Segmentation fault error in a subset of samples using LUMPY Express #129
Comments
|
To dig into this we will have to extract the problematic region of the BAM On Thu, Jul 21, 2016 at 12:49 PM, AAvalos82 notifications@github.com
Ryan Layer |
|
Hi, I got the same segmentation as #129 fault error leading to a core dump. It only happens on a subset of my samples (6/52, human whole genomes, aligned with BWA-MEM, -M). The output of these samples contains readable vcf headers without any calls. I would greatly appreciate any help solving this issue. Thanks in advance, amaia |
|
Can you check to see how big this file is /data/corpora/sge2/
lag/projects/lg-hand/working/Bordeaux/SV/lumpy/t0_397/t0_
397.discordants.bam?
…On Tue, May 9, 2017 at 2:21 AM, amaiacc ***@***.***> wrote:
Hi,
I got the same segmentation fault error leading to a core dump. It only
happens on a subset of my samples (6/52, human whole genomes, aligned with
BWA-MEM, -M).
The output of these samples contains readable vcf headers without any
calls.
I would greatly appreciate any help solving this issue.
Thanks in advance,
amaia
lumpyexpress \
> -B t0_397.reordered.bam \
> -S t0_397/t0_397.splitters.bam \
> -D t0_397/t0_397.discordants.bam \
> -T ./tmp \
> -v -k \
> -o BILGIN_t0_397_k_SV_lumpy.vcf
Sourcing executables from /data/corpora/MPI_workspace/lag/shared_spaces/Resource_DB/lumpy-sv/bin/lumpyexpress.config ...
Checking for required python modules (/usr/local/apps/python-2.7.11/bin/python)...
create temporary directory
Calculating insert distributions...
Library read groups: HKAIPI000472-70,HKAIPI000472-70.1,HKAIPI000472-70.2,HKAIPI000472-70.3
Library read length: 90
Removed 130 outliers with isize >= 557
Library read groups: HKAIPI000471-71
Library read length: 90
Removed 68 outliers with isize >= 558
done
0
0
Running LUMPY...
/data/corpora/MPI_workspace/lag/shared_spaces/Resource_DB/lumpy-sv/bin/lumpy \
-t ./tmp/BILGIN_t0_397_k_SV_lumpy.vcf \
-msw 4 \
-tt 0 \
\
\
-pe bam_file:/data/corpora/sge2/lag/projects/lg-hand/working/Bordeaux/SV/lumpy/t0_397/t0_397.discordants.bam,histo_file:./tmp/BILGIN_t0_397_k_SV_lumpy.vcf.sample1.lib1.x4.histo,mean:457.712174187,stdev:52.7052111789,read_length:90,min_non_overlap:90,discordant_z:5,back_distance:10,weight:1,id:t0_397,min_mapping_threshold:20,read_group:HKAIPI000472-70,read_group:HKAIPI000472-70.1,read_group:HKAIPI000472-70.2,read_group:HKAIPI000472-70.3 -pe bam_file:/data/corpora/sge2/lag/projects/lg-hand/working/Bordeaux/SV/lumpy/t0_397/t0_397.discordants.bam,histo_file:./tmp/BILGIN_t0_397_k_SV_lumpy.vcf.sample1.lib2.x4.histo,mean:457.844237813,stdev:53.707274301,read_length:90,min_non_overlap:90,discordant_z:5,back_distance:10,weight:1,id:t0_397,min_mapping_threshold:20,read_group:HKAIPI000471-71 \
-sr bam_file:/data/corpora/sge2/lag/projects/lg-hand/working/Bordeaux/SV/lumpy/t0_397/t0_397.splitters.bam,back_distance:10,min_mapping_threshold:20,weight:1,id:t0_397,min_clip:20 \
> BILGIN_t0_397_k_SV_lumpy.vcf
474 0
469 0
chrM 1000000
/data/corpora/MPI_workspace/lag/shared_spaces/Resource_DB/lumpy-sv/bin/lumpyexpress: line 480: 56317 Segmentation fault $LUMPY $PROB_CURVE -t ${TEMP_DIR}/${OUTBASE} -msw $MIN_SAMPLE_WEIGHT -tt $TRIM_THRES $LUMPY_DEPTH_STRING $EXCLUDE_BED_FMT $LUMPY_DISC_STRING $EXCLUDE_BED_FMT $LUMPY_SPL_STRING > $OUTPUT
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The file is 756M. Other samples that ran without problems had similar sized
discordants bam files (ranging: 373M-1.1G).
Thanks,
amaia
2017-06-06 19:20 GMT+02:00 Ryan Layer <notifications@github.com>:
… Can you check to see how big this file is /data/corpora/sge2/
lag/projects/lg-hand/working/Bordeaux/SV/lumpy/t0_397/t0_
397.discordants.bam?
On Tue, May 9, 2017 at 2:21 AM, amaiacc ***@***.***> wrote:
> Hi,
>
> I got the same segmentation fault error leading to a core dump. It only
> happens on a subset of my samples (6/52, human whole genomes, aligned
with
> BWA-MEM, -M).
>
> The output of these samples contains readable vcf headers without any
> calls.
>
> I would greatly appreciate any help solving this issue.
>
> Thanks in advance,
>
> amaia
>
> lumpyexpress \
> > -B t0_397.reordered.bam \
> > -S t0_397/t0_397.splitters.bam \
> > -D t0_397/t0_397.discordants.bam \
> > -T ./tmp \
> > -v -k \
> > -o BILGIN_t0_397_k_SV_lumpy.vcf
> Sourcing executables from /data/corpora/MPI_workspace/
lag/shared_spaces/Resource_DB/lumpy-sv/bin/lumpyexpress.config ...
>
> Checking for required python modules (/usr/local/apps/python-2.7.
11/bin/python)...
>
> create temporary directory
> Calculating insert distributions...
> Library read groups: HKAIPI000472-70,HKAIPI000472-
70.1,HKAIPI000472-70.2,HKAIPI000472-70.3
> Library read length: 90
> Removed 130 outliers with isize >= 557
> Library read groups: HKAIPI000471-71
> Library read length: 90
> Removed 68 outliers with isize >= 558
> done
> 0
> 0
> Running LUMPY...
>
> /data/corpora/MPI_workspace/lag/shared_spaces/Resource_DB/lumpy-sv/bin/lumpy
\
> -t ./tmp/BILGIN_t0_397_k_SV_lumpy.vcf \
> -msw 4 \
> -tt 0 \
> \
> \
> -pe bam_file:/data/corpora/sge2/lag/projects/lg-hand/working/
Bordeaux/SV/lumpy/t0_397/t0_397.discordants.bam,histo_
file:./tmp/BILGIN_t0_397_k_SV_lumpy.vcf.sample1.lib1.x4.
histo,mean:457.712174187,stdev:52.7052111789,read_
length:90,min_non_overlap:90,discordant_z:5,back_distance:
10,weight:1,id:t0_397,min_mapping_threshold:20,read_
group:HKAIPI000472-70,read_group:HKAIPI000472-70.1,read_
group:HKAIPI000472-70.2,read_group:HKAIPI000472-70.3 -pe
bam_file:/data/corpora/sge2/lag/projects/lg-hand/working/
Bordeaux/SV/lumpy/t0_397/t0_397.discordants.bam,histo_
file:./tmp/BILGIN_t0_397_k_SV_lumpy.vcf.sample1.lib2.x4.
histo,mean:457.844237813,stdev:53.707274301,read_
length:90,min_non_overlap:90,discordant_z:5,back_distance:
10,weight:1,id:t0_397,min_mapping_threshold:20,read_group:HKAIPI000471-71
\
> -sr bam_file:/data/corpora/sge2/lag/projects/lg-hand/working/
Bordeaux/SV/lumpy/t0_397/t0_397.splitters.bam,back_
distance:10,min_mapping_threshold:20,weight:1,id:t0_397,min_clip:20 \
> > BILGIN_t0_397_k_SV_lumpy.vcf
> 474 0
> 469 0
> chrM 1000000
> /data/corpora/MPI_workspace/lag/shared_spaces/Resource_DB/lumpy-sv/bin/lumpyexpress:
line 480: 56317 Segmentation fault $LUMPY $PROB_CURVE -t
${TEMP_DIR}/${OUTBASE} -msw $MIN_SAMPLE_WEIGHT -tt $TRIM_THRES
$LUMPY_DEPTH_STRING $EXCLUDE_BED_FMT $LUMPY_DISC_STRING $EXCLUDE_BED_FMT
$LUMPY_SPL_STRING > $OUTPUT
>
> —
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> Reply to this email directly, view it on GitHub
> <#129 (comment)>,
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Ryan Layer
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Do you think that you can send over these files:
/data/corpora/sge2/lag/projects/lg-hand/working/Bordeaux/SV/lumpy/t0_397/t0_397.discordants.bam
/tmp/BILGIN_t0_397_k_SV_lumpy.vcf.sample1.lib1.x4.histo
/data/corpora/sge2/lag/projects/lg-hand/working/Bordeaux/SV/lumpy/t0_397/t0_397.discordants.bam
/tmp/BILGIN_t0_397_k_SV_lumpy.vcf.sample1.lib2.x4.histo
/data/corpora/sge2/lag/projects/lg-hand/working/Bordeaux/SV/lumpy/t0_397/t0_397.splitters.bam
…On Tue, Jun 6, 2017 at 11:52 AM, amaiacc ***@***.***> wrote:
The file is 756M. Other samples that ran without problems had similar sized
discordants bam files (ranging: 373M-1.1G).
Thanks,
amaia
2017-06-06 19:20 GMT+02:00 Ryan Layer ***@***.***>:
> Can you check to see how big this file is /data/corpora/sge2/
> lag/projects/lg-hand/working/Bordeaux/SV/lumpy/t0_397/t0_
> 397.discordants.bam?
>
> On Tue, May 9, 2017 at 2:21 AM, amaiacc ***@***.***>
wrote:
>
> > Hi,
> >
> > I got the same segmentation fault error leading to a core dump. It only
> > happens on a subset of my samples (6/52, human whole genomes, aligned
> with
> > BWA-MEM, -M).
> >
> > The output of these samples contains readable vcf headers without any
> > calls.
> >
> > I would greatly appreciate any help solving this issue.
> >
> > Thanks in advance,
> >
> > amaia
> >
> > lumpyexpress \
> > > -B t0_397.reordered.bam \
> > > -S t0_397/t0_397.splitters.bam \
> > > -D t0_397/t0_397.discordants.bam \
> > > -T ./tmp \
> > > -v -k \
> > > -o BILGIN_t0_397_k_SV_lumpy.vcf
> > Sourcing executables from /data/corpora/MPI_workspace/
> lag/shared_spaces/Resource_DB/lumpy-sv/bin/lumpyexpress.config ...
> >
> > Checking for required python modules (/usr/local/apps/python-2.7.
> 11/bin/python)...
> >
> > create temporary directory
> > Calculating insert distributions...
> > Library read groups: HKAIPI000472-70,HKAIPI000472-
> 70.1,HKAIPI000472-70.2,HKAIPI000472-70.3
> > Library read length: 90
> > Removed 130 outliers with isize >= 557
> > Library read groups: HKAIPI000471-71
> > Library read length: 90
> > Removed 68 outliers with isize >= 558
> > done
> > 0
> > 0
> > Running LUMPY...
> >
> > /data/corpora/MPI_workspace/lag/shared_spaces/Resource_DB/
lumpy-sv/bin/lumpy
> \
> > -t ./tmp/BILGIN_t0_397_k_SV_lumpy.vcf \
> > -msw 4 \
> > -tt 0 \
> > \
> > \
> > -pe bam_file:/data/corpora/sge2/lag/projects/lg-hand/working/
> Bordeaux/SV/lumpy/t0_397/t0_397.discordants.bam,histo_
> file:./tmp/BILGIN_t0_397_k_SV_lumpy.vcf.sample1.lib1.x4.
> histo,mean:457.712174187,stdev:52.7052111789 <(705)%20211-1789>,read_
> length:90,min_non_overlap:90,discordant_z:5,back_distance:
> 10,weight:1,id:t0_397,min_mapping_threshold:20,read_
> group:HKAIPI000472-70,read_group:HKAIPI000472-70.1,read_
> group:HKAIPI000472-70.2,read_group:HKAIPI000472-70.3 -pe
> bam_file:/data/corpora/sge2/lag/projects/lg-hand/working/
> Bordeaux/SV/lumpy/t0_397/t0_397.discordants.bam,histo_
> file:./tmp/BILGIN_t0_397_k_SV_lumpy.vcf.sample1.lib2.x4.
> histo,mean:457.844237813,stdev:53.707274301,read_
> length:90,min_non_overlap:90,discordant_z:5,back_distance:
> 10,weight:1,id:t0_397,min_mapping_threshold:20,read_
group:HKAIPI000471-71
> \
> > -sr bam_file:/data/corpora/sge2/lag/projects/lg-hand/working/
> Bordeaux/SV/lumpy/t0_397/t0_397.splitters.bam,back_
> distance:10,min_mapping_threshold:20,weight:1,id:t0_397,min_clip:20 \
> > > BILGIN_t0_397_k_SV_lumpy.vcf
> > 474 0
> > 469 0
> > chrM 1000000
> > /data/corpora/MPI_workspace/lag/shared_spaces/Resource_DB/
lumpy-sv/bin/lumpyexpress:
> line 480: 56317 Segmentation fault $LUMPY $PROB_CURVE -t
> ${TEMP_DIR}/${OUTBASE} -msw $MIN_SAMPLE_WEIGHT -tt $TRIM_THRES
> $LUMPY_DEPTH_STRING $EXCLUDE_BED_FMT $LUMPY_DISC_STRING $EXCLUDE_BED_FMT
> $LUMPY_SPL_STRING > $OUTPUT
> >
> > —
> > You are receiving this because you commented.
> > Reply to this email directly, view it on GitHub
> > <#129 (comment)>,
> or mute
> > the thread
> > <https://github.com/notifications/unsubscribe-auth/
> AAlDUU2tKnMCE4cHPlp5GPlR1b-mzjsuks5r4CIXgaJpZM4JSGjo>
> > .
> >
>
>
>
> --
> Ryan Layer
>
> —
> You are receiving this because you commented.
> Reply to this email directly, view it on GitHub
> <#129 (comment)>,
or mute
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dWc9OVfjPXLTGks5sBYppgaJpZM4JSGjo>
> .
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Ryan Layer
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Dear Ryan,
I've uploaded the files here
<https://owncloud.gwdg.de/index.php/s/kSmRE86MN8cTJb0>.
I've noticed that a subset of my samples do not contain any split reads,
splitters.bam is empty.
However, some of these samples do create SV calls despite not having any
split reads. I've included one of these samples without SR, but with SV
calls in the vcf file (BILGIN_t0_508_SV_lumpy.vcf).
Thanks in advance for your help,
amaia
2017-06-06 20:19 GMT+02:00 Ryan Layer <notifications@github.com>:
… Do you think that you can send over these files:
/data/corpora/sge2/lag/projects/lg-hand/working/
Bordeaux/SV/lumpy/t0_397/t0_397.discordants.bam
/tmp/BILGIN_t0_397_k_SV_lumpy.vcf.sample1.lib1.x4.histo
/data/corpora/sge2/lag/projects/lg-hand/working/
Bordeaux/SV/lumpy/t0_397/t0_397.discordants.bam
/tmp/BILGIN_t0_397_k_SV_lumpy.vcf.sample1.lib2.x4.histo
/data/corpora/sge2/lag/projects/lg-hand/working/
Bordeaux/SV/lumpy/t0_397/t0_397.splitters.bam
On Tue, Jun 6, 2017 at 11:52 AM, amaiacc ***@***.***> wrote:
> The file is 756M. Other samples that ran without problems had similar
sized
> discordants bam files (ranging: 373M-1.1G).
>
> Thanks,
> amaia
>
> 2017-06-06 19:20 GMT+02:00 Ryan Layer ***@***.***>:
>
> > Can you check to see how big this file is /data/corpora/sge2/
> > lag/projects/lg-hand/working/Bordeaux/SV/lumpy/t0_397/t0_
> > 397.discordants.bam?
> >
> > On Tue, May 9, 2017 at 2:21 AM, amaiacc ***@***.***>
> wrote:
> >
> > > Hi,
> > >
> > > I got the same segmentation fault error leading to a core dump. It
only
> > > happens on a subset of my samples (6/52, human whole genomes, aligned
> > with
> > > BWA-MEM, -M).
> > >
> > > The output of these samples contains readable vcf headers without any
> > > calls.
> > >
> > > I would greatly appreciate any help solving this issue.
> > >
> > > Thanks in advance,
> > >
> > > amaia
> > >
> > > lumpyexpress \
> > > > -B t0_397.reordered.bam \
> > > > -S t0_397/t0_397.splitters.bam \
> > > > -D t0_397/t0_397.discordants.bam \
> > > > -T ./tmp \
> > > > -v -k \
> > > > -o BILGIN_t0_397_k_SV_lumpy.vcf
> > > Sourcing executables from /data/corpora/MPI_workspace/
> > lag/shared_spaces/Resource_DB/lumpy-sv/bin/lumpyexpress.config ...
> > >
> > > Checking for required python modules (/usr/local/apps/python-2.7.
> > 11/bin/python)...
> > >
> > > create temporary directory
> > > Calculating insert distributions...
> > > Library read groups: HKAIPI000472-70,HKAIPI000472-
>
> > 70.1,HKAIPI000472-70.2,HKAIPI000472-70.3
> > > Library read length: 90
> > > Removed 130 outliers with isize >= 557
> > > Library read groups: HKAIPI000471-71
> > > Library read length: 90
> > > Removed 68 outliers with isize >= 558
> > > done
> > > 0
> > > 0
> > > Running LUMPY...
> > >
> > > /data/corpora/MPI_workspace/lag/shared_spaces/Resource_DB/
> lumpy-sv/bin/lumpy
> > \
> > > -t ./tmp/BILGIN_t0_397_k_SV_lumpy.vcf \
> > > -msw 4 \
> > > -tt 0 \
> > > \
> > > \
> > > -pe bam_file:/data/corpora/sge2/lag/projects/lg-hand/working/
> > Bordeaux/SV/lumpy/t0_397/t0_397.discordants.bam,histo_
> > file:./tmp/BILGIN_t0_397_k_SV_lumpy.vcf.sample1.lib1.x4.
> > histo,mean:457.712174187,stdev:52.7052111789 <(705)%20211-1789>,read_
> > length:90,min_non_overlap:90,discordant_z:5,back_distance:
> > 10,weight:1,id:t0_397,min_mapping_threshold:20,read_
> > group:HKAIPI000472-70,read_group:HKAIPI000472-70.1,read_
> > group:HKAIPI000472-70.2,read_group:HKAIPI000472-70.3 -pe
> > bam_file:/data/corpora/sge2/lag/projects/lg-hand/working/
> > Bordeaux/SV/lumpy/t0_397/t0_397.discordants.bam,histo_
> > file:./tmp/BILGIN_t0_397_k_SV_lumpy.vcf.sample1.lib2.x4.
> > histo,mean:457.844237813,stdev:53.707274301,read_
> > length:90,min_non_overlap:90,discordant_z:5,back_distance:
> > 10,weight:1,id:t0_397,min_mapping_threshold:20,read_
> group:HKAIPI000471-71
> > \
> > > -sr bam_file:/data/corpora/sge2/lag/projects/lg-hand/working/
> > Bordeaux/SV/lumpy/t0_397/t0_397.splitters.bam,back_
> > distance:10,min_mapping_threshold:20,weight:1,id:t0_397,min_clip:20 \
> > > > BILGIN_t0_397_k_SV_lumpy.vcf
> > > 474 0
> > > 469 0
> > > chrM 1000000
> > > /data/corpora/MPI_workspace/lag/shared_spaces/Resource_DB/
> lumpy-sv/bin/lumpyexpress:
> > line 480: 56317 Segmentation fault $LUMPY $PROB_CURVE -t
> > ${TEMP_DIR}/${OUTBASE} -msw $MIN_SAMPLE_WEIGHT -tt $TRIM_THRES
> > $LUMPY_DEPTH_STRING $EXCLUDE_BED_FMT $LUMPY_DISC_STRING
$EXCLUDE_BED_FMT
> > $LUMPY_SPL_STRING > $OUTPUT
> > >
> > > —
> > > You are receiving this because you commented.
> > > Reply to this email directly, view it on GitHub
> > > <#129 (comment)
>,
> > or mute
> > > the thread
> > > <https://github.com/notifications/unsubscribe-auth/
> > AAlDUU2tKnMCE4cHPlp5GPlR1b-mzjsuks5r4CIXgaJpZM4JSGjo>
> > > .
> > >
> >
> >
> >
> > --
> > Ryan Layer
> >
> > —
> > You are receiving this because you commented.
> > Reply to this email directly, view it on GitHub
> > <#129 (comment)>,
> or mute
> > the thread
> > <https://github.com/notifications/unsubscribe-auth/APGbb9PeDxb5pNgd2U_
> dWc9OVfjPXLTGks5sBYppgaJpZM4JSGjo>
> > .
> >
>
> —
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> <#129 (comment)>,
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> .
>
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Hello, Im running like this: Here is my output: Checking for required python modules (/usr/bin/python)... |
|
This is the problem I'm having with lumpy express - but only when run via galaxy. I do not get the segfault on my mac. I want to be able to implement my analysis pipeline over to galaxy, so I'm interested in getting this resolved. My 27 bam files (10 of which lead to a segfault) are fairly small, ranging from 1Mb to 2.7Mb. |
|
HI, I am getting similar error. What's the solution for this? I can not share data as these are real patient samples. I will greatly appreciate your help. Thanks in advance! |
|
My fork is likely somewhat behind the current though... |
|
My fork is likely somewhat behind the current though... |
Hi,
I have been trying to use lumpyexpress on a set of 90 haploid genomes from honey bee drones. These genomes were aligned with BWA-MEM and did include the -M flag. However, although 80 of these samples ran with no issues, 10 of these encountered a segmentation fault error that lead to a core dump. The samples in question do not associate by population and alignments were done in separate parallel batches, so they also do not correlate with possible processing pipeline errors.
The analysis does produce readable vcf files but these are corrupted with a break around the second set of scaffolds (Group10.*). The error was consistent across these 10 samples generating similar corrupted vcf files.
Any help resolving this issue would be greatly appreciated.
Example command input from lumpyexpress -v flag as follows:
Sourcing executables from /home/apps/lumpy-sv/lumpy-sv-0.2.13/scripts/lumpyexpress.config ...
Checking for required python modules (/home/apps/python/python-2.7.3/bin/python)...
Warning: The index file is older than the data file: /home/a-m/aavalos/2015_12_hb_aggression_popgen/data/2016_5_11_realign_bam/W197_WHAIPI005553-18_EHB.realigned.bai
Calculating insert distributions...
Library read groups: W197_WHAIPI005553-18_EHB
Library read length: 100
Removed 1890 outliers with isize >= 586
done
0
Running LUMPY...
/home/apps/lumpy-sv/lumpy-sv-0.2.13/bin/lumpy -P$PROB_CURVE -t $ {TEMP_DIR}/${OUTBASE} -msw $MIN_SAMPLE_WEIGHT -tt $TRIM_THRES $EXCLUDE_BED_FMT $LUMPY_DISC_STRING $LUMPY_SPL_STRING > $OUTPUT
-t W197_WHAIPI005553-18_EHB.bam.vcf.g71iro19am1r/W197_WHAIPI005553-18_EHB.bam.vcf
-msw 4
-tt 0
-x /home/a-m/aavalos/2015_12_hb_aggression_popgen/data/ref/numt.bed
-pe bam_file:/home/a-m/aavalos/2015_12_hb_aggression_popgen/data/2016_7_5_discord_split/discordant_reads_bam/filtered_dis/W197_WHAIPI005553-18_EHB.filtered_disc.bam,histo_file:W197_WHAIPI005553-18_EHB.bam.vcf.g71iro19am1r/W197_WHAIPI005553-18_EHB.bam.vcf.sample1.lib1.x4.histo,mean:453.706583919,stdev:78.806904399,read_length:100,min_non_overlap:100,discordant_z:5,back_distance:10,weight:1,id:W197_WHAIPI005553-18_EHB,min_mapping_threshold:20,read_group:W197_WHAIPI005553-18_EHB
-sr bam_file:/home/a-m/aavalos/2015_12_hb_aggression_popgen/data/2016_7_5_discord_split/split_reads_bam/filtered_split/W197_WHAIPI005553-18_EHB.filtered_split.bam,back_distance:10,min_mapping_threshold:20,weight:1,id:W197_WHAIPI005553-18_EHB,min_clip:20
> W197_WHAIPI005553-18_EHB.bam.vcf
496 0
Group1.1 1000000
Group1.10 1000000
Group1.11 1000000
...
GroupUn993 1000000
GroupUn994 1000000
GroupUn995 1000000
GroupUn997 1000000
/home/apps/lumpy-sv/lumpy-sv-0.2.13/scripts/lumpyexpress: line 411: 79691 Segmentation fault (core dumped) $LUMPY
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