Segmentation fault error when there are two references

[mitenjain]

---JOBTREE SLAVE OUTPUT LOG--- /bin/sh: line 1: 24546 Done echo cigar: channel_439_read_57 0 1122 + DNA_CS 0 3 559 + 1 D 1838 I 1 M 7 D 1 M 3 I 2 M 6 D 1 M 13 I 1 M 2 I 1 M 7 I 1 M 16 D 1 M 35 D 1 M 47 I 1 M 1 I 2 M 11 D 3 M 45 I 2 M 26 I 1 M 2 I 1 M 18 D 2 M 17 I 1 M 36 D 2 M 4 D 1 M 8 I 2 M 7 D 1 M 9 I 1 M 52 D 1 M 8 D 1 M 9 D 3 M 29 D 1 M 18 D 3 M 12 D 1 M 19 I 2 M 103 D 1 M 18 D 1 M 8 D 1 M 14 I 1 M 9 D 1 M 10 I 1 M 3 D 1 M 5 D 1 M 9 I 2 M 14 D 1 M 14 D 1 M 2 I 1 M 4 I 1 M 46 D 1 M 2 I 1 M 66 I 1 M 1 I 1 M 17 I 2 M 5 D 1 M 20 I 1 M 12 D 1 M 71 I 1 M 15 I 2 M 9 D 2 M 23 I 1 M 6 D 1 M 6 D 1 M 6 D 1 M 19 D 2 M 26 I 1 M 36 I 1 M 9 D 605 I 10 24547 Segmentation fault (core dumped) | cPecanRealign /scratch/tmp/tmpivbY_w/localTempD ir/ref.fa /scratch/tmp/tmpivbY_w/localTempDir/read.fa --diagonalExpansion=10 --splitMatrixBiggerTh anThis=3000 --loadHmm /hive/users/miten/pipeline_full_runs/stats_marginAlign/margin/src/margin/map pers/last_hmm_20.txt --gapGamma=0.5 --matchGamma=0.0 >> /hive/users/miten/pipeline_full_runs/stats _marginAlign/margin/jobTreeM13NoEM/jobs/gTD1/tmp_zsbGhgPBdH/tempOutput_1814.txt Traceback (most recent call last): File "/hive/users/miten/pipeline_full_runs/stats_marginAlign/margin/submodules/jobTree/src/jobTr eeSlave.py", line 271, in main defaultMemory=defaultMemory, defaultCpu=defaultCpu, depth=depth) File "/hive/users/miten/pipeline_full_runs/stats_marginAlign/margin/submodules/jobTree/scriptTre e/stack.py", line 153, in execute self.target.run() File "/hive/users/miten/pipeline_full_runs/statsmarginAlign/margin/submodules/jobTree/scriptTre e/target.py", line 197, in run func(((self,) + tuple(self.args)), *_self.kwargs) File "/hive/users/miten/pipeline_full_runs/stats_marginAlign/margin/src/margin/marginAlignLib.py ", line 319, in realignCigarTargetFn options.gapGamma, options.matchGamma, outputCigarFile)) File "/hive/users/miten/pipeline_full_runs/stats_marginAlign/margin/submodules/sonLib/bioio.py", line 184, in system raise RuntimeError("Command: %s exited with non-zero status %i" % (command, sts)) RuntimeError: Command: echo cigar: channel_439_read_57 0 1122 + DNA_CS 0 3559 + 1 D 1838 I 1 M 7 D 1 M 3 I 2 M 6 D 1 M 13 I 1 M 2 I 1 M 7 I 1 M 16 D 1 M 35 D 1 M 47 I 1 M 1 I 2 M 11 D 3 M 45 I 2 M 26 I 1 M 2 I 1 M 18 D 2 M 17 I 1 M 36 D 2 M 4 D 1 M 8 I 2 M 7 D 1 M 9 I 1 M 52 D 1 M 8 D 1 M 9 D 3 M 29 D 1 M 18 D 3 M 12 D 1 M 19 I 2 M 103 D 1 M 18 D 1 M 8 D 1 M 14 I 1 M 9 D 1 M 10 I 1 M 3 D 1 M 5 D 1 M 9 I 2 M 14 D 1 M 14 D 1 M 2 I 1 M 4 I 1 M 46 D 1 M 2 I 1 M 66 I 1 M 1 I 1 M 17 I 2 M 5 D 1 M 20 I 1 M 12 D 1 M 71 I 1 M 15 I 2 M 9 D 2 M 23 I 1 M 6 D 1 M 6 D 1 M 6 D 1 M 19 D 2 M 26 I 1 M 36 I 1 M 9 D 605 I 10 | cPecanRealign /scratch/tmp/tmpivbY_w/localTempDir/ref.fa /scratch/tmp/t mpivbY_w/localTempDir/read.fa --diagonalExpansion=10 --splitMatrixBiggerThanThis=3000 --lo adHmm /hive/users/miten/pipeline_full_runs/stats_marginAlign/margin/src/margin/mappers/last_hmm_20 .txt --gapGamma=0.5 --matchGamma=0.0 >> /hive/users/miten/pipeline_full_runs/stats_marginAlign/mar gin/jobTreeM13NoEM/jobs/gTD1/tmp_zsbGhgPBdH/tempOutput_1814.txt exited with non-zero status 139 Exiting the slave because of a failed job on host juggernaut Due to failure we are reducing the remaining retry count of job /hive/users/miten/pipeline_full_ru ns/stats_marginAlign/margin/jobTreeM13NoEM/jobs/t3/t3/t3/t4/t2/t0/job to 0 We have set the default memory of the failed job to 2147483648 bytes

[benedictpaten]

Hi Miten,

Is this for marginAlign, marginCall or both?

[mitenjain]

Hi Ben,

I have not checked this for marginCall. I can check it right now and get back to you in a few minutes.

Best regards, Miten

On Wed, Feb 25, 2015 at 8:56 AM, Benedict Paten notifications@github.com wrote:

Hi Miten,

Is this for marginAlign, marginCall or both?

— Reply to this email directly or view it on GitHub https://github.com/benedictpaten/marginAlign/issues/6#issuecomment-76001007 .

[benedictpaten]

What would be most helpful would be if you could add a test to the unit-tests that has two references for marginAlign. That way I can fix this and we'll know it's fixed in future revisions.

[mitenjain]

Sure. I will do it ASAP.

On Wed, Feb 25, 2015 at 8:59 AM, Benedict Paten notifications@github.com wrote:

What would be most helpful would be if you could add a test to the unit-tests that has two references for marginAlign. That way I can fix this and we'll know it's fixed in future revisions.

— Reply to this email directly or view it on GitHub https://github.com/benedictpaten/marginAlign/issues/6#issuecomment-76001762 .

[benedictpaten]

Just pushed a fix - I note that some tests fail because the file "./tests/input2Refs.sam" is not in the repo.. possibly forgot to commit?

[mitenjain]

Committed. Sorry for forgetting earlier.

All tests working now.

On Sun, Mar 1, 2015 at 10:12 PM, Benedict Paten notifications@github.com wrote:

Just pushed a fix - I note that some tests fail because the file "./tests/input2Refs.sam" is not in the repo.. possibly forgot to commit?

— Reply to this email directly or view it on GitHub https://github.com/benedictpaten/marginAlign/issues/6#issuecomment-76663286 .

[benedictpaten]

Great, I'm working on the local alignment vs. global alignment issue.

On Sun, Mar 1, 2015 at 10:24 PM, Miten Jain notifications@github.com wrote:

Committed. Sorry for forgetting earlier.

All tests working now.

On Sun, Mar 1, 2015 at 10:12 PM, Benedict Paten notifications@github.com wrote:

Just pushed a fix - I note that some tests fail because the file "./tests/input2Refs.sam" is not in the repo.. possibly forgot to commit?

— Reply to this email directly or view it on GitHub < https://github.com/benedictpaten/marginAlign/issues/6#issuecomment-76663286

.

— Reply to this email directly or view it on GitHub https://github.com/benedictpaten/marginAlign/issues/6#issuecomment-76664060 .