[miten@ku margin]$ ./marginAlign tests/reads.fq tests/reference.fa tests/test.sam --jobTree ./jobTree
The job seems to have left a log file, indicating failure: /hive/users/miten/pipeline_full_runs/marginAlign/margin/jobTree/jobs/job
Reporting file: /hive/users/miten/pipeline_full_runs/marginAlign/margin/jobTree/jobs/log.txt
log.txt: ---JOBTREE SLAVE OUTPUT LOG---
log.txt: /bin/sh: line 1: 19327 Done echo cigar: RAT_1_read_1 0 38435 + HUMAN 0 57553 +
1 D 41310 I 23895 M 93 D 1 M 16 I 1 M 1 I 3 M 4 I 2 M 8 D 1 M 14 I 1 M 27 D 1 M 89 D 1 M 5 I 1 M 7
D 4 M 13 D 36 I 135 M 15 I 1 M 8 I 1 M 32 D 1 M 6 D 1 M 9 D 1 M 5 I 2 M 7 D 1 M 32 D 1 M 51 D 4 M
4 D 2 M 3 I 1 M 9 D 5 M 18 D 4 M 59 I 1 M 3 I 2 M 25 I 1 M 27 D 1 M 9 I 1 M 4 I 1 M 5 I 2 M 8 D 1
M 13 D 2 M 17 I 3 M 9 I 1 M 3 D 3 M 15 I 3 M 13 D 2 M 64 D 1 M 17 I 8 M 2 I 3 M 3 I 1 M 2 I 1 M 1
1 I 1 M 7 I 1 M 3 I 6 M 46 I 2 M 38 I 3 M 21 D 1 M 7 I 1 M 26 I 1 M 2 D 1 M 5 D 2 M 1 D 1 M 4 D 5
M 3 D 1 M 1 D 5 M 23 D 3 M 21 I 3 M 4 D 1 M 6 I 4 M 2 I 2 M 4 I 1 M 2 I 2 M 5 I 1 M 11 D 1 M 9 D 1
M 31 D 2 M 3 I 1 M 32 I 2 M 2 I 1 M 4 I 2 M 19 D 1 M 13 D 3 M 4 D 1 M 13 D 2 M 1 D 12 M 5 D 2 M 3
D 1 M 4 D 3 M 14 D 12 M 3 D 3 M 1 D 1 M 33 D 2 M 19 D 1 M 4 D 5 M 63 D 2 M 3 D 3 M 17 D 1 M 12 D
2 M 19 D 1 M 4 D 3 M 11 I 1 M 72 I 6 M 2 I 2 M 2 I 2 M 5 I 1 M 4 I 7 M 4 I 2 M 3 I 1 M 6 I 2 M 2 I
4 M 4 I 3 M 3 I 4 M 3 I 1 M 3 I 3 M 1 I 8 M 4 I 4 M 2 I 2 M 3 I 2 M 9 I 5 M 1 I 3 M 11 I 5 M 21 I
1 M 7 I 1 M 11 I 1 M 27 I 3 M 4 D 3 M 9 D 3 M 3 I 4 M 4 I 1 M 3 I 1 M 3 I 1 M 6 D 1 M 16 D 2 M 5
I 1 M 61 D 1 M 17 D 6 M 3 D 2 M 1 D 2 M 4 D 6 M 11 D 1 M 55 D 1 M 11 D 1 M 9 I 1 M 7 D 2 M 4 I 2 M
23 I 3 M 3 I 5 M 5 I 2 M 1 I 8 M 2 I 3 M 1 I 6 M 3 I 1 M 41 D 2 M 48 D 3 M 33 D 1 M 9 I 1 M 5 I 2
M 18 D 1 M 8 D 14027 I 12195
19328 Segmentation fault | cactus_realign /tmp/tmpiZzkHK/localTempDir/ref.fa /tmp/tmpiZz
kHK/localTempDir/read.fa --diagonalExpansion=10 --splitMatrixBiggerThanThis=3000 --loadHmm hmm.txt
--gapGamma=0.5 --matchGamma=0.0 >> /hive/users/miten/pipeline_full_runs/marginAlign/margin/jobTre
e/jobs/gTD1/tmp_BO6zheoVpY/tempOutput_1.txt
Traceback (most recent call last):
File "/hive/users/miten/pipeline_full_runs/marginAlign/margin/submodules/jobTree/src/jobTreeSlav
e.py", line 271, in main
defaultMemory=defaultMemory, defaultCpu=defaultCpu, depth=depth)
File "/hive/users/miten/pipeline_full_runs/marginAlign/margin/submodules/jobTree/scriptTree/stac
k.py", line 153, in execute
self.target.run()
File "/hive/users/miten/pipeline_fullruns/marginAlign/margin/submodules/jobTree/scriptTree/targ
et.py", line 197, in run
func(((self,) + tuple(self.args)), *_self.kwargs)
File "/hive/users/miten/pipeline_full_runs/marginAlign/margin/src/margin/marginAlignLib.py", lin
e 319, in realignCigarTargetFn
options.gapGamma, options.matchGamma, outputCigarFile))
File "/hive/users/miten/pipeline_full_runs/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: RAT_1_read_1 0 38435 + HUMAN 0 57553 + 1 D 41310 I 23895 M 93 D
1 M 16 I 1 M 1 I 3 M 4 I 2 M 8 D 1 M 14 I 1 M 27 D 1 M 89 D 1 M 5 I 1 M 7 D 4 M 13 D 36 I 135 M 1
5 I 1 M 8 I 1 M 32 D 1 M 6 D 1 M 9 D 1 M 5 I 2 M 7 D 1 M 32 D 1 M 51 D 4 M 4 D 2 M 3 I 1 M 9 D 5 M
18 D 4 M 59 I 1 M 3 I 2 M 25 I 1 M 27 D 1 M 9 I 1 M 4 I 1 M 5 I 2 M 8 D 1 M 13 D 2 M 17 I 3 M 9 I
1 M 3 D 3 M 15 I 3 M 13 D 2 M 64 D 1 M 17 I 8 M 2 I 3 M 3 I 1 M 2 I 1 M 11 I 1 M 7 I 1 M 3 I 6 M
46 I 2 M 38 I 3 M 21 D 1 M 7 I 1 M 26 I 1 M 2 D 1 M 5 D 2 M 1 D 1 M 4 D 5 M 3 D 1 M 1 D 5 M 23 D 3
M 21 I 3 M 4 D 1 M 6 I 4 M 2 I 2 M 4 I 1 M 2 I 2 M 5 I 1 M 11 D 1 M 9 D 1 M 31 D 2 M 3 I 1 M 32 I
2 M 2 I 1 M 4 I 2 M 19 D 1 M 13 D 3 M 4 D 1 M 13 D 2 M 1 D 12 M 5 D 2 M 3 D 1 M 4 D 3 M 14 D 12 M
3 D 3 M 1 D 1 M 33 D 2 M 19 D 1 M 4 D 5 M 63 D 2 M 3 D 3 M 17 D 1 M 12 D 2 M 19 D 1 M 4 D 3 M 11
I 1 M 72 I 6 M 2 I 2 M 2 I 2 M 5 I 1 M 4 I 7 M 4 I 2 M 3 I 1 M 6 I 2 M 2 I 4 M 4 I 3 M 3 I 4 M 3 I
1 M 3 I 3 M 1 I 8 M 4 I 4 M 2 I 2 M 3 I 2 M 9 I 5 M 1 I 3 M 11 I 5 M 21 I 1 M 7 I 1 M 11 I 1 M 27
I 3 M 4 D 3 M 9 D 3 M 3 I 4 M 4 I 1 M 3 I 1 M 3 I 1 M 6 D 1 M 16 D 2 M 5 I 1 M 61 D 1 M 17 D 6 M
3 D 2 M 1 D 2 M 4 D 6 M 11 D 1 M 55 D 1 M 11 D 1 M 9 I 1 M 7 D 2 M 4 I 2 M 23 I 3 M 3 I 5 M 5 I 2
M 1 I 8 M 2 I 3 M 1 I 6 M 3 I 1 M 41 D 2 M 48 D 3 M 33 D 1 M 9 I 1 M 5 I 2 M 18 D 1 M 8 D 14027 I
12195 | cactus_realign /tmp/tmpiZzkHK/localTempDir/ref.fa /tmp/tmpiZzkHK/localTempDir/read.fa --di
agonalExpansion=10 --splitMatrixBiggerThanThis=3000 --loadHmm hmm.txt --gapGamma=0.5 --mat
chGamma=0.0 >> /hive/users/miten/pipeline_full_runs/marginAlign/margin/jobTree/jobs/gTD1/tmp_BO6zh
eoVpY/tempOutput_1.txt exited with non-zero status 139
Exiting the slave because of a failed job on host ku.sdsc.edu
Due to failure we are reducing the remaining retry count of job /hive/users/miten/pipeline_full_ru
ns/marginAlign/margin/jobTree/jobs/job to 0
We have set the default memory of the failed job to 2147483648 bytes
[miten@ku margin]$ ./marginAlign tests/reads.fq tests/reference.fa tests/test.sam --jobTree ./jobTree The job seems to have left a log file, indicating failure: /hive/users/miten/pipeline_full_runs/marginAlign/margin/jobTree/jobs/job Reporting file: /hive/users/miten/pipeline_full_runs/marginAlign/margin/jobTree/jobs/log.txt log.txt: ---JOBTREE SLAVE OUTPUT LOG--- log.txt: /bin/sh: line 1: 19327 Done echo cigar: RAT_1_read_1 0 38435 + HUMAN 0 57553 + 1 D 41310 I 23895 M 93 D 1 M 16 I 1 M 1 I 3 M 4 I 2 M 8 D 1 M 14 I 1 M 27 D 1 M 89 D 1 M 5 I 1 M 7 D 4 M 13 D 36 I 135 M 15 I 1 M 8 I 1 M 32 D 1 M 6 D 1 M 9 D 1 M 5 I 2 M 7 D 1 M 32 D 1 M 51 D 4 M 4 D 2 M 3 I 1 M 9 D 5 M 18 D 4 M 59 I 1 M 3 I 2 M 25 I 1 M 27 D 1 M 9 I 1 M 4 I 1 M 5 I 2 M 8 D 1 M 13 D 2 M 17 I 3 M 9 I 1 M 3 D 3 M 15 I 3 M 13 D 2 M 64 D 1 M 17 I 8 M 2 I 3 M 3 I 1 M 2 I 1 M 1 1 I 1 M 7 I 1 M 3 I 6 M 46 I 2 M 38 I 3 M 21 D 1 M 7 I 1 M 26 I 1 M 2 D 1 M 5 D 2 M 1 D 1 M 4 D 5 M 3 D 1 M 1 D 5 M 23 D 3 M 21 I 3 M 4 D 1 M 6 I 4 M 2 I 2 M 4 I 1 M 2 I 2 M 5 I 1 M 11 D 1 M 9 D 1 M 31 D 2 M 3 I 1 M 32 I 2 M 2 I 1 M 4 I 2 M 19 D 1 M 13 D 3 M 4 D 1 M 13 D 2 M 1 D 12 M 5 D 2 M 3 D 1 M 4 D 3 M 14 D 12 M 3 D 3 M 1 D 1 M 33 D 2 M 19 D 1 M 4 D 5 M 63 D 2 M 3 D 3 M 17 D 1 M 12 D 2 M 19 D 1 M 4 D 3 M 11 I 1 M 72 I 6 M 2 I 2 M 2 I 2 M 5 I 1 M 4 I 7 M 4 I 2 M 3 I 1 M 6 I 2 M 2 I 4 M 4 I 3 M 3 I 4 M 3 I 1 M 3 I 3 M 1 I 8 M 4 I 4 M 2 I 2 M 3 I 2 M 9 I 5 M 1 I 3 M 11 I 5 M 21 I 1 M 7 I 1 M 11 I 1 M 27 I 3 M 4 D 3 M 9 D 3 M 3 I 4 M 4 I 1 M 3 I 1 M 3 I 1 M 6 D 1 M 16 D 2 M 5 I 1 M 61 D 1 M 17 D 6 M 3 D 2 M 1 D 2 M 4 D 6 M 11 D 1 M 55 D 1 M 11 D 1 M 9 I 1 M 7 D 2 M 4 I 2 M 23 I 3 M 3 I 5 M 5 I 2 M 1 I 8 M 2 I 3 M 1 I 6 M 3 I 1 M 41 D 2 M 48 D 3 M 33 D 1 M 9 I 1 M 5 I 2 M 18 D 1 M 8 D 14027 I 12195 19328 Segmentation fault | cactus_realign /tmp/tmpiZzkHK/localTempDir/ref.fa /tmp/tmpiZz kHK/localTempDir/read.fa --diagonalExpansion=10 --splitMatrixBiggerThanThis=3000 --loadHmm hmm.txt --gapGamma=0.5 --matchGamma=0.0 >> /hive/users/miten/pipeline_full_runs/marginAlign/margin/jobTre e/jobs/gTD1/tmp_BO6zheoVpY/tempOutput_1.txt Traceback (most recent call last): File "/hive/users/miten/pipeline_full_runs/marginAlign/margin/submodules/jobTree/src/jobTreeSlav e.py", line 271, in main defaultMemory=defaultMemory, defaultCpu=defaultCpu, depth=depth) File "/hive/users/miten/pipeline_full_runs/marginAlign/margin/submodules/jobTree/scriptTree/stac k.py", line 153, in execute self.target.run() File "/hive/users/miten/pipeline_fullruns/marginAlign/margin/submodules/jobTree/scriptTree/targ et.py", line 197, in run func(((self,) + tuple(self.args)), *_self.kwargs) File "/hive/users/miten/pipeline_full_runs/marginAlign/margin/src/margin/marginAlignLib.py", lin e 319, in realignCigarTargetFn options.gapGamma, options.matchGamma, outputCigarFile)) File "/hive/users/miten/pipeline_full_runs/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: RAT_1_read_1 0 38435 + HUMAN 0 57553 + 1 D 41310 I 23895 M 93 D 1 M 16 I 1 M 1 I 3 M 4 I 2 M 8 D 1 M 14 I 1 M 27 D 1 M 89 D 1 M 5 I 1 M 7 D 4 M 13 D 36 I 135 M 1 5 I 1 M 8 I 1 M 32 D 1 M 6 D 1 M 9 D 1 M 5 I 2 M 7 D 1 M 32 D 1 M 51 D 4 M 4 D 2 M 3 I 1 M 9 D 5 M 18 D 4 M 59 I 1 M 3 I 2 M 25 I 1 M 27 D 1 M 9 I 1 M 4 I 1 M 5 I 2 M 8 D 1 M 13 D 2 M 17 I 3 M 9 I 1 M 3 D 3 M 15 I 3 M 13 D 2 M 64 D 1 M 17 I 8 M 2 I 3 M 3 I 1 M 2 I 1 M 11 I 1 M 7 I 1 M 3 I 6 M 46 I 2 M 38 I 3 M 21 D 1 M 7 I 1 M 26 I 1 M 2 D 1 M 5 D 2 M 1 D 1 M 4 D 5 M 3 D 1 M 1 D 5 M 23 D 3 M 21 I 3 M 4 D 1 M 6 I 4 M 2 I 2 M 4 I 1 M 2 I 2 M 5 I 1 M 11 D 1 M 9 D 1 M 31 D 2 M 3 I 1 M 32 I 2 M 2 I 1 M 4 I 2 M 19 D 1 M 13 D 3 M 4 D 1 M 13 D 2 M 1 D 12 M 5 D 2 M 3 D 1 M 4 D 3 M 14 D 12 M 3 D 3 M 1 D 1 M 33 D 2 M 19 D 1 M 4 D 5 M 63 D 2 M 3 D 3 M 17 D 1 M 12 D 2 M 19 D 1 M 4 D 3 M 11 I 1 M 72 I 6 M 2 I 2 M 2 I 2 M 5 I 1 M 4 I 7 M 4 I 2 M 3 I 1 M 6 I 2 M 2 I 4 M 4 I 3 M 3 I 4 M 3 I 1 M 3 I 3 M 1 I 8 M 4 I 4 M 2 I 2 M 3 I 2 M 9 I 5 M 1 I 3 M 11 I 5 M 21 I 1 M 7 I 1 M 11 I 1 M 27 I 3 M 4 D 3 M 9 D 3 M 3 I 4 M 4 I 1 M 3 I 1 M 3 I 1 M 6 D 1 M 16 D 2 M 5 I 1 M 61 D 1 M 17 D 6 M 3 D 2 M 1 D 2 M 4 D 6 M 11 D 1 M 55 D 1 M 11 D 1 M 9 I 1 M 7 D 2 M 4 I 2 M 23 I 3 M 3 I 5 M 5 I 2 M 1 I 8 M 2 I 3 M 1 I 6 M 3 I 1 M 41 D 2 M 48 D 3 M 33 D 1 M 9 I 1 M 5 I 2 M 18 D 1 M 8 D 14027 I 12195 | cactus_realign /tmp/tmpiZzkHK/localTempDir/ref.fa /tmp/tmpiZzkHK/localTempDir/read.fa --di agonalExpansion=10 --splitMatrixBiggerThanThis=3000 --loadHmm hmm.txt --gapGamma=0.5 --mat chGamma=0.0 >> /hive/users/miten/pipeline_full_runs/marginAlign/margin/jobTree/jobs/gTD1/tmp_BO6zh eoVpY/tempOutput_1.txt exited with non-zero status 139 Exiting the slave because of a failed job on host ku.sdsc.edu Due to failure we are reducing the remaining retry count of job /hive/users/miten/pipeline_full_ru ns/marginAlign/margin/jobTree/jobs/job to 0 We have set the default memory of the failed job to 2147483648 bytes