jellyfish error

[hdashnow]

Hi,

I'm keen to try RUFUS. Just having a bit of trouble getting started.

When running runRufus I'm getting errors like this: /usr/bin/ld: cannot open output file /usr/local/installed/rufus/0.8.2/src/externals/jellyfish-2.2.5/bin/.libs/9641-lt-jellyfish: Permission denied

Where the number varies e.g.: 9641-lt-jellyfish 9639-lt-jellyfish

It does produce two .generator files (for the sample and control), then it hangs and doesn't do anything further (i.e. it's still running but not using any resources, I've tried letting it run overnight just in case).

It seems like it's trying to write to the install directory /usr/local/installed/rufus/0.8.2/src/externals/jellyfish-2.2.5/bin/.libs/ which I don't have write permissions for (it's installed centrally on our cluster). So, if that's the problem, is there a way to tell it to write temporary files to a given location?

I'm attaching the full output of the program here: rufus_err.txt

RUFUS versions tested v0.8.2 and master commit ab2f3eb (attached error is from the ab2f3eb version) Running on centos-release-6-7

[hdashnow]

Sorry, this issue might be premature. IT just tells me they don't think they installed it correctly. I'll close this for now and do some more tests.

[WilliamRichards2017]

Hello Harriet! Thank you so much for the interest and feedback. It appears the release tarball is not currently up to date with the master branch. Thank you for bringing this to our attention! We plan on putting out an updated release that should build without issues in the next day or two. We are also testing building this project on various linux environments to ensure a smooth install process. I will let you know when the new release is put out, and this should hopefully fix any install issues that you are having. Please let us know if you have any further trouble running the tool, and we are happy to help you every step of the way and fix any unknown issues the project may have. Sorry for the inconvenience, and thank you for your patience!

[WilliamRichards2017]

We have now put out a new release that should build more reliably, as well as provided some better documentation on how to get RUFUS to build on ubuntu. Give the new release a try, and let us know whether or not you have any more issues getting RUFUS to build!

[hdashnow]

Hi @WilliamRichards2017. Just to help pin down my problem: do you have a feel for how much memory RUFUS requires? For example for runTest.sh.

[WilliamRichards2017]

RUFUS uses a k-mer counting program called jellyfish. Jellyfish is provided with the amount of memory to use, and by default is large enough for all full genome sample to be counted. This is around 4.9 GB. For runTest, you can provide jellyfish with a much smaller amount of memory. To do this currently, two scripts that call jellyfish must be altered.

In cloud/RunJellyForRufus, line 28 should be changed from

/usr/bin/time -v $JELLYFISH count --disk -m $K -L $L -s 1G -t $T -o $GEN.Jhash -C $GEN.fq

to

/usr/bin/time -v $JELLYFISH count -m $K -L $L -s 100 -t $T -o $GEN.Jhash -C $GEN.fq

and in scripts/Overlap.sh, change line 128 from

$JellyFish count -m $HashSize -s 1G -t 20 -o ./$NameStub.overlap.hashcount.fastq.Jhash ./$NameStub.overlap.hashcount.fastq

to

$JellyFish count -m $HashSize -s 100 -t 20 -o ./$NameStub.overlap.hashcount.fastq.Jhash ./$NameStub.overlap.hashcount.fastq

and change scripts/Overlap.sh line 138 from:

$JellyFish count -m $HashSize -s 1G -t 20 -o ./$NameStub.overlap.asembly.hash.fastq.ref.fastq.Jhash ./$NameStub.overlap.asembly.hash.fastq.ref.fastq

to

$JellyFish count -m $HashSize -s 100 -t 20 -o ./$NameStub.overlap.hashcount.fastq.Jhash ./$NameStub.overlap.hashcount.fastq

We will soon add the memory to provide jellyfish with as a command line parameter to avoid future problems. If you run into any issue with threading, change the -t parameter to the number of threads your machine has. Good luck and let us know if this allows you to run runTest.sh!

[hdashnow]

Thanks @WilliamRichards2017

I gave the VM 6GB of memory, which fixed the memory failure message. So we're making progress.

I also limited threads like so: ./../runRufus.sh -s $PWD/../resources/testData/Child.bam -c $PWD/../resources/testData/Mother.bam $PWD/../resources/testData/Father.bam -k 25 -t 2 -m 8 -r $PWD/../resources/references/small_test_human_reference_v37_decoys.fa

I'm getting to the following stage then it appears to hang. But there are a few non-zero exit messages in there earlier, so I'm guessing some earlier stages failed. Any ideas what to try next?

@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
Final reference path being used is /group/bioi1/shared/tools/RUFUS/testRun/../resources/references/small_test_human_reference_v37_decoys.fa
Final bwa reference path being used is /group/bioi1/shared/tools/RUFUS/testRun/../resources/references/small_test_human_reference_v37_decoys.fa
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
proband extension is bam
you provided the proband bam file /group/bioi1/shared/tools/RUFUS/testRun/../resources/testData/Child.bam
parent file name is Mother.bam
parent file extension name is bam
You provided the control bam file /group/bioi1/shared/tools/RUFUS/testRun/../resources/testData/Mother.bam
parent file name is Father.bam
parent file extension name is bam
You provided the control bam file /group/bioi1/shared/tools/RUFUS/testRun/../resources/testData/Father.bam
~~~~~~~~~~~~ printing out paramater values used in script ~~~~~~~~~~~~~~~~
value of ProbandGenerator Child.bam.generator
Value of ParentGenerators:
 Mother.bam.generator
 Father.bam.generator
Value of K is: 25
Value of Threads is: 2
value of ref is: /group/bioi1/shared/tools/RUFUS/testRun/../resources/references/small_test_human_reference_v37_decoys.fa
value of min is: 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Did not provide refHash
$_arg_min is NOT empty
_arg_min is 8
MutantMinCov is 8
Building parentString...
parent is  Mother.bam.generator 
parents string equals  Mother.bam.generator.Jhash
parent is  Father.bam.generator 
parents string equals  Mother.bam.generator.Jhash Father.bam.generator.Jhash
ok lets do this
core file size          (blocks, -c) 0
data seg size           (kbytes, -d) unlimited
scheduling priority             (-e) 0
file size               (blocks, -f) unlimited
pending signals                 (-i) 14995
max locked memory       (kbytes, -l) 64
max memory size         (kbytes, -m) unlimited
open files                      (-n) 1024
pipe size            (512 bytes, -p) 8
POSIX message queues     (bytes, -q) 819200
real-time priority              (-r) 0
stack size              (kbytes, -s) 8192
cpu time               (seconds, -t) unlimited
max user processes              (-u) 4096
virtual memory          (kbytes, -v) 30000000
file locks                      (-x) unlimited
here
ok lets do this
core file size          (blocks, -c) 0
data seg size           (kbytes, -d) unlimited
scheduling priority             (-e) 0
file size               (blocks, -f) unlimited
pending signals                 (-i) 14995
max locked memory       (kbytes, -l) 64
max memory size         (kbytes, -m) unlimited
open files                      (-n) 1024
pipe size            (512 bytes, -p) 8
POSIX message queues     (bytes, -q) 819200
real-time priority              (-r) 0
stack size              (kbytes, -s) 8192
cpu time               (seconds, -t) unlimited
max user processes              (-u) 4096
virtual memory          (kbytes, -v) 30000000
file locks                      (-x) unlimited
here
ok lets do this
core file size          (blocks, -c) 0
data seg size           (kbytes, -d) unlimited
scheduling priority             (-e) 0
file size               (blocks, -f) unlimited
pending signals                 (-i) 14995
max locked memory       (kbytes, -l) 64
max memory size         (kbytes, -m) unlimited
open files                      (-n) 1024
pipe size            (512 bytes, -p) 8
POSIX message queues     (bytes, -q) 819200
real-time priority              (-r) 0
stack size              (kbytes, -s) 8192
cpu time               (seconds, -t) unlimited
max user processes              (-u) 4096
virtual memory          (kbytes, -v) 30000000
file locks                      (-x) unlimited
here
Command terminated by signal 9
    Command being timed: "/group/bioi1/shared/tools/RUFUS/src/externals/jellyfish-2.2.5/bin/jellyfish count --disk -m 25 -L 2 -s 1G -t 0 -o Father.bam.generator.Jhash -C Father.bam.generator.fq"
    User time (seconds): 0.08
    System time (seconds): 1.36
    Percent of CPU this job got: 35%
    Elapsed (wall clock) time (h:mm:ss or m:ss): 0:04.11
    Average shared text size (kbytes): 0
    Average unshared data size (kbytes): 0
    Average stack size (kbytes): 0
    Average total size (kbytes): 0
    Maximum resident set size (kbytes): 2005424
    Average resident set size (kbytes): 0
    Major (requiring I/O) page faults: 3
    Minor (reclaiming a frame) page faults: 306574
    Voluntary context switches: 2000
    Involuntary context switches: 135
    Swaps: 0
    File system inputs: 1776
    File system outputs: 0
    Socket messages sent: 0
    Socket messages received: 0
    Signals delivered: 0
    Page size (bytes): 4096
    Exit status: 0
Failed to open input file 'Father.bam.generator.Jhash'
Command exited with non-zero status 1
    Command being timed: "/group/bioi1/shared/tools/RUFUS/src/externals/jellyfish-2.2.5/bin/jellyfish histo -f -o Father.bam.generator.Jhash.histo Father.bam.generator.Jhash"
    User time (seconds): 0.00
    System time (seconds): 0.00
    Percent of CPU this job got: 9%
    Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.01
    Average shared text size (kbytes): 0
    Average unshared data size (kbytes): 0
    Average stack size (kbytes): 0
    Average total size (kbytes): 0
    Maximum resident set size (kbytes): 1464
    Average resident set size (kbytes): 0
    Major (requiring I/O) page faults: 1
    Minor (reclaiming a frame) page faults: 420
    Voluntary context switches: 5
    Involuntary context switches: 1
    Swaps: 0
    File system inputs: 1512
    File system outputs: 0
    Socket messages sent: 0
    Socket messages received: 0
    Signals delivered: 0
    Page size (bytes): 4096
    Exit status: 1
Command terminated by signal 9
    Command being timed: "/group/bioi1/shared/tools/RUFUS/src/externals/jellyfish-2.2.5/bin/jellyfish count --disk -m 25 -L 2 -s 1G -t 0 -o Mother.bam.generator.Jhash -C Mother.bam.generator.fq"
    User time (seconds): 0.13
    System time (seconds): 2.14
    Percent of CPU this job got: 41%
    Elapsed (wall clock) time (h:mm:ss or m:ss): 0:05.53
    Average shared text size (kbytes): 0
    Average unshared data size (kbytes): 0
    Average stack size (kbytes): 0
    Average total size (kbytes): 0
    Maximum resident set size (kbytes): 3317028
    Average resident set size (kbytes): 0
    Major (requiring I/O) page faults: 19
    Minor (reclaiming a frame) page faults: 514476
    Voluntary context switches: 2433
    Involuntary context switches: 204
    Swaps: 0
    File system inputs: 10112
    File system outputs: 0
    Socket messages sent: 0
    Socket messages received: 0
    Signals delivered: 0
    Page size (bytes): 4096
    Exit status: 0
Failed to open input file 'Mother.bam.generator.Jhash'
Command exited with non-zero status 1
    Command being timed: "/group/bioi1/shared/tools/RUFUS/src/externals/jellyfish-2.2.5/bin/jellyfish histo -f -o Mother.bam.generator.Jhash.histo Mother.bam.generator.Jhash"
    User time (seconds): 0.00
    System time (seconds): 0.00
    Percent of CPU this job got: 2%
    Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.13
    Average shared text size (kbytes): 0
    Average unshared data size (kbytes): 0
    Average stack size (kbytes): 0
    Average total size (kbytes): 0
    Maximum resident set size (kbytes): 1460
    Average resident set size (kbytes): 0
    Major (requiring I/O) page faults: 4
    Minor (reclaiming a frame) page faults: 417
    Voluntary context switches: 12
    Involuntary context switches: 0
    Swaps: 0
    File system inputs: 12032
    File system outputs: 0
    Socket messages sent: 0
    Socket messages received: 0
    Signals delivered: 0
    Page size (bytes): 4096
    Exit status: 1
    Command being timed: "/group/bioi1/shared/tools/RUFUS/src/externals/jellyfish-2.2.5/bin/jellyfish count --disk -m 25 -L 2 -s 1G -t 0 -o Child.bam.generator.Jhash -C Child.bam.generator.fq"
    User time (seconds): 0.15
    System time (seconds): 2.80
    Percent of CPU this job got: 48%
    Elapsed (wall clock) time (h:mm:ss or m:ss): 0:06.07
    Average shared text size (kbytes): 0
    Average unshared data size (kbytes): 0
    Average stack size (kbytes): 0
    Average total size (kbytes): 0
    Maximum resident set size (kbytes): 3949400
    Average resident set size (kbytes): 0
    Major (requiring I/O) page faults: 105
    Minor (reclaiming a frame) page faults: 536436
    Voluntary context switches: 2839
    Involuntary context switches: 295
    Swaps: 0
    File system inputs: 9568
    File system outputs: 8
    Socket messages sent: 0
    Socket messages received: 0
    Signals delivered: 0
    Page size (bytes): 4096
    Exit status: 0
    Command being timed: "/group/bioi1/shared/tools/RUFUS/src/externals/jellyfish-2.2.5/bin/jellyfish histo -f -o Child.bam.generator.Jhash.histo Child.bam.generator.Jhash"
    User time (seconds): 0.00
    System time (seconds): 0.00
    Percent of CPU this job got: 8%
    Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.03
    Average shared text size (kbytes): 0
    Average unshared data size (kbytes): 0
    Average stack size (kbytes): 0
    Average total size (kbytes): 0
    Maximum resident set size (kbytes): 1700
    Average resident set size (kbytes): 0
    Major (requiring I/O) page faults: 0
    Minor (reclaiming a frame) page faults: 479
    Voluntary context switches: 8
    Involuntary context switches: 0
    Swaps: 0
    File system inputs: 0
    File system outputs: 136
    Socket messages sent: 0
    Socket messages received: 0
    Signals delivered: 0
    Page size (bytes): 4096
    Exit status: 0
    Command being timed: "bash /group/bioi1/shared/tools/RUFUS/cloud/RunJellyForRUFUS Child.bam.generator 25 0 2"
    User time (seconds): 0.17
    System time (seconds): 2.80
    Percent of CPU this job got: 47%
    Elapsed (wall clock) time (h:mm:ss or m:ss): 0:06.22
    Average shared text size (kbytes): 0
    Average unshared data size (kbytes): 0
    Average stack size (kbytes): 0
    Average total size (kbytes): 0
    Maximum resident set size (kbytes): 3949400
    Average resident set size (kbytes): 0
    Major (requiring I/O) page faults: 135
    Minor (reclaiming a frame) page faults: 540805
    Voluntary context switches: 2935
    Involuntary context switches: 300
    Swaps: 0
    File system inputs: 15568
    File system outputs: 152
    Socket messages sent: 0
    Socket messages received: 0
    Signals delivered: 0
    Page size (bytes): 4096
    Exit status: 0

For reference, I'm now using CentOS-7. A fresh VM with the following installed:

Python 2.7.5

sudo yum install cmake
sudo yum install gcc
sudo yum install gcc-c++
sudo yum install zlib
sudo yum install bc
sudo yum install bzip2-libs 
sudo yum install ncurses-devel
sudo yum install bzip2-devel
sudo yum install xz-devel
sudo yum install time```

[WilliamRichards2017]

There are some calculations that require the assumption that you are using at least three threads. runRUFUS must be provided with a minimum of 3 threads. This is because in RunJellyForRUFUS, each bam file is given 1/3 of the threads passed to runRUFUS. If your machine has only two cores, this is no issue, Jellyfish will run on two bam files first, then will run on the third. We will fix this in the source code so any number of threads will work, but I would provided runRUFUS with 3 threads for the time being. This explains why the jellyfish count commands all have a -t 0 when you provide two threads.

Let us know if this fixes your issue. Thank you for all your help, interest, and patience!

[hdashnow]

Currently running with 3 threads on a machine with 6 GB memory. 24 hours so far. Is that to be expected? Not all previous commands completed with a zero exit status, so I have suspicions that all is not quite fine. Will let you know when (if?) it finishes.

[hdashnow]

Okay, so I let it run for 3 days (well, about 70 hours). The jellyfish program is still running, but nothing has been written to file since the first day, so I'm guessing it's stalled. Here's the command and output. Can you see anything to suggest what's going wrong?

$ cat runTest.sh 
./../runRufus.sh -s $PWD/../resources/testData/Child.bam -c $PWD/../resources/testData/Mother.bam $PWD/../resources/testData/Father.bam -k 25 -t 3 -m 8 -r $PWD/../resources/references/small_test_human_reference_v37_decoys.fa
$ bash runTest.sh 
arg ref without fa is /group/bioi1/shared/tools/RUFUS/testRun/../resources/references/small_test_human_reference_v37_decoys
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
Final reference path being used is /group/bioi1/shared/tools/RUFUS/testRun/../resources/references/small_test_human_reference_v37_decoys.fa
Final bwa reference path being used is /group/bioi1/shared/tools/RUFUS/testRun/../resources/references/small_test_human_reference_v37_decoys.fa
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
proband extension is bam
you provided the proband bam file /group/bioi1/shared/tools/RUFUS/testRun/../resources/testData/Child.bam
parent file name is Mother.bam
parent file extension name is bam
You provided the control bam file /group/bioi1/shared/tools/RUFUS/testRun/../resources/testData/Mother.bam
parent file name is Father.bam
parent file extension name is bam
You provided the control bam file /group/bioi1/shared/tools/RUFUS/testRun/../resources/testData/Father.bam
~~~~~~~~~~~~ printing out paramater values used in script ~~~~~~~~~~~~~~~~
value of ProbandGenerator Child.bam.generator
Value of ParentGenerators:
 Mother.bam.generator
 Father.bam.generator
Value of K is: 25
Value of Threads is: 3
value of ref is: /group/bioi1/shared/tools/RUFUS/testRun/../resources/references/small_test_human_reference_v37_decoys.fa
value of min is: 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Did not provide refHash
$_arg_min is NOT empty
_arg_min is 8
MutantMinCov is 8
Building parentString...
parent is  Mother.bam.generator 
parents string equals  Mother.bam.generator.Jhash
parent is  Father.bam.generator 
parents string equals  Mother.bam.generator.Jhash Father.bam.generator.Jhash
ok lets do this
core file size          (blocks, -c) 0
data seg size           (kbytes, -d) unlimited
scheduling priority             (-e) 0
file size               (blocks, -f) unlimited
pending signals                 (-i) 14995
max locked memory       (kbytes, -l) 64
max memory size         (kbytes, -m) unlimited
open files                      (-n) 1024
pipe size            (512 bytes, -p) 8
POSIX message queues     (bytes, -q) 819200
real-time priority              (-r) 0
stack size              (kbytes, -s) 8192
cpu time               (seconds, -t) unlimited
max user processes              (-u) 4096
virtual memory          (kbytes, -v) 30000000
file locks                      (-x) unlimited
here
ok lets do this
core file size          (blocks, -c) 0
data seg size           (kbytes, -d) unlimited
scheduling priority             (-e) 0
file size               (blocks, -f) unlimited
pending signals                 (-i) 14995
max locked memory       (kbytes, -l) 64
max memory size         (kbytes, -m) unlimited
open files                      (-n) 1024
pipe size            (512 bytes, -p) 8
POSIX message queues     (bytes, -q) 819200
real-time priority              (-r) 0
stack size              (kbytes, -s) 8192
cpu time               (seconds, -t) unlimited
max user processes              (-u) 4096
virtual memory          (kbytes, -v) 30000000
file locks                      (-x) unlimited
here
ok lets do this
core file size          (blocks, -c) 0
data seg size           (kbytes, -d) unlimited
scheduling priority             (-e) 0
file size               (blocks, -f) unlimited
pending signals                 (-i) 14995
max locked memory       (kbytes, -l) 64
max memory size         (kbytes, -m) unlimited
open files                      (-n) 1024
pipe size            (512 bytes, -p) 8
POSIX message queues     (bytes, -q) 819200
real-time priority              (-r) 0
stack size              (kbytes, -s) 8192
cpu time               (seconds, -t) unlimited
max user processes              (-u) 4096
virtual memory          (kbytes, -v) 30000000
file locks                      (-x) unlimited
here
Command terminated by signal 9
    Command being timed: "/group/bioi1/shared/tools/RUFUS/src/externals/jellyfish-2.2.5/bin/jellyfish count --disk -m 25 -L 2 -s 1G -t 1 -o Father.bam.generator.Jhash -C Father.bam.generator.fq"
    User time (seconds): 0.08
    System time (seconds): 1.17
    Percent of CPU this job got: 33%
    Elapsed (wall clock) time (h:mm:ss or m:ss): 0:03.71
    Average shared text size (kbytes): 0
    Average unshared data size (kbytes): 0
    Average stack size (kbytes): 0
    Average total size (kbytes): 0
    Maximum resident set size (kbytes): 1940212
    Average resident set size (kbytes): 0
    Major (requiring I/O) page faults: 5
    Minor (reclaiming a frame) page faults: 334253
    Voluntary context switches: 1746
    Involuntary context switches: 110
    Swaps: 0
    File system inputs: 440
    File system outputs: 0
    Socket messages sent: 0
    Socket messages received: 0
    Signals delivered: 0
    Page size (bytes): 4096
    Exit status: 0
Command terminated by signal 9
    Command being timed: "/group/bioi1/shared/tools/RUFUS/src/externals/jellyfish-2.2.5/bin/jellyfish count --disk -m 25 -L 2 -s 1G -t 1 -o Mother.bam.generator.Jhash -C Mother.bam.generator.fq"
    User time (seconds): 0.12
    System time (seconds): 1.73
    Percent of CPU this job got: 39%
    Elapsed (wall clock) time (h:mm:ss or m:ss): 0:04.71
    Average shared text size (kbytes): 0
    Average unshared data size (kbytes): 0
    Average stack size (kbytes): 0
    Average total size (kbytes): 0
    Maximum resident set size (kbytes): 2939160
    Average resident set size (kbytes): 0
    Major (requiring I/O) page faults: 5
    Minor (reclaiming a frame) page faults: 513800
    Voluntary context switches: 2425
    Involuntary context switches: 177
    Swaps: 0
    File system inputs: 512
    File system outputs: 0
    Socket messages sent: 0
    Socket messages received: 0
    Signals delivered: 0
    Page size (bytes): 4096
    Exit status: 0
Command terminated by signal 9
    Command being timed: "/group/bioi1/shared/tools/RUFUS/src/externals/jellyfish-2.2.5/bin/jellyfish count --disk -m 25 -L 2 -s 1G -t 1 -o Child.bam.generator.Jhash -C Child.bam.generator.fq"
    User time (seconds): 0.12
    System time (seconds): 1.73
    Percent of CPU this job got: 39%
    Elapsed (wall clock) time (h:mm:ss or m:ss): 0:04.71
    Average shared text size (kbytes): 0
    Average unshared data size (kbytes): 0
    Average stack size (kbytes): 0
    Average total size (kbytes): 0
    Maximum resident set size (kbytes): 2670296
    Average resident set size (kbytes): 0
    Major (requiring I/O) page faults: 8
    Minor (reclaiming a frame) page faults: 512055
    Voluntary context switches: 2072
    Involuntary context switches: 177
    Swaps: 0
    File system inputs: 376
    File system outputs: 0
    Socket messages sent: 0
    Socket messages received: 0
    Signals delivered: 0
    Page size (bytes): 4096
    Exit status: 0
Failed to open input file 'Child.bam.generator.Jhash'
Command exited with non-zero status 1
    Command being timed: "/group/bioi1/shared/tools/RUFUS/src/externals/jellyfish-2.2.5/bin/jellyfish histo -f -o Child.bam.generator.Jhash.histo Child.bam.generator.Jhash"
    User time (seconds): 0.00
    System time (seconds): 0.00
    Percent of CPU this job got: 14%
    Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.00
    Average shared text size (kbytes): 0
    Average unshared data size (kbytes): 0
    Average stack size (kbytes): 0
    Average total size (kbytes): 0
    Maximum resident set size (kbytes): 1460
    Average resident set size (kbytes): 0
    Major (requiring I/O) page faults: 0
    Minor (reclaiming a frame) page faults: 419
    Voluntary context switches: 7
    Involuntary context switches: 0
    Swaps: 0
    File system inputs: 3840
    File system outputs: 0
    Socket messages sent: 0
    Socket messages received: 0
    Signals delivered: 0
    Page size (bytes): 4096
    Exit status: 1
Failed to open input file 'Father.bam.generator.Jhash'
Command exited with non-zero status 1
    Command being timed: "/group/bioi1/shared/tools/RUFUS/src/externals/jellyfish-2.2.5/bin/jellyfish histo -f -o Father.bam.generator.Jhash.histo Father.bam.generator.Jhash"
    User time (seconds): 0.00
    System time (seconds): 0.00
    Percent of CPU this job got: 2%
    Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.14
    Average shared text size (kbytes): 0
    Average unshared data size (kbytes): 0
    Average stack size (kbytes): 0
    Average total size (kbytes): 0
    Maximum resident set size (kbytes): 1464
    Average resident set size (kbytes): 0
    Major (requiring I/O) page faults: 5
    Minor (reclaiming a frame) page faults: 415
    Voluntary context switches: 19
    Involuntary context switches: 5
    Swaps: 0
    File system inputs: 11384
    File system outputs: 0
    Socket messages sent: 0
    Socket messages received: 0
    Signals delivered: 0
    Page size (bytes): 4096
    Exit status: 1
Failed to open input file 'Mother.bam.generator.Jhash'
Command exited with non-zero status 1
    Command being timed: "/group/bioi1/shared/tools/RUFUS/src/externals/jellyfish-2.2.5/bin/jellyfish histo -f -o Mother.bam.generator.Jhash.histo Mother.bam.generator.Jhash"
    User time (seconds): 0.00
    System time (seconds): 0.00
    Percent of CPU this job got: 12%
    Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.00
    Average shared text size (kbytes): 0
    Average unshared data size (kbytes): 0
    Average stack size (kbytes): 0
    Average total size (kbytes): 0
    Maximum resident set size (kbytes): 1464
    Average resident set size (kbytes): 0
    Major (requiring I/O) page faults: 0
    Minor (reclaiming a frame) page faults: 420
    Voluntary context switches: 5
    Involuntary context switches: 0
    Swaps: 0
    File system inputs: 0
    File system outputs: 0
    Socket messages sent: 0
    Socket messages received: 0
    Signals delivered: 0
    Page size (bytes): 4096
    Exit status: 1

[WilliamRichards2017]

The runTest should complete in about a minute, so something is definitely wrong. It looks like the .Jhash files containing the k-mer counts was never produced, so my guess is RUFUS was unable to build Jellyfish. Can you try removing the bin directory, then rerun ./configure as well as bin/cmake .. && bin/make and show me the output produced by the build commands?

[hdashnow]

I wonder if you could generate a binary and attach it to your release?

I did a git pull, then re-installed. Installation output and testRun.sh output also at the bottom (with new errors):

$ ./configure.sh
update script paths
Can't open scripts/RunJellyForRUFUS: No such file or directory.
Can't open scripts/RunRUFUS.sarcoma.sh: No such file or directory.
--2018-09-18 12:33:28--  https://github.com/samtools/samtools/releases/download/1.9/samtools-1.9.tar.bz2
Resolving github.com (github.com)... 192.30.255.112, 192.30.255.113
Connecting to github.com (github.com)|192.30.255.112|:443... connected.
HTTP request sent, awaiting response... 302 Found
Location: https://github-production-release-asset-2e65be.s3.amazonaws.com/3666841/fe586164-8a73-11e8-84ad-bb90bbd3b7c0?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20180918%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20180918T023329Z&X-Amz-Expires=300&X-Amz-Signature=3db88ad619fe5171f1e2ad9020655f85ccb46f50ab37eaedfc4e21eb11013799&X-Amz-SignedHeaders=host&actor_id=0&response-content-disposition=attachment%3B%20filename%3Dsamtools-1.9.tar.bz2&response-content-type=application%2Foctet-stream [following]
--2018-09-18 12:33:29--  https://github-production-release-asset-2e65be.s3.amazonaws.com/3666841/fe586164-8a73-11e8-84ad-bb90bbd3b7c0?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20180918%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20180918T023329Z&X-Amz-Expires=300&X-Amz-Signature=3db88ad619fe5171f1e2ad9020655f85ccb46f50ab37eaedfc4e21eb11013799&X-Amz-SignedHeaders=host&actor_id=0&response-content-disposition=attachment%3B%20filename%3Dsamtools-1.9.tar.bz2&response-content-type=application%2Foctet-stream
Resolving github-production-release-asset-2e65be.s3.amazonaws.com (github-production-release-asset-2e65be.s3.amazonaws.com)... 54.231.98.160
Connecting to github-production-release-asset-2e65be.s3.amazonaws.com (github-production-release-asset-2e65be.s3.amazonaws.com)|54.231.98.160|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 4440405 (4.2M) [application/octet-stream]
Saving to: ‘samtools-1.9.tar.bz2’

100%[===============================================================>] 4,440,405    750KB/s   in 14s    

2018-09-18 12:33:44 (318 KB/s) - ‘samtools-1.9.tar.bz2’ saved [4440405/4440405]

./configure.sh: line 32: ./configure: No such file or directory
make: *** No targets specified and no makefile found.  Stop.
make: *** No rule to make target `install'.  Stop.
current pwd is /group/bioi1/shared/tools/RUFUS/src/externals
jellyfish already installed: skipping
jellyfish-2.2.5/
jellyfish-2.2.5/tests/
jellyfish-2.2.5/tests/large_key.sh
jellyfish-2.2.5/tests/parallel_hashing.sh
jellyfish-2.2.5/tests/generate_sequence.sh
jellyfish-2.2.5/tests/subset_hashing.sh
jellyfish-2.2.5/tests/merge.sh
jellyfish-2.2.5/tests/bloom_counter.sh
jellyfish-2.2.5/tests/swig_perl.sh
jellyfish-2.2.5/tests/big.sh
jellyfish-2.2.5/tests/multi_file.sh
jellyfish-2.2.5/tests/swig_python.sh
jellyfish-2.2.5/tests/compat.sh.in
jellyfish-2.2.5/tests/bloom_filter.sh
jellyfish-2.2.5/tests/swig_ruby.sh
jellyfish-2.2.5/include/
jellyfish-2.2.5/include/jellyfish/
jellyfish-2.2.5/include/jellyfish/atomic_bits_array.hpp
jellyfish-2.2.5/include/jellyfish/allocators_mmap.hpp
jellyfish-2.2.5/include/jellyfish/offsets_key_value.hpp
jellyfish-2.2.5/include/jellyfish/time.hpp
jellyfish-2.2.5/include/jellyfish/mer_heap.hpp
jellyfish-2.2.5/include/jellyfish/large_hash_iterator.hpp
jellyfish-2.2.5/include/jellyfish/circular_buffer.hpp
jellyfish-2.2.5/include/jellyfish/hash_counter.hpp
jellyfish-2.2.5/include/jellyfish/file_header.hpp
jellyfish-2.2.5/include/jellyfish/rectangular_binary_matrix.hpp
jellyfish-2.2.5/include/jellyfish/dumper.hpp
jellyfish-2.2.5/include/jellyfish/misc.hpp
jellyfish-2.2.5/include/jellyfish/err.hpp
jellyfish-2.2.5/include/jellyfish/stdio_filebuf.hpp
jellyfish-2.2.5/include/jellyfish/simple_circular_buffer.hpp
jellyfish-2.2.5/include/jellyfish/token_ring.hpp
jellyfish-2.2.5/include/jellyfish/bloom_counter2.hpp
jellyfish-2.2.5/include/jellyfish/large_hash_array.hpp
jellyfish-2.2.5/include/jellyfish/mer_overlap_sequence_parser.hpp
jellyfish-2.2.5/include/jellyfish/atomic_field.hpp
jellyfish-2.2.5/include/jellyfish/binary_dumper.hpp
jellyfish-2.2.5/include/jellyfish/text_dumper.hpp
jellyfish-2.2.5/include/jellyfish/generic_file_header.hpp
jellyfish-2.2.5/include/jellyfish/atomic_gcc.hpp
jellyfish-2.2.5/include/jellyfish/whole_sequence_parser.hpp
jellyfish-2.2.5/include/jellyfish/divisor.hpp
jellyfish-2.2.5/include/jellyfish/bloom_common.hpp
jellyfish-2.2.5/include/jellyfish/storage.hpp
jellyfish-2.2.5/include/jellyfish/mer_qual_iterator.hpp
jellyfish-2.2.5/include/jellyfish/mapped_file.hpp
jellyfish-2.2.5/include/jellyfish/locks_pthread.hpp
jellyfish-2.2.5/include/jellyfish/sorted_dumper.hpp
jellyfish-2.2.5/include/jellyfish/cooperative_pool.hpp
jellyfish-2.2.5/include/jellyfish/json.h
jellyfish-2.2.5/include/jellyfish/backtrace.hpp
jellyfish-2.2.5/include/jellyfish/generator_manager.hpp
jellyfish-2.2.5/include/jellyfish/mer_iterator.hpp
jellyfish-2.2.5/include/jellyfish/thread_exec.hpp
jellyfish-2.2.5/include/jellyfish/bloom_filter.hpp
jellyfish-2.2.5/include/jellyfish/mer_dna.hpp
jellyfish-2.2.5/include/jellyfish/jellyfish.hpp
jellyfish-2.2.5/include/jellyfish/compare_and_swap.hpp
jellyfish-2.2.5/include/jellyfish/stream_iterator.hpp
jellyfish-2.2.5/include/jellyfish/cpp_array.hpp
jellyfish-2.2.5/include/jellyfish/cooperative_pool2.hpp
jellyfish-2.2.5/include/jellyfish/stream_manager.hpp
jellyfish-2.2.5/include/jellyfish/mer_dna_bloom_counter.hpp
jellyfish-2.2.5/include/jellyfish/int128.hpp
jellyfish-2.2.5/sub_commands/
jellyfish-2.2.5/sub_commands/info_main_cmdline.hpp
jellyfish-2.2.5/sub_commands/merge_main_cmdline.hpp
jellyfish-2.2.5/sub_commands/mem_main_cmdline.hpp
jellyfish-2.2.5/sub_commands/count_main_cmdline.hpp
jellyfish-2.2.5/sub_commands/cite_main_cmdline.hpp
jellyfish-2.2.5/sub_commands/info_main.cc
jellyfish-2.2.5/sub_commands/histo_main_cmdline.hpp
jellyfish-2.2.5/sub_commands/count_main.cc
jellyfish-2.2.5/sub_commands/dump_main.cc
jellyfish-2.2.5/sub_commands/stats_main.cc
jellyfish-2.2.5/sub_commands/merge_main.cc
jellyfish-2.2.5/sub_commands/jellyfish.cc
jellyfish-2.2.5/sub_commands/query_main.cc
jellyfish-2.2.5/sub_commands/histo_main.cc
jellyfish-2.2.5/sub_commands/stats_main_cmdline.hpp
jellyfish-2.2.5/sub_commands/query_main_cmdline.hpp
jellyfish-2.2.5/sub_commands/dump_main_cmdline.hpp
jellyfish-2.2.5/sub_commands/mem_main.cc
jellyfish-2.2.5/sub_commands/bc_main_cmdline.hpp
jellyfish-2.2.5/sub_commands/bc_main.cc
jellyfish-2.2.5/sub_commands/cite_main.cc
jellyfish-2.2.5/config.sub
jellyfish-2.2.5/m4/
jellyfish-2.2.5/m4/m4-ax_pkg_swig.m4
jellyfish-2.2.5/m4/m4-ax_perl_ext.m4
jellyfish-2.2.5/m4/m4-ax_ruby_ext.m4
jellyfish-2.2.5/m4/m4-ax_python_devel.m4
jellyfish-2.2.5/m4/m4-ax_swig_enable_cxx.m4
jellyfish-2.2.5/m4/lt~obsolete.m4
jellyfish-2.2.5/m4/ltversion.m4
jellyfish-2.2.5/m4/ltsugar.m4
jellyfish-2.2.5/m4/ltoptions.m4
jellyfish-2.2.5/m4/libtool.m4
jellyfish-2.2.5/README
jellyfish-2.2.5/gtest.mk
jellyfish-2.2.5/jellyfish/
jellyfish-2.2.5/jellyfish/merge_files.hpp
jellyfish-2.2.5/jellyfish/generate_sequence.cc
jellyfish-2.2.5/jellyfish/randomc.h
jellyfish-2.2.5/jellyfish/mersenne.cpp
jellyfish-2.2.5/jellyfish/generate_sequence_cmdline.hpp
jellyfish-2.2.5/jellyfish/fstream_default.hpp
jellyfish-2.2.5/jellyfish/dbg.hpp
jellyfish-2.2.5/jellyfish/dbg.cc
jellyfish-2.2.5/jellyfish/merge_files.cc
jellyfish-2.2.5/jellyfish/backtrace.cc
jellyfish-2.2.5/depcomp
jellyfish-2.2.5/install-sh
jellyfish-2.2.5/Makefile.in
jellyfish-2.2.5/configure.ac
jellyfish-2.2.5/config.h.in
jellyfish-2.2.5/swig/
jellyfish-2.2.5/swig/hash_set.i
jellyfish-2.2.5/swig/mer_file.i
jellyfish-2.2.5/swig/mer_dna.i
jellyfish-2.2.5/swig/python/
jellyfish-2.2.5/swig/python/test_mer_file.py
jellyfish-2.2.5/swig/python/test_hash_counter.py
jellyfish-2.2.5/swig/python/jellyfish.py
jellyfish-2.2.5/swig/python/test_string_mers.py
jellyfish-2.2.5/swig/python/swig_wrap.cpp
jellyfish-2.2.5/swig/hash_counter.i
jellyfish-2.2.5/swig/perl5/
jellyfish-2.2.5/swig/perl5/swig_wrap.cpp
jellyfish-2.2.5/swig/perl5/jellyfish.pm
jellyfish-2.2.5/swig/perl5/t/
jellyfish-2.2.5/swig/perl5/t/test_string_mers.t
jellyfish-2.2.5/swig/perl5/t/test_hash_counter.t
jellyfish-2.2.5/swig/perl5/t/test_mer_file.t
jellyfish-2.2.5/swig/Makefile.am
jellyfish-2.2.5/swig/ruby/
jellyfish-2.2.5/swig/ruby/test_hash_counter.rb
jellyfish-2.2.5/swig/ruby/test_mer_file.rb
jellyfish-2.2.5/swig/ruby/swig_wrap.cpp
jellyfish-2.2.5/swig/ruby/test_string_mers.rb
jellyfish-2.2.5/swig/jellyfish.i
jellyfish-2.2.5/swig/string_mers.i
jellyfish-2.2.5/missing
jellyfish-2.2.5/jellyfish-2.0.pc.in
jellyfish-2.2.5/aclocal.m4
jellyfish-2.2.5/config.guess
jellyfish-2.2.5/Makefile.am
jellyfish-2.2.5/compile
jellyfish-2.2.5/configure
jellyfish-2.2.5/doc/
jellyfish-2.2.5/doc/jellyfish.pdf
jellyfish-2.2.5/doc/jellyfish.man
jellyfish-2.2.5/test-driver
jellyfish-2.2.5/unit_tests/
jellyfish-2.2.5/unit_tests/test_generator_manager.cc
jellyfish-2.2.5/unit_tests/test_stream_iterator.cc
jellyfish-2.2.5/unit_tests/test_stdio_filebuf.cc
jellyfish-2.2.5/unit_tests/test_hash_counter.cc
jellyfish-2.2.5/unit_tests/test_allocators_mmap.cc
jellyfish-2.2.5/unit_tests/test_mer_dna_bloom_counter.cc
jellyfish-2.2.5/unit_tests/test_mer_overlap_sequence_parser.cc
jellyfish-2.2.5/unit_tests/test_whole_sequence_parser.cc
jellyfish-2.2.5/unit_tests/test_simple_circular_buffer.cc
jellyfish-2.2.5/unit_tests/test_atomic_bits_array.cc
jellyfish-2.2.5/unit_tests/test_token_ring.cc
jellyfish-2.2.5/unit_tests/unit_tests.sh
jellyfish-2.2.5/unit_tests/test_mer_iterator.cc
jellyfish-2.2.5/unit_tests/test_mer_heap.cc
jellyfish-2.2.5/unit_tests/test_main_cmdline.hpp
jellyfish-2.2.5/unit_tests/test_text_dumper.cc
jellyfish-2.2.5/unit_tests/test_main.cc
jellyfish-2.2.5/unit_tests/test_rectangular_binary_matrix.cc
jellyfish-2.2.5/unit_tests/test_mapped_file.cc
jellyfish-2.2.5/unit_tests/test_mer_dna.cc
jellyfish-2.2.5/unit_tests/test_offsets_key_value.cc
jellyfish-2.2.5/unit_tests/gtest/
jellyfish-2.2.5/unit_tests/gtest/gtest.h
jellyfish-2.2.5/unit_tests/gtest/src/
jellyfish-2.2.5/unit_tests/gtest/src/gtest-all.cc
jellyfish-2.2.5/unit_tests/gtest/src/gtest_main.cc
jellyfish-2.2.5/unit_tests/test_file_header.cc
jellyfish-2.2.5/unit_tests/test_dumpers.cc
jellyfish-2.2.5/unit_tests/test_int128.cc
jellyfish-2.2.5/unit_tests/test_main.hpp
jellyfish-2.2.5/unit_tests/test_cooperative_pool2.cc
jellyfish-2.2.5/unit_tests/test_misc.cc
jellyfish-2.2.5/unit_tests/test_large_hash_array.cc
jellyfish-2.2.5/LICENSE
jellyfish-2.2.5/ltmain.sh
jellyfish-2.2.5/lib/
jellyfish-2.2.5/lib/int128.cc
jellyfish-2.2.5/lib/misc.cc
jellyfish-2.2.5/lib/time.cc
jellyfish-2.2.5/lib/generator_manager.cc
jellyfish-2.2.5/lib/jsoncpp.cpp
jellyfish-2.2.5/lib/allocators_mmap.cc
jellyfish-2.2.5/lib/rectangular_binary_matrix.cc
jellyfish-2.2.5/lib/storage.cc
jellyfish-2.2.5/lib/thread_exec.cc
jellyfish-2.2.5/lib/mer_dna.cc
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /usr/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking whether make supports nested variables... (cached) yes
checking how to print strings... printf
checking for style of include used by make... GNU
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking dependency style of gcc... gcc3
checking for a sed that does not truncate output... /usr/bin/sed
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for fgrep... /usr/bin/grep -F
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking how to convert x86_64-unknown-linux-gnu file names to x86_64-unknown-linux-gnu format... func_convert_file_noop
checking how to convert x86_64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for ar... ar
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for sysroot... no
checking for mt... no
checking if : is a manifest tool... no
checking how to run the C preprocessor... gcc -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for dlfcn.h... yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... no
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking dependency style of g++... gcc3
checking how to run the C++ preprocessor... g++ -E
checking for ld used by g++... /usr/bin/ld -m elf_x86_64
checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes
checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking for g++ option to produce PIC... -fPIC -DPIC
checking if g++ PIC flag -fPIC -DPIC works... yes
checking if g++ static flag -static works... no
checking if g++ supports -c -o file.o... yes
checking if g++ supports -c -o file.o... (cached) yes
checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for md5sum... md5sum
checking for yaggo... false
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for __int128... yes
checking for std::numeric_limits<__int128>... no
checking for _NSGetExecutablePath... no
checking for execinfo.h... yes
checking for ext/stdio_filebuf.h... yes
checking for siginfo_t.si_int... yes
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating tests/compat.sh
config.status: creating jellyfish-2.0.pc
config.status: creating config.h
config.status: executing depfiles commands
config.status: executing libtool commands
make  all-am
make[1]: Entering directory `/group/bioi1/shared/tools/RUFUS/cloud/jellyfish-MODIFIED-merge'
  CXX      lib/rectangular_binary_matrix.lo
  CXX      lib/mer_dna.lo
  CXX      lib/storage.lo
  CXX      lib/allocators_mmap.lo
  CXX      lib/misc.lo
  CXX      lib/int128.lo
  CXX      lib/thread_exec.lo
  CXX      lib/jsoncpp.lo
  CXX      lib/time.lo
  CXX      lib/generator_manager.lo
  CXXLD    libjellyfish-2.0.la
  CXX      sub_commands/jellyfish.o
  CXX      sub_commands/count_main.o
  CXX      sub_commands/info_main.o
  CXX      sub_commands/dump_main.o
  CXX      sub_commands/histo_main.o
  CXX      sub_commands/stats_main.o
  CXX      sub_commands/merge_main.o
  CXX      sub_commands/bc_main.o
  CXX      sub_commands/query_main.o
  CXX      sub_commands/cite_main.o
  CXX      sub_commands/mem_main.o
  CXX      jellyfish/merge_files.o
jellyfish/merge_files.cc: In instantiation of ‘void do_merge(jellyfish::cpp_array<file_info>&, std::ostream&, writer_type&, uint64_t, uint64_t) [with reader_type = jellyfish::binary_reader<jellyfish::mer_dna_ns::mer_base_static<long unsigned int, 0>, long unsigned int>; writer_type = jellyfish::binary_writer<jellyfish::mer_dna_ns::mer_base_static<long unsigned int, 0>, long unsigned int>; std::ostream = std::basic_ostream<char>; uint64_t = long unsigned int]’:
jellyfish/merge_files.cc:216:72:   required from here
jellyfish/merge_files.cc:101:10: warning: unused variable ‘unique’ [-Wunused-variable]
     bool unique = false; 
          ^
jellyfish/merge_files.cc:102:9: warning: unused variable ‘ucount’ [-Wunused-variable]
     int ucount = -1;
         ^
jellyfish/merge_files.cc:103:9: warning: unused variable ‘check’ [-Wunused-variable]
     int check = 0;
         ^
jellyfish/merge_files.cc: In instantiation of ‘void do_merge(jellyfish::cpp_array<file_info>&, std::ostream&, writer_type&, uint64_t, uint64_t) [with reader_type = jellyfish::text_reader<jellyfish::mer_dna_ns::mer_base_static<long unsigned int, 0>, long unsigned int>; writer_type = jellyfish::text_writer<jellyfish::mer_dna_ns::mer_base_static<long unsigned int, 0>, long unsigned int>; std::ostream = std::basic_ostream<char>; uint64_t = long unsigned int]’:
jellyfish/merge_files.cc:220:68:   required from here
jellyfish/merge_files.cc:101:10: warning: unused variable ‘unique’ [-Wunused-variable]
     bool unique = false; 
          ^
jellyfish/merge_files.cc:102:9: warning: unused variable ‘ucount’ [-Wunused-variable]
     int ucount = -1;
         ^
jellyfish/merge_files.cc:103:9: warning: unused variable ‘check’ [-Wunused-variable]
     int check = 0;
         ^
  CXXLD    bin/jellyfish
make[1]: Leaving directory `/group/bioi1/shared/tools/RUFUS/cloud/jellyfish-MODIFIED-merge'
make  install-am
make[1]: Entering directory `/group/bioi1/shared/tools/RUFUS/cloud/jellyfish-MODIFIED-merge'
make[2]: Entering directory `/group/bioi1/shared/tools/RUFUS/cloud/jellyfish-MODIFIED-merge'
 /usr/bin/mkdir -p '/group/bioi1/shared/tools/RUFUS/cloud/jellyfish-MODIFIED_merge/lib'
 /bin/sh ./libtool   --mode=install /usr/bin/install -c   libjellyfish-2.0.la '/group/bioi1/shared/tools/RUFUS/cloud/jellyfish-MODIFIED_merge/lib'
libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.so.2.0.0 /group/bioi1/shared/tools/RUFUS/cloud/jellyfish-MODIFIED_merge/lib/libjellyfish-2.0.so.2.0.0
libtool: install: (cd /group/bioi1/shared/tools/RUFUS/cloud/jellyfish-MODIFIED_merge/lib && { ln -s -f libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so.2 || { rm -f libjellyfish-2.0.so.2 && ln -s libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so.2; }; })
libtool: install: (cd /group/bioi1/shared/tools/RUFUS/cloud/jellyfish-MODIFIED_merge/lib && { ln -s -f libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so || { rm -f libjellyfish-2.0.so && ln -s libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so; }; })
libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.lai /group/bioi1/shared/tools/RUFUS/cloud/jellyfish-MODIFIED_merge/lib/libjellyfish-2.0.la
libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.a /group/bioi1/shared/tools/RUFUS/cloud/jellyfish-MODIFIED_merge/lib/libjellyfish-2.0.a
libtool: install: chmod 644 /group/bioi1/shared/tools/RUFUS/cloud/jellyfish-MODIFIED_merge/lib/libjellyfish-2.0.a
libtool: install: ranlib /group/bioi1/shared/tools/RUFUS/cloud/jellyfish-MODIFIED_merge/lib/libjellyfish-2.0.a
libtool: finish: PATH="/group/bioi1/harrietd/src/google-cloud-sdk/bin:/group/bioi1/harrietd/src/bpipe-0.9.9.6/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/harriet.dashnow/bin:/sbin" ldconfig -n /group/bioi1/shared/tools/RUFUS/cloud/jellyfish-MODIFIED_merge/lib
----------------------------------------------------------------------
Libraries have been installed in:
   /group/bioi1/shared/tools/RUFUS/cloud/jellyfish-MODIFIED_merge/lib

If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the `-LLIBDIR'
flag during linking and do at least one of the following:
   - add LIBDIR to the `LD_LIBRARY_PATH' environment variable
     during execution
   - add LIBDIR to the `LD_RUN_PATH' environment variable
     during linking
   - use the `-Wl,-rpath -Wl,LIBDIR' linker flag
   - have your system administrator add LIBDIR to `/etc/ld.so.conf'

See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
----------------------------------------------------------------------
 /usr/bin/mkdir -p '/group/bioi1/shared/tools/RUFUS/cloud/jellyfish-MODIFIED_merge/bin'
  /bin/sh ./libtool   --mode=install /usr/bin/install -c bin/jellyfish '/group/bioi1/shared/tools/RUFUS/cloud/jellyfish-MODIFIED_merge/bin'
libtool: install: /usr/bin/install -c bin/.libs/jellyfish /group/bioi1/shared/tools/RUFUS/cloud/jellyfish-MODIFIED_merge/bin/jellyfish
 /usr/bin/mkdir -p '/group/bioi1/shared/tools/RUFUS/cloud/jellyfish-MODIFIED_merge/include/jellyfish-2.2.5/jellyfish'
 /usr/bin/install -c -m 644 include/jellyfish/allocators_mmap.hpp include/jellyfish/backtrace.hpp include/jellyfish/atomic_gcc.hpp include/jellyfish/large_hash_array.hpp include/jellyfish/err.hpp include/jellyfish/misc.hpp include/jellyfish/offsets_key_value.hpp include/jellyfish/int128.hpp include/jellyfish/rectangular_binary_matrix.hpp include/jellyfish/mer_dna.hpp include/jellyfish/storage.hpp include/jellyfish/simple_circular_buffer.hpp include/jellyfish/circular_buffer.hpp include/jellyfish/atomic_field.hpp include/jellyfish/compare_and_swap.hpp include/jellyfish/divisor.hpp include/jellyfish/large_hash_iterator.hpp include/jellyfish/jellyfish.hpp include/jellyfish/thread_exec.hpp include/jellyfish/stream_iterator.hpp include/jellyfish/mer_overlap_sequence_parser.hpp include/jellyfish/whole_sequence_parser.hpp include/jellyfish/binary_dumper.hpp include/jellyfish/sorted_dumper.hpp include/jellyfish/text_dumper.hpp include/jellyfish/dumper.hpp include/jellyfish/time.hpp include/jellyfish/mer_heap.hpp include/jellyfish/token_ring.hpp include/jellyfish/locks_pthread.hpp include/jellyfish/file_header.hpp include/jellyfish/generic_file_header.hpp include/jellyfish/json.h include/jellyfish/hash_counter.hpp include/jellyfish/mapped_file.hpp include/jellyfish/mer_dna_bloom_counter.hpp include/jellyfish/bloom_common.hpp include/jellyfish/bloom_counter2.hpp include/jellyfish/bloom_filter.hpp include/jellyfish/cooperative_pool.hpp '/group/bioi1/shared/tools/RUFUS/cloud/jellyfish-MODIFIED_merge/include/jellyfish-2.2.5/jellyfish'
 /usr/bin/install -c -m 644 include/jellyfish/cooperative_pool2.hpp include/jellyfish/stream_manager.hpp include/jellyfish/generator_manager.hpp include/jellyfish/cpp_array.hpp include/jellyfish/mer_iterator.hpp include/jellyfish/atomic_bits_array.hpp include/jellyfish/stdio_filebuf.hpp include/jellyfish/mer_qual_iterator.hpp '/group/bioi1/shared/tools/RUFUS/cloud/jellyfish-MODIFIED_merge/include/jellyfish-2.2.5/jellyfish'
 /usr/bin/mkdir -p '/group/bioi1/shared/tools/RUFUS/cloud/jellyfish-MODIFIED_merge/share/man/man1'
 /usr/bin/install -c -m 644 'doc/jellyfish.man' '/group/bioi1/shared/tools/RUFUS/cloud/jellyfish-MODIFIED_merge/share/man/man1/jellyfish.1'
 /usr/bin/mkdir -p '/group/bioi1/shared/tools/RUFUS/cloud/jellyfish-MODIFIED_merge/lib/pkgconfig'
 /usr/bin/install -c -m 644 jellyfish-2.0.pc '/group/bioi1/shared/tools/RUFUS/cloud/jellyfish-MODIFIED_merge/lib/pkgconfig'
make[2]: Leaving directory `/group/bioi1/shared/tools/RUFUS/cloud/jellyfish-MODIFIED-merge'
make[1]: Leaving directory `/group/bioi1/shared/tools/RUFUS/cloud/jellyfish-MODIFIED-merge'
PWD FOR jelly-Modified-merge is /group/bioi1/shared/tools/RUFUS

$ cd bin
$ cmake ..
-- The C compiler identification is GNU 4.8.5
-- The CXX compiler identification is GNU 4.8.5
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Found Git: /usr/bin/git (found version "1.8.3.1") 
TEST: ENV{CPLUS_INCLUDE_PATH}
-- Configuring done
-- Generating done
-- Build files have been written to: /group/bioi1/shared/tools/RUFUS/bin

$ make
Scanning dependencies of target zlib_project
[  1%] Creating directories for 'zlib_project'
[  2%] Performing download step (git clone) for 'zlib_project'
Cloning into 'zlib_project'...
remote: Counting objects: 5059, done.
remote: Compressing objects: 100% (2/2), done.
remote: Total 5059 (delta 0), reused 0 (delta 0), pack-reused 5057
Receiving objects: 100% (5059/5059), 2.60 MiB | 611.00 KiB/s, done.
Resolving deltas: 100% (3564/3564), done.
Checking out files: 100% (254/254), done.
Checking out files: 100% (96/96), done.
Note: checking out '50893291621658f355bc5b4d450a8d06a563053d'.

You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by performing another checkout.

If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -b with the checkout command again. Example:

  git checkout -b new_branch_name

HEAD is now at 5089329... zlib 1.2.8
[  4%] No patch step for 'zlib_project'
[  5%] No update step for 'zlib_project'
[  7%] No configure step for 'zlib_project'
[  8%] Performing build step for 'zlib_project'
Checking for gcc...
Checking for shared library support...
Building shared library libz.so.1.2.8 with gcc.
Checking for off64_t... Yes.
Checking for fseeko... Yes.
Checking for strerror... Yes.
Checking for unistd.h... Yes.
Checking for stdarg.h... Yes.
Checking whether to use vs[n]printf() or s[n]printf()... using vs[n]printf().
Checking for vsnprintf() in stdio.h... Yes.
Checking for return value of vsnprintf()... Yes.
Checking for attribute(visibility) support... Yes.
[ 10%] Performing install step for 'zlib_project'
[ 11%] Completed 'zlib_project'
[ 11%] Built target zlib_project
Scanning dependencies of target bedtools2_project
[ 12%] Creating directories for 'bedtools2_project'
[ 14%] Performing download step (git clone) for 'bedtools2_project'
Cloning into 'bedtools2_project'...
remote: Counting objects: 16860, done.
remote: Compressing objects: 100% (4647/4647), done.
remote: Total 16860 (delta 11899), reused 16853 (delta 11892), pack-reused 0
Receiving objects: 100% (16860/16860), 38.47 MiB | 8.63 MiB/s, done.
Resolving deltas: 100% (11899/11899), done.
Checking out files: 100% (974/974), done.
Already on 'master'
[ 15%] No patch step for 'bedtools2_project'
[ 17%] No update step for 'bedtools2_project'
[ 18%] No configure step for 'bedtools2_project'
[ 20%] Performing build step for 'bedtools2_project'
$CXXFLAGS is [-Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -I./zlib/src/zlib_project -std=c++11]
Building BEDTools:
=========================================================
DETECTED_VERSION = 4bae9e5
CURRENT_VERSION  = 
Updating version file.
 * Creating BamTools API
- Building in src/utils/FileRecordTools
  * compiling FileRecordMgr.cpp
  * compiling FileRecordMergeMgr.cpp
make[4]: Warning: File `../../../obj//FileRecordMergeMgr.o' has modification time 0.012 s in the future
- Building in FileReaders
  * compiling FileReader.cpp
  * compiling SingleLineDelimTextFileReader.cpp
  * compiling BamFileReader.cpp
  * compiling BufferedStreamMgr.cpp
  * compiling InputStreamMgr.cpp
- Building in Records
  * compiling Record.cpp
  * compiling EmptyRecord.cpp
  * compiling Bed3Interval.cpp
  * compiling Bed4Interval.cpp
  * compiling BedGraphInterval.cpp
  * compiling Bed5Interval.cpp
  * compiling Bed6Interval.cpp
  * compiling PlusFields.cpp
  * compiling BedPlusInterval.cpp
  * compiling Bed12Interval.cpp
  * compiling BamRecord.cpp
  * compiling GffRecord.cpp
  * compiling GffPlusRecord.cpp
  * compiling VcfRecord.cpp
  * compiling NoPosPlusRecord.cpp
  * compiling BlockMgr.cpp
  * compiling StrandQueue.cpp
  * compiling RecordMgr.cpp
  * compiling RecordList.cpp
  * compiling RecordKeyList.cpp
  * compiling RecordKeyVector.cpp
make[4]: warning:  Clock skew detected.  Your build may be incomplete.
- Building in src/utils/FileRecordTools/FileReaders
- Building in src/utils/FileRecordTools/Records
- Building in src/utils/bedFile
  * compiling bedFile.cpp
- Building in src/utils/BinTree
  * compiling BinTree.cpp
- Building in src/utils/version
  * compiling version.cpp
- Building in src/utils/bedGraphFile
  * compiling bedGraphFile.cpp
- Building in src/utils/chromsweep
  * compiling chromsweep.cpp
- Building in src/utils/Contexts
  * compiling ContextBase.cpp
  * compiling ContextIntersect.cpp
  * compiling ContextFisher.cpp
  * compiling ContextMap.cpp
  * compiling ContextSample.cpp
  * compiling ContextSpacing.cpp
  * compiling ContextMerge.cpp
  * compiling ContextJaccard.cpp
  * compiling ContextClosest.cpp
  * compiling ContextSubtract.cpp
  * compiling ContextCoverage.cpp
  * compiling ContextComplement.cpp
  * compiling ContextGroupBy.cpp
- Building in src/utils/general
  * compiling ParseTools.cpp
  * compiling PushBackStreamBuf.cpp
  * compiling CompressionTools.cpp
  * compiling Tokenizer.cpp
  * compiling CommonHelp.cpp
- Building in src/utils/gzstream
- Building in src/utils/fileType
  * compiling fileType.cpp
  * compiling FileRecordTypeChecker.cpp
FileRecordTypeChecker.cpp: In member function ‘bool FileRecordTypeChecker::isTextDelimtedFormat(const char*, size_t)’:
FileRecordTypeChecker.cpp:365:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int j=0; j < len; j++) {
                     ^
- Building in src/utils/bedFilePE
  * compiling bedFilePE.cpp
- Building in src/utils/KeyListOps
  * compiling KeyListOps.cpp
  * compiling KeyListOpsMethods.cpp
- Building in src/utils/NewChromsweep
  * compiling NewChromsweep.cpp
  * compiling CloseSweep.cpp
- Building in src/utils/sequenceUtilities
  * compiling sequenceUtils.cpp
- Building in src/utils/tabFile
  * compiling tabFile.cpp
- Building in src/utils/BamTools
 * compiling BamAlignment.cpp
 * compiling BamMultiReader.cpp
 * compiling BamReader.cpp
 * compiling BamWriter.cpp
 * compiling SamHeader.cpp
 * compiling SamProgram.cpp
 * compiling SamProgramChain.cpp
 * compiling SamReadGroup.cpp
 * compiling SamReadGroupDictionary.cpp
 * compiling SamSequence.cpp
 * compiling SamSequenceDictionary.cpp
 * compiling BamHeader_p.cpp
 * compiling BamMultiReader_p.cpp
 * compiling BamRandomAccessController_p.cpp
 * compiling BamReader_p.cpp
 * compiling BamWriter_p.cpp
 * compiling BamIndexFactory_p.cpp
 * compiling BamStandardIndex_p.cpp
src/api/internal/index/BamStandardIndex_p.cpp: In member function ‘void BamTools::Internal::BamStandardIndex::WriteLinearOffsets(const int&, BamTools::Internal::BaiLinearOffsetVector&)’:
src/api/internal/index/BamStandardIndex_p.cpp:958:89: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if ( numBytesWritten != (sizeof(offsetCount) + linearOffsets.size()*sizeof(uint64_t)) )
                                                                                         ^
 * compiling BamToolsIndex_p.cpp
 * compiling BamDeviceFactory_p.cpp
 * compiling BamFile_p.cpp
 * compiling BamFtp_p.cpp
 * compiling BamHttp_p.cpp
src/api/internal/io/BamHttp_p.cpp: In member function ‘bool BamTools::Internal::BamHttp::SendRequest(size_t)’:
src/api/internal/io/BamHttp_p.cpp:396:66: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     return ( WriteToSocket(requestHeader.c_str(), headerSize) == headerSize );
                                                                  ^
 * compiling BamPipe_p.cpp
 * compiling BgzfStream_p.cpp
 * compiling ByteArray_p.cpp
 * compiling HostAddress_p.cpp
 * compiling HostInfo_p.cpp
 * compiling HttpHeader_p.cpp
 * compiling ILocalIODevice_p.cpp
 * compiling RollingBuffer_p.cpp
 * compiling TcpSocketEngine_p.cpp
 * compiling TcpSocketEngine_unix_p.cpp
 * compiling TcpSocket_p.cpp
 * compiling SamFormatParser_p.cpp
 * compiling SamFormatPrinter_p.cpp
 * compiling SamHeaderValidator_p.cpp
 * compiling BamException_p.cpp
 * linking lib/libbamtools.a
- Building in src/utils/BamTools-Ancillary
  * compiling BamAncillary.cpp
  * compiling BamAncillary.cpp
- Building in src/utils/BlockedIntervals
  * compiling BlockedIntervals.cpp
- Building in src/utils/Fasta
  * compiling Fasta.cpp
  * compiling split.cpp
- Building in src/utils/VectorOps
  * compiling VectorOps.cpp
- Building in src/utils/GenomeFile
  * compiling GenomeFile.cpp
GenomeFile.cpp: In member function ‘void GenomeFile::loadGenomeFileIntoMap()’:
GenomeFile.cpp:60:26: warning: variable ‘c2’ set but not used [-Wunused-but-set-variable]
                     long c2;
                          ^
  * compiling NewGenomeFile.cpp
- Building in src/utils/RecordOutputMgr
  * compiling RecordOutputMgr.cpp
- Building in src/utils/ToolBase
  * compiling ToolBase.cpp
- Building in src/utils/driver
  * compiling BedtoolsDriver.cpp
- Building in src/annotateBed
  * compiling annotateMain.cpp
annotateMain.cpp: In function ‘int annotate_main(int, char**)’:
annotateMain.cpp:39:10: warning: variable ‘haveTitles’ set but not used [-Wunused-but-set-variable]
     bool haveTitles     = false;
          ^
  * compiling annotateBed.cpp
- Building in src/bamToBed
  * compiling bamToBed.cpp
bamToBed.cpp: In function ‘int bamtobed_main(int, char**)’:
bamToBed.cpp:88:10: warning: variable ‘useAlignmentScore’ set but not used [-Wunused-but-set-variable]
     bool useAlignmentScore = false;
          ^
- Building in src/bamToFastq
  * compiling bamToFastqMain.cpp
bamToFastqMain.cpp: In function ‘int bamtofastq_main(int, char**)’:
bamToFastqMain.cpp:38:10: warning: variable ‘haveFastq2’ set but not used [-Wunused-but-set-variable]
     bool haveFastq2    = false;
          ^
  * compiling bamToFastq.cpp
- Building in src/bedToBam
  * compiling bedToBam.cpp
bedToBam.cpp: In function ‘int bedtobam_main(int, char**)’:
bedToBam.cpp:60:10: warning: variable ‘haveMapQual’ set but not used [-Wunused-but-set-variable]
     bool haveMapQual     = false;
          ^
- Building in src/bedpeToBam
  * compiling bedpeToBam.cpp
bedpeToBam.cpp: In function ‘int bedpetobam_main(int, char**)’:
bedpeToBam.cpp:61:10: warning: variable ‘haveMapQual’ set but not used [-Wunused-but-set-variable]
     bool haveMapQual     = false;
          ^
- Building in src/bedToIgv
  * compiling bedToIgv.cpp
- Building in src/bed12ToBed6
  * compiling bed12ToBed6.cpp
- Building in src/closestFile
  * compiling closestHelp.cpp
  * compiling closestFile.cpp
- Building in src/clusterBed
  * compiling clusterMain.cpp
clusterMain.cpp: In function ‘int cluster_main(int, char**)’:
clusterMain.cpp:38:10: warning: variable ‘haveMaxDistance’ set but not used [-Wunused-but-set-variable]
     bool haveMaxDistance = false;
          ^
  * compiling clusterBed.cpp
- Building in src/complementFile
  * compiling complementHelp.cpp
  * compiling complementFile.cpp
- Building in src/coverageFile
  * compiling coverageHelp.cpp
  * compiling coverageFile.cpp
- Building in src/expand
  * compiling expand.cpp
- Building in src/fastaFromBed
  * compiling fastaFromBedMain.cpp
  * compiling fastaFromBed.cpp
- Building in src/flankBed
  * compiling flankBedMain.cpp
  * compiling flankBed.cpp
- Building in src/genomeCoverageBed
  * compiling genomeCoverageMain.cpp
  * compiling genomeCoverageBed.cpp
genomeCoverageBed.cpp: In member function ‘void BedGenomeCoverage::CoverageBam(std::string)’:
genomeCoverageBed.cpp:324:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 if(end<_fragmentSize) { //sometimes fragmentSize is bigger :(
                        ^
- Building in src/getOverlap
  * compiling getOverlap.cpp
getOverlap.cpp: In function ‘int getoverlap_main(int, char**)’:
getOverlap.cpp:44:10: warning: variable ‘haveColumns’ set but not used [-Wunused-but-set-variable]
     bool haveColumns = false;
          ^
- Building in src/groupBy
  * compiling groupBy.cpp
  * compiling groupByHelp.cpp
- Building in src/intersectFile
  * compiling intersectHelp.cpp
  * compiling intersectFile.cpp
intersectFile.cpp: In member function ‘virtual void IntersectFile::processHits(RecordOutputMgr*, RecordKeyVector&)’:
intersectFile.cpp:70:33: warning: variable ‘hitListIter’ set but not used [-Wunused-but-set-variable]
  RecordKeyVector::iterator_type hitListIter = hits.begin();
                                 ^
- Building in src/fisher
  * compiling fisherHelp.cpp
  * compiling fisher.cpp
  * compiling kfunc.cpp
- Building in src/jaccard
  * compiling jaccardHelp.cpp
  * compiling jaccard.cpp
- Building in src/linksBed
  * compiling linksMain.cpp
  * compiling linksBed.cpp
- Building in src/maskFastaFromBed
  * compiling maskFastaFromBedMain.cpp
  * compiling maskFastaFromBed.cpp
- Building in src/mapFile
  * compiling mapHelp.cpp
  * compiling mapFile.cpp
- Building in src/mergeFile
  * compiling mergeHelp.cpp
  * compiling mergeFile.cpp
- Building in src/multiBamCov
  * compiling multiBamCovMain.cpp
multiBamCovMain.cpp: In function ‘int multibamcov_main(int, char**)’:
multiBamCovMain.cpp:38:10: warning: variable ‘haveBed’ set but not used [-Wunused-but-set-variable]
     bool haveBed           = false;
          ^
multiBamCovMain.cpp:39:10: warning: variable ‘haveBams’ set but not used [-Wunused-but-set-variable]
     bool haveBams          = false;
          ^
multiBamCovMain.cpp:47:10: warning: variable ‘haveFraction’ set but not used [-Wunused-but-set-variable]
     bool haveFraction       = false;
          ^
  * compiling multiBamCov.cpp
- Building in src/multiIntersectBed
  * compiling multiIntersectBedMain.cpp
multiIntersectBedMain.cpp: In function ‘int multiintersect_main(int, char**)’:
multiIntersectBedMain.cpp:45:10: warning: variable ‘haveFiles’ set but not used [-Wunused-but-set-variable]
     bool haveFiles         = false;
          ^
multiIntersectBedMain.cpp:47:10: warning: variable ‘haveGenome’ set but not used [-Wunused-but-set-variable]
     bool haveGenome        = false;
          ^
multiIntersectBedMain.cpp:48:10: warning: variable ‘haveFiller’ set but not used [-Wunused-but-set-variable]
     bool haveFiller        = true;
          ^
  * compiling multiIntersectBed.cpp
- Building in src/nucBed
  * compiling nucBedMain.cpp
  * compiling nucBed.cpp
- Building in src/pairToBed
  * compiling pairToBedMain.cpp
pairToBedMain.cpp: In function ‘int pairtobed_main(int, char**)’:
pairToBedMain.cpp:43:10: warning: variable ‘haveFraction’ set but not used [-Wunused-but-set-variable]
     bool haveFraction       = false;
          ^
  * compiling pairToBed.cpp
pairToBed.cpp: In member function ‘void BedIntersectPE::FindSpanningOverlaps(const BEDPE&, std::vector<BED>&, const string&)’:
pairToBed.cpp:257:12: warning: variable ‘spanLength’ set but not used [-Wunused-but-set-variable]
     CHRPOS spanLength = 0;
            ^
pairToBed.cpp: In member function ‘bool BedIntersectPE::FindOneOrMoreSpanningOverlaps(const BEDPE&, const string&)’:
pairToBed.cpp:310:9: warning: variable ‘spanLength’ set but not used [-Wunused-but-set-variable]
     int spanLength = 0;
         ^
- Building in src/pairToPair
  * compiling pairToPairMain.cpp
pairToPairMain.cpp: In function ‘int pairtopair_main(int, char**)’:
pairToPairMain.cpp:44:10: warning: variable ‘haveFraction’ set but not used [-Wunused-but-set-variable]
     bool haveFraction = false;
          ^
  * compiling pairToPair.cpp
pairToPair.cpp: In member function ‘void PairToPair::FindOverlaps(const BEDPE&)’:
pairToPair.cpp:112:14: warning: variable ‘found1’ set but not used [-Wunused-but-set-variable]
         bool found1 = false;
              ^
pairToPair.cpp:113:14: warning: variable ‘found2’ set but not used [-Wunused-but-set-variable]
         bool found2 = false;
              ^
- Building in src/randomBed
  * compiling randomBedMain.cpp
  * compiling randomBed.cpp
- Building in src/regressTest
compiling RegressTest.cpp
compiling regressTestMain.cpp
- Building in src/reldist
  * compiling reldistMain.cpp
  * compiling reldist.cpp
- Building in src/sampleFile
  * compiling sampleHelp.cpp
  * compiling sampleFile.cpp
- Building in src/shiftBed
  * compiling shiftBedMain.cpp
  * compiling shiftBed.cpp
- Building in src/shuffleBed
  * compiling shuffleBedMain.cpp
  * compiling shuffleBed.cpp
- Building in src/slopBed
  * compiling slopBedMain.cpp
  * compiling slopBed.cpp
- Building in src/sortBed
  * compiling sortMain.cpp
  * compiling sortBed.cpp
- Building in src/spacingFile
  * compiling spacingHelp.cpp
  * compiling spacingFile.cpp
- Building in src/split
  * compiling splitBed.cpp
  * compiling splitBedMain.cpp
- Building in src/subtractFile
  * compiling subtractHelp.cpp
  * compiling subtractFile.cpp
- Building in src/tagBam
  * compiling tagBamMain.cpp
  * compiling tagBam.cpp
- Building in src/unionBedGraphs
  * compiling unionBedGraphsMain.cpp
unionBedGraphsMain.cpp: In function ‘int unionbedgraphs_main(int, char**)’:
unionBedGraphsMain.cpp:46:10: warning: variable ‘haveFiles’ set but not used [-Wunused-but-set-variable]
     bool haveFiles         = false;
          ^
unionBedGraphsMain.cpp:48:10: warning: variable ‘haveGenome’ set but not used [-Wunused-but-set-variable]
     bool haveGenome        = false;
          ^
unionBedGraphsMain.cpp:49:10: warning: variable ‘haveFiller’ set but not used [-Wunused-but-set-variable]
     bool haveFiller        = true;
          ^
  * compiling unionBedGraphs.cpp
- Building in src/windowBed
  * compiling windowMain.cpp
  * compiling windowBed.cpp
- Building in src/windowMaker
  * compiling windowMakerMain.cpp
  * compiling windowMaker.cpp
- Building main bedtools binary.
done.
- Creating executables for old CLI.
done.
[ 21%] No install step for 'bedtools2_project'
[ 22%] Completed 'bedtools2_project'
[ 22%] Built target bedtools2_project
Scanning dependencies of target bwa_project
[ 24%] Creating directories for 'bwa_project'
[ 25%] Performing download step (git clone) for 'bwa_project'
Cloning into 'bwa_project'...
remote: Counting objects: 4261, done.
remote: Total 4261 (delta 0), reused 0 (delta 0), pack-reused 4261
Receiving objects: 100% (4261/4261), 1.65 MiB | 578.00 KiB/s, done.
Resolving deltas: 100% (3028/3028), done.
Already on 'master'
[ 27%] No patch step for 'bwa_project'
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[ 30%] No configure step for 'bwa_project'
[ 31%] Performing build step for 'bwa_project'
bwt_gen.c: In function ‘BWTIncBuildRelativeRank’:
bwt_gen.c:879:10: warning: variable ‘oldInverseSa0RelativeRank’ set but not used [-Wunused-but-set-variable]
  bgint_t oldInverseSa0RelativeRank = 0;
          ^
bwt_gen.c: In function ‘BWTIncMergeBwt’:
bwt_gen.c:953:15: warning: variable ‘bitsInWordMinusBitPerChar’ set but not used [-Wunused-but-set-variable]
  unsigned int bitsInWordMinusBitPerChar;
               ^
[ 32%] No install step for 'bwa_project'
[ 34%] Completed 'bwa_project'
[ 34%] Built target bwa_project
Scanning dependencies of target fastahack_project
[ 35%] Creating directories for 'fastahack_project'
[ 37%] Performing download step (git clone) for 'fastahack_project'
Cloning into 'fastahack_project'...
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[ 38%] No patch step for 'fastahack_project'
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loading initial cache file /group/bioi1/shared/tools/RUFUS/bin/externals/fastahack/tmp/fastahack_project-cache.cmake
-- The C compiler identification is GNU 4.8.5
-- The CXX compiler identification is GNU 4.8.5
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Configuring done
-- Generating done
-- Build files have been written to: /group/bioi1/shared/tools/RUFUS/bin/externals/fastahack/src/fastahack_project-build
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[ 25%] Building C object src/CMakeFiles/fastahack_src_lib.dir/disorder.c.o
[ 50%] Building CXX object src/CMakeFiles/fastahack_src_lib.dir/Fasta.cpp.o
[ 75%] Building CXX object src/CMakeFiles/fastahack_src_lib.dir/split.cpp.o
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[100%] Built target fastahack
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[ 45%] Completed 'fastahack_project'
[ 45%] Built target fastahack_project
Scanning dependencies of target rufalu_project
[ 47%] Creating directories for 'rufalu_project'
[ 48%] Performing download step (git clone) for 'rufalu_project'
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remote: Total 918 (delta 0), reused 2 (delta 0), pack-reused 908
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Already on 'master'
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loading initial cache file /group/bioi1/shared/tools/RUFUS/bin/externals/rufalu/tmp/rufalu_project-cache.cmake
-- The C compiler identification is GNU 4.8.5
-- The CXX compiler identification is GNU 4.8.5
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
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-- Found Git: /usr/bin/git (found version "1.8.3.1") 
BAMTOOLS INCLUDE: /group/bioi1/shared/tools/RUFUS/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/include
BINARY_DIR: /group/bioi1/shared/tools/RUFUS/bin/externals/rufalu/src/rufalu_project-build/externals/minimap2/src/minimap2_project
SRC_DIR: /group/bioi1/shared/tools/RUFUS/bin/externals/rufalu/src/rufalu_project-build/externals/minimap2/src/minimap2_project
BAMTOOLS LIB DIR: /group/bioi1/shared/tools/RUFUS/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/include
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Scanning dependencies of target minimap2_project
[  2%] Creating directories for 'minimap2_project'
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Cloning into 'minimap2_project'...
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remote: Total 3786 (delta 25), reused 40 (delta 23), pack-reused 3730
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Already on 'master'
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[ 14%] No install step for 'minimap2_project'
[ 16%] Completed 'minimap2_project'
[ 16%] Built target minimap2_project
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Note: checking out '50893291621658f355bc5b4d450a8d06a563053d'.

You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by performing another checkout.

If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -b with the checkout command again. Example:

  git checkout -b new_branch_name

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[ 22%] No patch step for 'zlib_project'
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loading initial cache file /group/bioi1/shared/tools/RUFUS/bin/externals/rufalu/src/rufalu_project-build/externals/zlib/tmp/zlib_project-cache.cmake
-- The C compiler identification is GNU 4.8.5
-- Check for working C compiler: /usr/bin/cc
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-- Detecting C compiler ABI info
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-- Looking for sys/types.h
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-- Renaming
--     /group/bioi1/shared/tools/RUFUS/bin/externals/rufalu/src/rufalu_project-build/externals/zlib/src/zlib_project/zconf.h
-- to 'zconf.h.included' because this file is included with zlib
-- but CMake generates it automatically in the build directory.
-- Configuring done
-- Generating done
-- Build files have been written to: /group/bioi1/shared/tools/RUFUS/bin/externals/rufalu/src/rufalu_project-build/externals/zlib/src/zlib_project-build
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[ 58%] Building C object CMakeFiles/zlibstatic.dir/adler32.o
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[100%] Built target zlibstatic
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[ 32%] Built target zlib_project
Scanning dependencies of target bamtools_project
[ 34%] Creating directories for 'bamtools_project'
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Checking out files: 100% (184/184), done.
Note: checking out '45129fa9035847f54baa2c1750d4d3f526793e82'.

You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by performing another checkout.

If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -b with the checkout command again. Example:

  git checkout -b new_branch_name

HEAD is now at 45129fa... Switched order of directory processing
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loading initial cache file /group/bioi1/shared/tools/RUFUS/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/tmp/bamtools_project-cache.cmake
-- The C compiler identification is GNU 4.8.5
-- The CXX compiler identification is GNU 4.8.5
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
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-- Configuring done
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/group/bioi1/shared/tools/RUFUS/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/api/internal/index/BamStandardIndex_p.cpp: In member function ‘void BamTools::Internal::BamStandardIndex::WriteLinearOffsets(const int&, BamTools::Internal::BaiLinearOffsetVector&)’:
/group/bioi1/shared/tools/RUFUS/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/api/internal/index/BamStandardIndex_p.cpp:958:89: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if ( numBytesWritten != (sizeof(offsetCount) + linearOffsets.size()*sizeof(uint64_t)) )
                                                                                         ^
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/group/bioi1/shared/tools/RUFUS/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/api/internal/io/BamHttp_p.cpp: In member function ‘bool BamTools::Internal::BamHttp::SendGetRequest(size_t)’:
/group/bioi1/shared/tools/RUFUS/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/api/internal/io/BamHttp_p.cpp:409:62: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if ( WriteToSocket(requestHeader.c_str(), headerSize) != headerSize ) {
                                                              ^
/group/bioi1/shared/tools/RUFUS/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/api/internal/io/BamHttp_p.cpp: In member function ‘bool BamTools::Internal::BamHttp::SendHeadRequest()’:
/group/bioi1/shared/tools/RUFUS/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/api/internal/io/BamHttp_p.cpp:501:62: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if ( WriteToSocket(requestHeader.c_str(), headerSize) != headerSize ) {
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[ 52%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamReadGroup.cpp.o
[ 53%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamReadGroupDictionary.cpp.o
[ 54%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamSequence.cpp.o
[ 55%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamSequenceDictionary.cpp.o
[ 56%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/bam/BamHeader_p.cpp.o
[ 57%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/bam/BamMultiReader_p.cpp.o
[ 58%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/bam/BamRandomAccessController_p.cpp.o
[ 59%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/bam/BamReader_p.cpp.o
[ 60%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/bam/BamWriter_p.cpp.o
[ 61%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/index/BamIndexFactory_p.cpp.o
[ 62%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/index/BamStandardIndex_p.cpp.o
/group/bioi1/shared/tools/RUFUS/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/api/internal/index/BamStandardIndex_p.cpp: In member function ‘void BamTools::Internal::BamStandardIndex::WriteLinearOffsets(const int&, BamTools::Internal::BaiLinearOffsetVector&)’:
/group/bioi1/shared/tools/RUFUS/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/api/internal/index/BamStandardIndex_p.cpp:958:89: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if ( numBytesWritten != (sizeof(offsetCount) + linearOffsets.size()*sizeof(uint64_t)) )
                                                                                         ^
[ 63%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/index/BamToolsIndex_p.cpp.o
[ 64%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/BamDeviceFactory_p.cpp.o
[ 65%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/BamFile_p.cpp.o
[ 66%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/BamFtp_p.cpp.o
[ 67%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/BamHttp_p.cpp.o
/group/bioi1/shared/tools/RUFUS/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/api/internal/io/BamHttp_p.cpp: In member function ‘bool BamTools::Internal::BamHttp::SendGetRequest(size_t)’:
/group/bioi1/shared/tools/RUFUS/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/api/internal/io/BamHttp_p.cpp:409:62: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if ( WriteToSocket(requestHeader.c_str(), headerSize) != headerSize ) {
                                                              ^
/group/bioi1/shared/tools/RUFUS/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/api/internal/io/BamHttp_p.cpp: In member function ‘bool BamTools::Internal::BamHttp::SendHeadRequest()’:
/group/bioi1/shared/tools/RUFUS/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/api/internal/io/BamHttp_p.cpp:501:62: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if ( WriteToSocket(requestHeader.c_str(), headerSize) != headerSize ) {
                                                              ^
[ 68%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/BamPipe_p.cpp.o
[ 69%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/BgzfStream_p.cpp.o
[ 70%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/ByteArray_p.cpp.o
[ 71%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/HostAddress_p.cpp.o
[ 72%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/HostInfo_p.cpp.o
[ 73%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/HttpHeader_p.cpp.o
[ 74%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/ILocalIODevice_p.cpp.o
[ 75%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/RollingBuffer_p.cpp.o
[ 76%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/TcpSocket_p.cpp.o
[ 77%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/TcpSocketEngine_p.cpp.o
[ 78%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/TcpSocketEngine_unix_p.cpp.o
[ 79%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/sam/SamFormatParser_p.cpp.o
[ 80%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/sam/SamFormatPrinter_p.cpp.o
[ 81%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/sam/SamHeaderValidator_p.cpp.o
[ 82%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/utils/BamException_p.cpp.o
Linking CXX static library /group/bioi1/shared/tools/RUFUS/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/lib/libbamtools.a
[ 82%] Built target BamTools-static
Scanning dependencies of target BamTools-utils
[ 83%] Building CXX object src/utils/CMakeFiles/BamTools-utils.dir/bamtools_fasta.cpp.o
[ 84%] Building CXX object src/utils/CMakeFiles/BamTools-utils.dir/bamtools_options.cpp.o
[ 85%] Building CXX object src/utils/CMakeFiles/BamTools-utils.dir/bamtools_pileup_engine.cpp.o
[ 86%] Building CXX object src/utils/CMakeFiles/BamTools-utils.dir/bamtools_utilities.cpp.o
Linking CXX static library /group/bioi1/shared/tools/RUFUS/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/lib/libbamtools-utils.a
[ 86%] Built target BamTools-utils
Scanning dependencies of target bamtools_cmd
[ 87%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_convert.cpp.o
[ 88%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_count.cpp.o
[ 89%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_coverage.cpp.o
[ 90%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_filter.cpp.o
[ 91%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_header.cpp.o
[ 92%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_index.cpp.o
[ 93%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_merge.cpp.o
[ 94%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_random.cpp.o
[ 95%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_resolve.cpp.o
[ 96%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_revert.cpp.o
[ 97%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_sort.cpp.o
[ 98%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_split.cpp.o
/group/bioi1/shared/tools/RUFUS/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/toolkit/bamtools_split.cpp: In member function ‘bool BamTools::SplitTool::SplitToolPrivate::SplitListTagImpl(BamTools::BamAlignment&)’:
/group/bioi1/shared/tools/RUFUS/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/toolkit/bamtools_split.cpp:474:23: warning: typedef ‘TagElementType’ locally defined but not used [-Wunused-local-typedefs]
     typedef T         TagElementType;
                       ^
In file included from /group/bioi1/shared/tools/RUFUS/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/api/BamReader.h:14:0,
                 from /group/bioi1/shared/tools/RUFUS/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/toolkit/bamtools_split.cpp:14:
/group/bioi1/shared/tools/RUFUS/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/api/BamAlignment.h: In instantiation of ‘bool BamTools::BamAlignment::GetTag(const string&, std::vector<T>&) const [with T = signed char; std::string = std::basic_string<char>]’:
/group/bioi1/shared/tools/RUFUS/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/toolkit/bamtools_split.cpp:499:13:   required from ‘bool BamTools::SplitTool::SplitToolPrivate::SplitListTagImpl(BamTools::BamAlignment&) [with T = signed char]’
/group/bioi1/shared/tools/RUFUS/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/toolkit/bamtools_split.cpp:415:95:   required from here
/group/bioi1/shared/tools/RUFUS/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/api/BamAlignment.h:581:9: warning: variable ‘elementLength’ set but not used [-Wunused-but-set-variable]
     int elementLength = 0;
         ^
/group/bioi1/shared/tools/RUFUS/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/api/BamAlignment.h: In instantiation of ‘bool BamTools::BamAlignment::GetTag(const string&, std::vector<T>&) const [with T = short int; std::string = std::basic_string<char>]’:
/group/bioi1/shared/tools/RUFUS/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/toolkit/bamtools_split.cpp:499:13:   required from ‘bool BamTools::SplitTool::SplitToolPrivate::SplitListTagImpl(BamTools::BamAlignment&) [with T = short int]’
/group/bioi1/shared/tools/RUFUS/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/toolkit/bamtools_split.cpp:416:96:   required from here
/group/bioi1/shared/tools/RUFUS/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/api/BamAlignment.h:581:9: warning: variable ‘elementLength’ set but not used [-Wunused-but-set-variable]
/group/bioi1/shared/tools/RUFUS/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/api/BamAlignment.h: In instantiation of ‘bool BamTools::BamAlignment::GetTag(const string&, std::vector<T>&) const [with T = int; std::string = std::basic_string<char>]’:
/group/bioi1/shared/tools/RUFUS/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/toolkit/bamtools_split.cpp:499:13:   required from ‘bool BamTools::SplitTool::SplitToolPrivate::SplitListTagImpl(BamTools::BamAlignment&) [with T = int]’
/group/bioi1/shared/tools/RUFUS/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/toolkit/bamtools_split.cpp:417:96:   required from here
/group/bioi1/shared/tools/RUFUS/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/api/BamAlignment.h:581:9: warning: variable ‘elementLength’ set but not used [-Wunused-but-set-variable]
/group/bioi1/shared/tools/RUFUS/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/api/BamAlignment.h: In instantiation of ‘bool BamTools::BamAlignment::GetTag(const string&, std::vector<T>&) const [with T = unsigned char; std::string = std::basic_string<char>]’:
/group/bioi1/shared/tools/RUFUS/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/toolkit/bamtools_split.cpp:499:13:   required from ‘bool BamTools::SplitTool::SplitToolPrivate::SplitListTagImpl(BamTools::BamAlignment&) [with T = unsigned char]’
/group/bioi1/shared/tools/RUFUS/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/toolkit/bamtools_split.cpp:418:96:   required from here
/group/bioi1/shared/tools/RUFUS/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/api/BamAlignment.h:581:9: warning: variable ‘elementLength’ set but not used [-Wunused-but-set-variable]
/group/bioi1/shared/tools/RUFUS/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/api/BamAlignment.h: In instantiation of ‘bool BamTools::BamAlignment::GetTag(const string&, std::vector<T>&) const [with T = short unsigned int; std::string = std::basic_string<char>]’:
/group/bioi1/shared/tools/RUFUS/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/toolkit/bamtools_split.cpp:499:13:   required from ‘bool BamTools::SplitTool::SplitToolPrivate::SplitListTagImpl(BamTools::BamAlignment&) [with T = short unsigned int]’
/group/bioi1/shared/tools/RUFUS/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/toolkit/bamtools_split.cpp:419:97:   required from here
/group/bioi1/shared/tools/RUFUS/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/api/BamAlignment.h:581:9: warning: variable ‘elementLength’ set but not used [-Wunused-but-set-variable]
/group/bioi1/shared/tools/RUFUS/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/api/BamAlignment.h: In instantiation of ‘bool BamTools::BamAlignment::GetTag(const string&, std::vector<T>&) const [with T = unsigned int; std::string = std::basic_string<char>]’:
/group/bioi1/shared/tools/RUFUS/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/toolkit/bamtools_split.cpp:499:13:   required from ‘bool BamTools::SplitTool::SplitToolPrivate::SplitListTagImpl(BamTools::BamAlignment&) [with T = unsigned int]’
/group/bioi1/shared/tools/RUFUS/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/toolkit/bamtools_split.cpp:420:97:   required from here
/group/bioi1/shared/tools/RUFUS/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/api/BamAlignment.h:581:9: warning: variable ‘elementLength’ set but not used [-Wunused-but-set-variable]
/group/bioi1/shared/tools/RUFUS/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/api/BamAlignment.h: In instantiation of ‘bool BamTools::BamAlignment::GetTag(const string&, std::vector<T>&) const [with T = float; std::string = std::basic_string<char>]’:
/group/bioi1/shared/tools/RUFUS/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/toolkit/bamtools_split.cpp:499:13:   required from ‘bool BamTools::SplitTool::SplitToolPrivate::SplitListTagImpl(BamTools::BamAlignment&) [with T = float]’
/group/bioi1/shared/tools/RUFUS/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/toolkit/bamtools_split.cpp:421:94:   required from here
/group/bioi1/shared/tools/RUFUS/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/api/BamAlignment.h:581:9: warning: variable ‘elementLength’ set but not used [-Wunused-but-set-variable]
[ 99%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_stats.cpp.o
[100%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools.cpp.o
Linking CXX executable /group/bioi1/shared/tools/RUFUS/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/bin/bamtools
[100%] Built target bamtools_cmd
[ 46%] No install step for 'bamtools_project'
[ 48%] Completed 'bamtools_project'
[ 48%] Built target bamtools_project
Scanning dependencies of target gtest_project
[ 51%] Creating directories for 'gtest_project'
[ 53%] Performing download step (git clone) for 'gtest_project'
Cloning into 'gtest_project'...
remote: Counting objects: 13994, done.
remote: Compressing objects: 100% (19/19), done.
remote: Total 13994 (delta 4), reused 9 (delta 2), pack-reused 13972
Receiving objects: 100% (13994/13994), 4.78 MiB | 3.70 MiB/s, done.
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Checking out files: 100% (330/330), done.
Checking out files: 100% (370/370), done.
Note: checking out '9ae086a9ebafabdc49b71bb7f3879f551adee09a'.

You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by performing another checkout.

If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -b with the checkout command again. Example:

  git checkout -b new_branch_name

HEAD is now at 9ae086a... Merge pull request #874 from sejr/master
[ 55%] No patch step for 'gtest_project'
[ 57%] No update step for 'gtest_project'
[ 59%] Performing configure step for 'gtest_project'
loading initial cache file /group/bioi1/shared/tools/RUFUS/bin/externals/rufalu/src/rufalu_project-build/externals/gtest/tmp/gtest_project-cache.cmake
-- The C compiler identification is GNU 4.8.5
-- The CXX compiler identification is GNU 4.8.5
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Found PythonInterp: /usr/bin/python (found version "2.7.5") 
-- Looking for include file pthread.h
-- Looking for include file pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - not found
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE  
-- Configuring done
-- Generating done
-- Build files have been written to: /group/bioi1/shared/tools/RUFUS/bin/externals/rufalu/src/rufalu_project-build/externals/gtest/src/gtest_project-build
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Scanning dependencies of target gmock
[ 14%] Building CXX object googlemock/CMakeFiles/gmock.dir/__/googletest/src/gtest-all.cc.o
[ 28%] Building CXX object googlemock/CMakeFiles/gmock.dir/src/gmock-all.cc.o
Linking CXX static library libgmock.a
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Scanning dependencies of target gmock_main
[ 42%] Building CXX object googlemock/CMakeFiles/gmock_main.dir/__/googletest/src/gtest-all.cc.o
[ 57%] Building CXX object googlemock/CMakeFiles/gmock_main.dir/src/gmock-all.cc.o
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Linking CXX static library libgmock_main.a
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[ 85%] Building CXX object googlemock/gtest/CMakeFiles/gtest.dir/src/gtest-all.cc.o
Linking CXX static library libgtest.a
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Scanning dependencies of target gtest_main
[100%] Building CXX object googlemock/gtest/CMakeFiles/gtest_main.dir/src/gtest_main.cc.o
Linking CXX static library libgtest_main.a
[100%] Built target gtest_main
[ 63%] No install step for 'gtest_project'
[ 65%] Completed 'gtest_project'
[ 65%] Built target gtest_project
Scanning dependencies of target aludetect_external_project
[ 67%] Creating directories for 'aludetect_external_project'
[ 69%] No download step for 'aludetect_external_project'
[ 71%] No patch step for 'aludetect_external_project'
[ 73%] No update step for 'aludetect_external_project'
[ 75%] Performing configure step for 'aludetect_external_project'
loading initial cache file /group/bioi1/shared/tools/RUFUS/bin/externals/rufalu/src/rufalu_project-build/externals/aludetect_external_project-prefix/tmp/aludetect_external_project-cache.cmake
-- The C compiler identification is GNU 4.8.5
-- The CXX compiler identification is GNU 4.8.5
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Configuring done
-- Generating done
-- Build files have been written to: /group/bioi1/shared/tools/RUFUS/bin/externals/rufalu/src/rufalu_project-build/externals/aludetect_external_project/bin
[ 77%] Performing build step for 'aludetect_external_project'
[ 79%] No install step for 'aludetect_external_project'
[ 81%] Completed 'aludetect_external_project'
[ 81%] Built target aludetect_external_project
Scanning dependencies of target aludetect_core
[ 83%] Building CXX object libs/CMakeFiles/aludetect_core.dir/contig.cpp.o
[ 85%] Building CXX object libs/CMakeFiles/aludetect_core.dir/vcfWriter.cpp.o
[ 87%] Building CXX object libs/CMakeFiles/aludetect_core.dir/aluHead.cpp.o
[ 89%] Building CXX object libs/CMakeFiles/aludetect_core.dir/denovo.cpp.o
[ 91%] Building CXX object libs/CMakeFiles/aludetect_core.dir/polyATail.cpp.o
[ 93%] Building CXX object libs/CMakeFiles/aludetect_core.dir/util.cpp.o
[ 95%] Building CXX object libs/CMakeFiles/aludetect_core.dir/knownAlus.cpp.o
Linking CXX static library libaludetect_core.a
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Scanning dependencies of target rufalu_tests
[ 97%] Building CXX object tests/CMakeFiles/rufalu_tests.dir/gtest.cpp.o
Linking CXX executable /group/bioi1/shared/tools/RUFUS/bin/externals/rufalu/src/rufalu_project/tests/rufalu_tests
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Scanning dependencies of target aluDetect
[100%] Building CXX object src/CMakeFiles/aluDetect.dir/aluDetect.cpp.o
Linking CXX executable /group/bioi1/shared/tools/RUFUS/bin/externals/rufalu/src/rufalu_project/src/aluDetect
[100%] Built target aluDetect
[ 55%] No install step for 'rufalu_project'
[ 57%] Completed 'rufalu_project'
[ 57%] Built target rufalu_project
Scanning dependencies of target rufus_external_project
[ 58%] Creating directories for 'rufus_external_project'
[ 60%] No download step for 'rufus_external_project'
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loading initial cache file /group/bioi1/shared/tools/RUFUS/bin/externals/rufus_external_project-prefix/tmp/rufus_external_project-cache.cmake
-- The C compiler identification is GNU 4.8.5
-- The CXX compiler identification is GNU 4.8.5
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Configuring done
-- Generating done
-- Build files have been written to: /group/bioi1/shared/tools/RUFUS/bin/externals/rufus_external_project/bin
[ 65%] Performing build step for 'rufus_external_project'
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[ 68%] Built target rufus_external_project
Scanning dependencies of target rufus_util
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$ cat runTest.sh 
./../runRufus.sh -s $PWD/../resources/testData/Child.bam -c $PWD/../resources/testData/Mother.bam $PWD/../resources/testData/Father.bam -k 25 -t 3 -m 8 -r $PWD/../resources/references/small_test_human_reference_v37_decoys.fa
[harriet.dashnow@U-harrietD-01v testRun]$ bash runTest.sh 
arg ref without fa is /group/bioi1/shared/tools/RUFUS/testRun/../resources/references/small_test_human_reference_v37_decoys
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
Final reference path being used is /group/bioi1/shared/tools/RUFUS/testRun/../resources/references/small_test_human_reference_v37_decoys.fa
Final bwa reference path being used is /group/bioi1/shared/tools/RUFUS/testRun/../resources/references/small_test_human_reference_v37_decoys.fa
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
proband extension is bam
you provided the proband bam file /group/bioi1/shared/tools/RUFUS/testRun/../resources/testData/Child.bam
parent file name is Mother.bam
parent file extension name is bam
You provided the control bam file /group/bioi1/shared/tools/RUFUS/testRun/../resources/testData/Mother.bam
parent file name is Father.bam
parent file extension name is bam
You provided the control bam file /group/bioi1/shared/tools/RUFUS/testRun/../resources/testData/Father.bam
~~~~~~~~~~~~ printing out paramater values used in script ~~~~~~~~~~~~~~~~
value of ProbandGenerator Child.bam.generator
Value of ParentGenerators:
 Mother.bam.generator
 Father.bam.generator
Value of K is: 25
Value of Threads is: 3
value of ref is: /group/bioi1/shared/tools/RUFUS/testRun/../resources/references/small_test_human_reference_v37_decoys.fa
value of min is: 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Did not provide refHash
$_arg_min is NOT empty
_arg_min is 8
MutantMinCov is 8
Building parentString...
parent is  Mother.bam.generator 
parents string equals  Mother.bam.generator.Jhash
parent is  Father.bam.generator 
parents string equals  Mother.bam.generator.Jhash Father.bam.generator.Jhash
./../runRufus.sh: line 489: [!: command not found
ok lets do this
ok lets do this
core file size          (blocks, -c) 0
data seg size           (kbytes, -d) unlimited
core file size          (blocks, -c) 0
scheduling priority             (-e) 0
data seg size           (kbytes, -d) unlimited
file size               (blocks, -f) unlimited
scheduling priority             (-e) 0
pending signals                 (-i) 14995
file size               (blocks, -f) unlimited
max locked memory       (kbytes, -l) 64
pending signals                 (-i) 14995
max memory size         (kbytes, -m) unlimited
max locked memory       (kbytes, -l) 64
open files                      (-n) 1024
max memory size         (kbytes, -m) unlimited
pipe size            (512 bytes, -p) 8
open files                      (-n) 1024
POSIX message queues     (bytes, -q) 819200
pipe size            (512 bytes, -p) 8
real-time priority              (-r) 0
POSIX message queues     (bytes, -q) 819200
stack size              (kbytes, -s) 8192
real-time priority              (-r) 0
cpu time               (seconds, -t) unlimited
stack size              (kbytes, -s) 8192
max user processes              (-u) 4096
cpu time               (seconds, -t) unlimited
virtual memory          (kbytes, -v) 30000000
max user processes              (-u) 4096
file locks                      (-x) unlimited
virtual memory          (kbytes, -v) 30000000
file locks                      (-x) unlimited
here
here
ok lets do this
core file size          (blocks, -c) 0
data seg size           (kbytes, -d) unlimited
scheduling priority             (-e) 0
file size               (blocks, -f) unlimited
pending signals                 (-i) 14995
max locked memory       (kbytes, -l) 64
max memory size         (kbytes, -m) unlimited
open files                      (-n) 1024
pipe size            (512 bytes, -p) 8
POSIX message queues     (bytes, -q) 819200
real-time priority              (-r) 0
stack size              (kbytes, -s) 8192
cpu time               (seconds, -t) unlimited
max user processes              (-u) 4096
virtual memory          (kbytes, -v) 30000000
file locks                      (-x) unlimited
here
Child.bam.generator: line 1: /group/bioi1/shared/tools/RUFUS/bin/externals/samtools/samtools: No such file or directory
Father.bam.generator: line 1: /group/bioi1/shared/tools/RUFUS/bin/externals/samtools/samtools: No such file or directory
Mother.bam.generator: line 1: /group/bioi1/shared/tools/RUFUS/bin/externals/samtools/samtools: No such file or directory
Command terminated by signal 9
    Command being timed: "/group/bioi1/shared/tools/RUFUS/src/externals/jellyfish-2.2.5/bin/jellyfish count --disk -m 25 -L 2 -s 1G -t 1 -o Child.bam.generator.Jhash -C Child.bam.generator.fq"
    User time (seconds): 0.04
    System time (seconds): 0.81
    Percent of CPU this job got: 37%
    Elapsed (wall clock) time (h:mm:ss or m:ss): 0:02.31
    Average shared text size (kbytes): 0
    Average unshared data size (kbytes): 0
    Average stack size (kbytes): 0
    Average total size (kbytes): 0
    Maximum resident set size (kbytes): 1954044
    Average resident set size (kbytes): 0
    Major (requiring I/O) page faults: 4
    Minor (reclaiming a frame) page faults: 246739
    Voluntary context switches: 1950
    Involuntary context switches: 86
    Swaps: 0
    File system inputs: 240
    File system outputs: 0
    Socket messages sent: 0
    Socket messages received: 0
    Signals delivered: 0
    Page size (bytes): 4096
    Exit status: 0
Failed to open input file 'Child.bam.generator.Jhash'
Command exited with non-zero status 1
    Command being timed: "/group/bioi1/shared/tools/RUFUS/src/externals/jellyfish-2.2.5/bin/jellyfish histo -f -o Child.bam.generator.Jhash.histo Child.bam.generator.Jhash"
    User time (seconds): 0.00
    System time (seconds): 0.00
    Percent of CPU this job got: 1%
    Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.22
    Average shared text size (kbytes): 0
    Average unshared data size (kbytes): 0
    Average stack size (kbytes): 0
    Average total size (kbytes): 0
    Maximum resident set size (kbytes): 1464
    Average resident set size (kbytes): 0
    Major (requiring I/O) page faults: 5
    Minor (reclaiming a frame) page faults: 416
    Voluntary context switches: 15
    Involuntary context switches: 0
    Swaps: 0
    File system inputs: 13440
    File system outputs: 0
    Socket messages sent: 0
    Socket messages received: 0
    Signals delivered: 0
    Page size (bytes): 4096
    Exit status: 1
Command terminated by signal 9
    Command being timed: "/group/bioi1/shared/tools/RUFUS/src/externals/jellyfish-2.2.5/bin/jellyfish count --disk -m 25 -L 2 -s 1G -t 1 -o Mother.bam.generator.Jhash -C Mother.bam.generator.fq"
    User time (seconds): 0.07
    System time (seconds): 1.38
    Percent of CPU this job got: 42%
    Elapsed (wall clock) time (h:mm:ss or m:ss): 0:03.41
    Average shared text size (kbytes): 0
    Average unshared data size (kbytes): 0
    Average stack size (kbytes): 0
    Average total size (kbytes): 0
    Maximum resident set size (kbytes): 2994080
    Average resident set size (kbytes): 0
    Major (requiring I/O) page faults: 20
    Minor (reclaiming a frame) page faults: 406205
    Voluntary context switches: 2544
    Involuntary context switches: 162
    Swaps: 0
    File system inputs: 6128
    File system outputs: 0
    Socket messages sent: 0
    Socket messages received: 0
    Signals delivered: 0
    Page size (bytes): 4096
    Exit status: 0
Failed to open input file 'Mother.bam.generator.Jhash'
Command exited with non-zero status 1
    Command being timed: "/group/bioi1/shared/tools/RUFUS/src/externals/jellyfish-2.2.5/bin/jellyfish histo -f -o Mother.bam.generator.Jhash.histo Mother.bam.generator.Jhash"
    User time (seconds): 0.00
    System time (seconds): 0.00
    Percent of CPU this job got: 33%
    Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.00
    Average shared text size (kbytes): 0
    Average unshared data size (kbytes): 0
    Average stack size (kbytes): 0
    Average total size (kbytes): 0
    Maximum resident set size (kbytes): 1464
    Average resident set size (kbytes): 0
    Major (requiring I/O) page faults: 2
    Minor (reclaiming a frame) page faults: 418
    Voluntary context switches: 6
    Involuntary context switches: 1
    Swaps: 0
    File system inputs: 4376
    File system outputs: 0
    Socket messages sent: 0
    Socket messages received: 0
    Signals delivered: 0
    Page size (bytes): 4096
    Exit status: 1
    Command being timed: "/group/bioi1/shared/tools/RUFUS/src/externals/jellyfish-2.2.5/bin/jellyfish count --disk -m 25 -L 2 -s 1G -t 1 -o Father.bam.generator.Jhash -C Father.bam.generator.fq"
    User time (seconds): 13.09
    System time (seconds): 2.54
    Percent of CPU this job got: 54%
    Elapsed (wall clock) time (h:mm:ss or m:ss): 0:28.52
    Average shared text size (kbytes): 0
    Average unshared data size (kbytes): 0
    Average stack size (kbytes): 0
    Average total size (kbytes): 0
    Maximum resident set size (kbytes): 4689332
    Average resident set size (kbytes): 0
    Major (requiring I/O) page faults: 16337
    Minor (reclaiming a frame) page faults: 861193
    Voluntary context switches: 20735
    Involuntary context switches: 218
    Swaps: 0
    File system inputs: 881552
    File system outputs: 8
    Socket messages sent: 0
    Socket messages received: 0
    Signals delivered: 0
    Page size (bytes): 4096
    Exit status: 0
    Command being timed: "/group/bioi1/shared/tools/RUFUS/src/externals/jellyfish-2.2.5/bin/jellyfish histo -f -o Father.bam.generator.Jhash.histo Father.bam.generator.Jhash"
    User time (seconds): 0.00
    System time (seconds): 0.00
    Percent of CPU this job got: 11%
    Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.01
    Average shared text size (kbytes): 0
    Average unshared data size (kbytes): 0
    Average stack size (kbytes): 0
    Average total size (kbytes): 0
    Maximum resident set size (kbytes): 1700
    Average resident set size (kbytes): 0
    Major (requiring I/O) page faults: 0
    Minor (reclaiming a frame) page faults: 480
    Voluntary context switches: 10
    Involuntary context switches: 1
    Swaps: 0
    File system inputs: 0
    File system outputs: 136
    Socket messages sent: 0
    Socket messages received: 0
    Signals delivered: 0
    Page size (bytes): 4096
    Exit status: 0
    Command being timed: "bash /group/bioi1/shared/tools/RUFUS/cloud/RunJellyForRUFUS Father.bam.generator 25 1 2"
    User time (seconds): 13.10
    System time (seconds): 2.55
    Percent of CPU this job got: 54%
    Elapsed (wall clock) time (h:mm:ss or m:ss): 0:28.62
    Average shared text size (kbytes): 0
    Average unshared data size (kbytes): 0
    Average stack size (kbytes): 0
    Average total size (kbytes): 0
    Maximum resident set size (kbytes): 4689332
    Average resident set size (kbytes): 0
    Major (requiring I/O) page faults: 16351
    Minor (reclaiming a frame) page faults: 865166
    Voluntary context switches: 20813
    Involuntary context switches: 233
    Swaps: 0
    File system inputs: 882576
    File system outputs: 152
    Socket messages sent: 0
    Socket messages received: 0
    Signals delivered: 0
    Page size (bytes): 4096
    Exit status: 0