://github.com/vgteam/vg/issues/21 Source "src/snarls.cpp",

line 145, in recursively_emit_snarls [0x94e53d]

20 https://github.com/vgteam/vg/issues/20 Source "src/snarls.cpp",

line 180, in recursively_emit_snarls [0x94e5fe]

19 https://github.com/vgteam/vg/issues/19 Source "src/snarls.cpp",

line 145, in recursively_emit_snarls [0x94e53d]

18 https://github.com/vgteam/vg/issues/18 Source "src/snarls.cpp",

line 180, in recursively_emit_snarls [0x94e5fe]

17 https://github.com/vgteam/vg/issues/17 Source "src/snarls.cpp",

line 145, in recursively_emit_snarls [0x94e53d]

16 https://github.com/vgteam/vg/issues/16 Source "src/snarls.cpp",

line 180, in recursively_emit_snarls [0x94e5fe]

15 https://github.com/vgteam/vg/issues/15 Source "src/snarls.cpp",

line 145, in recursively_emit_snarls [0x94e53d]

14 https://github.com/vgteam/vg/issues/14 Source "src/snarls.cpp",

line 180, in recursively_emit_snarls [0x94e5fe]

13 https://github.com/vgteam/vg/issues/13 Source "src/snarls.cpp",

line 145, in recursively_emit_snarls [0x94e53d]

12 https://github.com/vgteam/vg/issues/12 Source "src/snarls.cpp",

line 180, in recursively_emit_snarls [0x94e5fe]

11 https://github.com/vgteam/vg/issues/11 Source "src/snarls.cpp",

line 145, in recursively_emit_snarls [0x94e53d]

10 https://github.com/vgteam/vg/issues/10 Source "src/snarls.cpp",

line 180, in recursively_emit_snarls [0x94e5fe]

9 https://github.com/vgteam/vg/issues/9 Source "src/snarls.cpp", line

145, in recursively_emit_snarls [0x94e53d]

8 https://github.com/vgteam/vg/issues/8 Source "src/snarls.cpp", line

180, in recursively_emit_snarls [0x94e5fe]

7 https://github.com/vgteam/vg/issues/7 Source "src/snarls.cpp", line

145, in recursively_emit_snarls [0x94e53d]

6 https://github.com/vgteam/vg/issues/6 Source "src/snarls.cpp", line

180, in recursively_emit_snarls [0x94e5fe]

5 https://github.com/vgteam/vg/issues/5 Source "src/snarls.cpp", line

180, in recursively_emit_snarls [0x94e5fe]

4 https://github.com/vgteam/vg/pull/4 Source "src/snarls.cpp", line

145, in recursively_emit_snarls [0x94e53d]

3 https://github.com/vgteam/vg/issues/3 Source "src/snarls.cpp", line

180, in recursively_emit_snarls [0x94e5fe]

2 https://github.com/vgteam/vg/issues/2 Source "src/snarls.cpp", line

145, in recursively_emit_snarls [0x94e53d]

1 https://github.com/vgteam/vg/issues/1 Source "src/snarls.cpp", line

180, in recursively_emit_snarls [0x94e5fe]

0 Source "src/snarls.cpp", line 73, in recursively_emit_snarls [0x94e331]

Segmentation fault (Address not mapped to object [0x7ffeb3d39f18])

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