gargs command?

[HGENETIC]

Hi again,

i have progressed so far with the installation but run aground while trying to run this command:

ls *.bed | ../gargs -p 30 "bgzip {}"

i've googled it and found a command xargs and so wondered if this is a typo? However, to me it looks like you are trying to zip all the .bed files in the /split folder? If so I am unable to make this work, I have run the following:

ls *.bed | xargs -p 30 "bgzip {}"

but this just resulted in every file name being printed in the terminal window so can you help clarify what this command is doing and suggest a way to make it work.

Cheers

Hywel

[ryanlayer]

gargs is much like xargs, but I better. You can get it here:

https://github.com/brentp/gargs/releases

Which example are you following? I may have forgotten to add the gargs download step to a few example files.

On Wed, Jul 12, 2017 at 4:46 AM, Hywel Williams notifications@github.com wrote:

Hi again,

i have progressed so far with the installation but run aground while trying to run this command:

ls *.bed | ../gargs -p 30 "bgzip {}"

i've googled it and found a command xargs and so wondered if this is a typo? However, to me it looks like you are trying to zip all the .bed files in the /split folder? If so I am unable to make this work, I have run the following:

ls *.bed | xargs -p 30 "bgzip {}"

but this just resulted in every file name being printed in the terminal window so can you help clarify what this command is doing and suggest a way to make it work.

Cheers

Hywel

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/ryanlayer/giggle/issues/24, or mute the thread https://github.com/notifications/unsubscribe-auth/AAlDUVF_q47RU0Qii6_3pEH14YHb0U1Oks5sNKPpgaJpZM4OVct0 .

-- Ryan Layer

[HGENETIC]

OK I see, I couldn’t find a link to gargs but will download using the link provided. I am using the example at this web address:

https://github.com/ryanlayer/giggle/blob/master/examples/rme/README.md

for clarity, can you briefly describe what this command is doing?

Many thanks

Hywel

From: Ryan Layer [mailto:notifications@github.com] Sent: 12 July 2017 14:55 To: ryanlayer/giggle Cc: Williams, Hywel; Author Subject: Re: [ryanlayer/giggle] gargs command? (#24)

gargs is much like xargs, but I better. You can get it here:

https://github.com/brentp/gargs/releases

Which example are you following? I may have forgotten to add the gargs download step to a few example files.

On Wed, Jul 12, 2017 at 4:46 AM, Hywel Williams notifications@github.com wrote:

Hi again,

i have progressed so far with the installation but run aground while trying to run this command:

ls *.bed | ../gargs -p 30 "bgzip {}"

i've googled it and found a command xargs and so wondered if this is a typo? However, to me it looks like you are trying to zip all the .bed files in the /split folder? If so I am unable to make this work, I have run the following:

ls *.bed | xargs -p 30 "bgzip {}"

but this just resulted in every file name being printed in the terminal window so can you help clarify what this command is doing and suggest a way to make it work.

Cheers

Hywel

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/ryanlayer/giggle/issues/24, or mute the thread https://github.com/notifications/unsubscribe-auth/AAlDUVF_q47RU0Qii6_3pEH14YHb0U1Oks5sNKPpgaJpZM4OVct0 .

-- Ryan Layer

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/ryanlayer/giggle/issues/24#issuecomment-314776448, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AMWdj1Ab3piCXSXY4XSY5vRlB5GEY0iMks5sNNAYgaJpZM4OVct0.

[ryanlayer]

It looks like the gargs download step was the last entry in the "Get source code" section of that examples.

ls *.bed | ../gargs -p 30 "bgzip {}" uses 30 threads to compress bed files.

gargs takes input from STDIN, and for every line maps fields in the line to arguments in a command. In this case ls *bed give a list of bed files, and gargs maps each line to the command bgzip FILE. -p 30 says use up to 30 threads.

[HGENETIC]

Hi Ryan,

I have managed to download all the rme data as described in your giggle examples section. However, when I ran the test (./giggle_tests.sh) I received the following:

[sejjhwi@login08 func]$ ./giggle_tests.sh which: no bedtools in (/home/sejjhwi/.python2local/bin:/shared/ucl/apps/python/bundles/python2-2.0.0/venv/bin:/shared/ucl/apps/openblas/0.2.14/gnu-4.9.2/bin:/shared/ucl/apps/python/2.7.12/gnu-4.9.2/bin:/shared/ucl/apps/intel-mpi/ucl-wrapper/bin:/shared/ucl/apps/intel/2017.Update1/impi/2017.1.132/intel64/bin:/shared/ucl/apps/intel/2017.Update1/debugger_2017/gdb/intel64_mic/bin:/shared/ucl/apps/intel/2017.Update1/compilers_and_libraries_2017.1.132/linux/mpi/intel64/bin:/shared/ucl/apps/intel/2017.Update1/compilers_and_libraries_2017.1.132/linux/bin/intel64:/shared/ucl/sysops/lquota/bin:/shared/ucl/apps/cluster-bin:/shared/ucl/apps/cluster-scripts:/shared/ucl/apps/mrxvt/0.5.4/bin:/shared/ucl/apps/tmux/2.2/gnu-4.9.2/bin:/shared/ucl/apps/emacs/24.5/gnu-4.9.2/bin:/shared/ucl/apps/giflib/5.1.1/gnu-4.9.2/bin:/shared/ucl/apps/dos2unix/7.3/gnu-4.9.2/bin:/shared/ucl/apps/NEdit/5.6-Aug15/bin:/shared/ucl/apps/nano/2.4.2/gnu-4.9.2//bin:/shared/ucl/apps/GERun:/shared/ucl/apps/screen/4.2.1/bin:/shared/ucl/apps/subversion/1.8.13/bin:/shared/ucl/apps/apr-util/1.5.4/bin:/shared/ucl/apps/apr/1.5.2/bin:/shared/ucl/apps/git/2.10.2/gnu-4.9.2/bin:/shared/ucl/apps/flex/2.5.39/gnu-4.9.2/bin:/shared/ucl/apps/cmake/3.2.1/gnu-4.9.2/bin:/shared/ucl/apps/gcc/4.9.2/bin:/opt/sge/bin:/opt/sge/bin/lx-amd64:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/sejjhwi/bin)

check_chr_v_nochr_search_1 ran in 0 sec with 1/0 lines to STDERR/OUT FAIL "11" != "0" (LINE 55) ./giggle_tests.sh: line 56: ../../bin/giggle: No such file or directory PASS "0" == "0" (LINE 56)

check_chr_v_nochr_search_2 ran in 0 sec with 1/0 lines to STDERR/OUT FAIL "11" != "0" (LINE 55) ./giggle_tests.sh: line 56: ../../bin/giggle: No such file or directory PASS "0" == "0" (LINE 56)

check_chr_v_nochr_search_3 ran in 0 sec with 1/0 lines to STDERR/OUT FAIL "11" != "0" (LINE 55) ./giggle_tests.sh: line 56: ../../bin/giggle: No such file or directory PASS "0" == "0" (LINE 56)

check_chr_v_nochr_search_4 ran in 0 sec with 1/0 lines to STDERR/OUT FAIL "11" != "0" (LINE 55) ./giggle_tests.sh: line 56: ../../bin/giggle: No such file or directory PASS "0" == "0" (LINE 56)

check_chr_v_nochr_search_5 ran in 0 sec with 1/0 lines to STDERR/OUT FAIL "11" != "0" (LINE 55) ./giggle_tests.sh: line 56: ../../bin/giggle: No such file or directory PASS "0" == "0" (LINE 56)

check_chr_v_nochr_search_6 ran in 0 sec with 1/0 lines to STDERR/OUT FAIL "11" != "0" (LINE 55) ./giggle_tests.sh: line 56: ../../bin/giggle: No such file or directory PASS "0" == "0" (LINE 56)

check_chr_v_nochr_search_7 ran in 0 sec with 1/0 lines to STDERR/OUT FAIL "11" != "0" (LINE 55) ./giggle_tests.sh: line 56: ../../bin/giggle: No such file or directory PASS "0" == "0" (LINE 56)

check_chr_v_nochr_search_8 ran in 0 sec with 1/0 lines to STDERR/OUT FAIL "11" != "0" (LINE 55) ./giggle_tests.sh: line 56: ../../bin/giggle: No such file or directory PASS "0" == "0" (LINE 56)

check_chr_v_nochr_search_9 ran in 0 sec with 1/0 lines to STDERR/OUT FAIL "11" != "0" (LINE 55) ./giggle_tests.sh: line 56: ../../bin/giggle: No such file or directory PASS "0" == "0" (LINE 56)

check_chr_v_nochr_search_10 ran in 0 sec with 1/0 lines to STDERR/OUT FAIL "11" != "0" (LINE 55) ./giggle_tests.sh: line 56: ../../bin/giggle: No such file or directory PASS "0" == "0" (LINE 56)

check_bulk_insert ran in 0 sec with 1/0 lines to STDERR/OUT FAIL "23" != "0" (LINE 79) ./giggle_tests.sh: line 80: ../../bin/giggle: No such file or directory PASS "0" == "0" (LINE 80)

check_offset_additional_data ran in 0 sec with 1/0 lines to STDERR/OUT FAIL "72" != "0" (LINE 87) PASS "0" == "0" (LINE 88)

check_dense_index ran in 0 sec with 1/0 lines to STDERR/OUT FAIL EXIT CODE (LINE 102) --> expected EX_OK, observed Unknown code: 127

sshtest v0.1.5

25 Tests 13 Failures 12 Successes

I assume there shouldn’t be any failures? I then ran the next command:

[sejjhwi@login08 func]$ cd ../unit/ [sejjhwi@login08 unit]$ make rm -f test_hash_list test_cache test_bulk_insert test_leaf_data test_genetic_offset_index test_lists test_offset_index test_giggle test_bpt test_disk_store test_ll test_file_read rm -f _Runner.c rm -rf dSYM/

ruby ./unity/auto/generate_test_runner.rb test_hash_list.c

ruby ./unity/generate_test_runner.rb test_hash_list.c gcc -Werror -g -o test_hash_list \ -I./unity \ -I../../src/ \ -I../../lib/htslib/ \ -DTEST ./unity/unity.c \ -DSAMTOOLS=1 \ -pthread \ ../../src/disk_store.c ../../src/cache.c ../../src/giggle_index.c ../../src/lists.c ../../src/util.c ../../src/ll.c ../../src/timer.c ../../src/file_read.c ../../src/bpt.c ../../src/wah.c ../../src/leaf.c ../../src/jsw_avltree.c ../../src/pq.c ../../src/offset_index.c ../../src/fastlz.c \ test_hash_list.c test_hash_list_Runner.c \ ../../lib/htslib//libhts.a \ -lz -lm -lcurl -lcrypto -lssl ../../lib/htslib//libhts.a(bgzf.o): In function bgzf_open': /home/sejjhwi/GIGGLE/giggle/lib/htslib/bgzf.c:290: undefined reference to__intel_sse2_strchr' /home/sejjhwi/GIGGLE/giggle/lib/htslib/bgzf.c:74: undefined reference to `_intel_fast_memset'

There are basically hundreds of lines that give the same error message relating to intel….. I am running my scripts on a HPC cluster and I’m not sure if I need to change any of my settings or download supporting programs to overcome this problem?

Any help will be much appreciated, best wishes

Hywel

From: Ryan Layer [mailto:notifications@github.com] Sent: 12 July 2017 15:05 To: ryanlayer/giggle Cc: Williams, Hywel; Author Subject: Re: [ryanlayer/giggle] gargs command? (#24)

It looks like the gargs download step was the last entry in the "Get source code" section of that examples.

ls *.bed | ../gargs -p 30 "bgzip {}" uses 30 threads to compress bed files.

gargs takes input from STDIN, and for every line maps fields in the line to arguments in a command. In this case ls *bed give a list of bed files, and gargs maps each line to the command bgzip FILE. -p 30 says use up to 30 threads.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/ryanlayer/giggle/issues/24#issuecomment-314779650, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AMWdj2sR2cpHdudSIPUyh7V9QSAO65TZks5sNNKjgaJpZM4OVct0.

[ryanlayer]

There are 2 issues here:

1. You need bedtools in your path to run the tests. I will update the README to make this clear.
2. There is a problem compiling htslib. What environment are you using (OS version, gcc version etc.)? I want to try and replicate that error. I think the issue is the order in which libraries are linked, but I cannot be sure without testing.

On Thu, Jul 13, 2017 at 8:54 AM, Hywel Williams notifications@github.com wrote:

Hi Ryan,

I have managed to download all the rme data as described in your giggle examples section. However, when I ran the test (./giggle_tests.sh) I received the following:

[sejjhwi@login08 func]$ ./giggle_tests.sh which: no bedtools in (/home/sejjhwi/.python2local/ bin:/shared/ucl/apps/python/bundles/python2-2.0.0/venv/ bin:/shared/ucl/apps/openblas/0.2.14/gnu-4.9.2/bin:/shared/ ucl/apps/python/2.7.12/gnu-4.9.2/bin:/shared/ucl/apps/ intel-mpi/ucl-wrapper/bin:/shared/ucl/apps/intel/2017. Update1/impi/2017.1.132/intel64/bin:/shared/ucl/apps/ intel/2017.Update1/debugger_2017/gdb/intel64_mic/bin:/ shared/ucl/apps/intel/2017.Update1/compilersand libraries_2017.1.132/linux/mpi/intel64/bin:/shared/ucl/ apps/intel/2017.Update1/compilers_and_libraries_2017. 1.132/linux/bin/intel64:/shared/ucl/sysops/lquota/bin:/ shared/ucl/apps/cluster-bin:/shared/ucl/apps/cluster- scripts:/shared/ucl/apps/mrxvt/0.5.4/bin:/shared/ucl/ apps/tmux/2.2/gnu-4.9.2/bin:/shared/ucl/apps/emacs/24.5/ gnu-4.9.2/bin:/shared/ucl/apps/giflib/5.1.1/gnu-4.9.2/ bin:/shared/ucl/apps/dos2unix/7.3/gnu-4.9.2/bin:/shared/ucl/ apps/NEdit/5.6-Aug15/bin:/shared/ucl/apps/nano/2.4.2/ gnu-4.9.2//bin:/shared/ucl/apps/GERun:/shared/ucl/apps/ screen/4.2.1/bin:/shared/ucl/apps/subversion/1.8.13/bin:/ shared/ucl/apps/apr-util/1.5.4/bin:/shared/ucl/apps/apr/1. 5.2/bin:/shared/ucl/apps/git/2.10.2/gnu-4.9.2/bin:/shared/ ucl/apps/flex/2.5.39/gnu-4.9.2/bin:/shared/ucl/apps/cmake/ 3.2.1/gnu-4.9.2/bin:/shared/ucl/apps/gcc/4.9.2/bin:/opt/ sge/bin:/opt/sge/bin/lx-amd64:/usr/local/bin:/usr/bin:/usr/ local/sbin:/usr/sbin:/home/sejjhwi/bin)

check_chr_v_nochr_search_1 ran in 0 sec with 1/0 lines to STDERR/OUT FAIL "11" != "0" (LINE 55) ./giggle_tests.sh: line 56: ../../bin/giggle: No such file or directory PASS "0" == "0" (LINE 56)

check_chr_v_nochr_search_2 ran in 0 sec with 1/0 lines to STDERR/OUT FAIL "11" != "0" (LINE 55) ./giggle_tests.sh: line 56: ../../bin/giggle: No such file or directory PASS "0" == "0" (LINE 56)

check_chr_v_nochr_search_3 ran in 0 sec with 1/0 lines to STDERR/OUT FAIL "11" != "0" (LINE 55) ./giggle_tests.sh: line 56: ../../bin/giggle: No such file or directory PASS "0" == "0" (LINE 56)

check_chr_v_nochr_search_4 ran in 0 sec with 1/0 lines to STDERR/OUT FAIL "11" != "0" (LINE 55) ./giggle_tests.sh: line 56: ../../bin/giggle: No such file or directory PASS "0" == "0" (LINE 56)

check_chr_v_nochr_search_5 ran in 0 sec with 1/0 lines to STDERR/OUT FAIL "11" != "0" (LINE 55) ./giggle_tests.sh: line 56: ../../bin/giggle: No such file or directory PASS "0" == "0" (LINE 56)

check_chr_v_nochr_search_6 ran in 0 sec with 1/0 lines to STDERR/OUT FAIL "11" != "0" (LINE 55) ./giggle_tests.sh: line 56: ../../bin/giggle: No such file or directory PASS "0" == "0" (LINE 56)

check_chr_v_nochr_search_7 ran in 0 sec with 1/0 lines to STDERR/OUT FAIL "11" != "0" (LINE 55) ./giggle_tests.sh: line 56: ../../bin/giggle: No such file or directory PASS "0" == "0" (LINE 56)

check_chr_v_nochr_search_8 ran in 0 sec with 1/0 lines to STDERR/OUT FAIL "11" != "0" (LINE 55) ./giggle_tests.sh: line 56: ../../bin/giggle: No such file or directory PASS "0" == "0" (LINE 56)

check_chr_v_nochr_search_9 ran in 0 sec with 1/0 lines to STDERR/OUT FAIL "11" != "0" (LINE 55) ./giggle_tests.sh: line 56: ../../bin/giggle: No such file or directory PASS "0" == "0" (LINE 56)

check_chr_v_nochr_search_10 ran in 0 sec with 1/0 lines to STDERR/OUT FAIL "11" != "0" (LINE 55) ./giggle_tests.sh: line 56: ../../bin/giggle: No such file or directory PASS "0" == "0" (LINE 56)

check_bulk_insert ran in 0 sec with 1/0 lines to STDERR/OUT FAIL "23" != "0" (LINE 79) ./giggle_tests.sh: line 80: ../../bin/giggle: No such file or directory PASS "0" == "0" (LINE 80)

check_offset_additional_data ran in 0 sec with 1/0 lines to STDERR/OUT FAIL "72" != "0" (LINE 87) PASS "0" == "0" (LINE 88)

check_dense_index ran in 0 sec with 1/0 lines to STDERR/OUT FAIL EXIT CODE (LINE 102) --> expected EX_OK, observed Unknown code: 127

sshtest v0.1.5

25 Tests 13 Failures 12 Successes

I assume there shouldn’t be any failures? I then ran the next command:

[sejjhwi@login08 func]$ cd ../unit/ [sejjhwi@login08 unit]$ make rm -f test_hash_list test_cache test_bulk_insert test_leaf_data test_genetic_offset_index test_lists test_offset_index test_giggle test_bpt test_disk_store test_ll test_file_read rm -f _Runner.c rm -rf dSYM/

ruby ./unity/auto/generate_test_runner.rb test_hash_list.c

ruby ./unity/generate_test_runner.rb test_hash_list.c gcc -Werror -g -o test_hash_list \ -I./unity \ -I../../src/ \ -I../../lib/htslib/ \ -DTEST ./unity/unity.c \ -DSAMTOOLS=1 \ -pthread \ ../../src/disk_store.c ../../src/cache.c ../../src/giggle_index.c ../../src/lists.c ../../src/util.c ../../src/ll.c ../../src/timer.c ../../src/file_read.c ../../src/bpt.c ../../src/wah.c ../../src/leaf.c ../../src/jsw_avltree.c ../../src/pq.c ../../src/offset_index.c ../../src/fastlz.c \ test_hash_list.c test_hash_list_Runner.c \ ../../lib/htslib//libhts.a \ -lz -lm -lcurl -lcrypto -lssl ../../lib/htslib//libhts.a(bgzf.o): In function bgzf_open': /home/sejjhwi/GIGGLE/giggle/lib/htslib/bgzf.c:290: undefined reference to __intel_sse2_strchr' /home/sejjhwi/GIGGLE/giggle/lib/htslib/bgzf.c:74: undefined reference to `_intel_fast_memset'

There are basically hundreds of lines that give the same error message relating to intel….. I am running my scripts on a HPC cluster and I’m not sure if I need to change any of my settings or download supporting programs to overcome this problem?

Any help will be much appreciated, best wishes

Hywel

From: Ryan Layer [mailto:notifications@github.com] Sent: 12 July 2017 15:05 To: ryanlayer/giggle Cc: Williams, Hywel; Author Subject: Re: [ryanlayer/giggle] gargs command? (#24)

It looks like the gargs download step was the last entry in the "Get source code" section of that examples.

ls *.bed | ../gargs -p 30 "bgzip {}" uses 30 threads to compress bed files.

gargs takes input from STDIN, and for every line maps fields in the line to arguments in a command. In this case ls *bed give a list of bed files, and gargs maps each line to the command bgzip FILE. -p 30 says use up to 30 threads.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/ ryanlayer/giggle/issues/24#issuecomment-314779650, or mute the thread< https://github.com/notifications/unsubscribe-auth/ AMWdj2sR2cpHdudSIPUyh7V9QSAO65TZks5sNNKjgaJpZM4OVct0>.

— You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub https://github.com/ryanlayer/giggle/issues/24#issuecomment-315102542, or mute the thread https://github.com/notifications/unsubscribe-auth/AAlDUddxEqJLtRHZ8SMp2iO4hEt7gux7ks5sNi-mgaJpZM4OVct0 .

-- Ryan Layer

[HGENETIC]

Thanks for the help.

Here is a list of some of my settings: BASH_VERSINFO=([0]="4" [1]="2" [2]="46" [3]="1" [4]="release" [5]="x86_64-redhat-linux-gnu") BASH_VERSION='4.2.46(1)-release' COMPILER_TAG=intel-2017 CPATH=/shared/ucl/apps/python/bundles/python2-2.0.0/venv/include:/shared/ucl/apps/openblas/0.2.14/gnu-4.9.2/include:/shared/ucl/apps/python/2.7.12/gnu-4.9.2/include:/shared/ucl/apps/intel/2017.Update1/impi/2017.1.132/intel64/include:/shared/ucl/apps/intel/2017.Update1/compilers_and_libraries_2017.1.132/linux/daal/include:/shared/ucl/apps/intel/2017.Update1/compilers_and_libraries_2017.1.132/linux/tbb/include:/shared/ucl/apps/intel/2017.Update1/compilers_and_libraries_2017.1.132/linux/mkl/include:/shared/ucl/apps/intel/2017.Update1/compilers_and_libraries_2017.1.132/linux/ipp/include:/shared/ucl/apps/giflib/5.1.1/gnu-4.9.2/include:/shared/ucl/apps/apr-util/1.5.4/include:/shared/ucl/apps/apr/1.5.2/include:/shared/ucl/apps/flex/2.5.39/gnu-4.9.2/include

LOADEDMODULES=gcc-libs/4.9.2:cmake/3.2.1:flex/2.5.39:git/2.10.2:apr/1.5.2:apr-util/1.5.4:subversion/1.8.13:screen/4.2.1:gerun:nano/2.4.2:nedit/5.6-aug15:dos2unix/7.3:giflib/5.1.1:emacs/24.5:tmux/2.2:mrxvt/0.5.4:userscripts/1.3.0:rcps-core/1.0.0:compilers/intel/2017/update1:mpi/intel/2017/update1/intel:default-modules/2017:python/2.7.12:openblas/0.2.14/gnu-4.9.2:python2/recommended

If this doesn’t include any particular piece of information please let me know and I will find it for you. For reference I simply used the ‘set’ command to extract this info.

Best wishes

Hywel

From: Ryan Layer [mailto:notifications@github.com] Sent: 13 July 2017 16:06 To: ryanlayer/giggle Cc: Williams, Hywel; Author Subject: Re: [ryanlayer/giggle] gargs command? (#24)

There are 2 issues here:

1. You need bedtools in your path to run the tests. I will update the README to make this clear.
2. There is a problem compiling htslib. What environment are you using (OS version, gcc version etc.)? I want to try and replicate that error. I think the issue is the order in which libraries are linked, but I cannot be sure without testing.

On Thu, Jul 13, 2017 at 8:54 AM, Hywel Williams notifications@github.com wrote:

Hi Ryan,

I have managed to download all the rme data as described in your giggle examples section. However, when I ran the test (./giggle_tests.sh) I received the following:

[sejjhwi@login08 func]$ ./giggle_tests.sh which: no bedtools in (/home/sejjhwi/.python2local/ bin:/shared/ucl/apps/python/bundles/python2-2.0.0/venv/ bin:/shared/ucl/apps/openblas/0.2.14/gnu-4.9.2/bin:/shared/ ucl/apps/python/2.7.12/gnu-4.9.2/bin:/shared/ucl/apps/ intel-mpi/ucl-wrapper/bin:/shared/ucl/apps/intel/2017. Update1/impi/2017.1.132/intel64/bin:/shared/ucl/apps/ intel/2017.Update1/debugger_2017/gdb/intel64_mic/bin:/ shared/ucl/apps/intel/2017.Update1/compilersand libraries_2017.1.132/linux/mpi/intel64/bin:/shared/ucl/ apps/intel/2017.Update1/compilers_and_libraries_2017. 1.132/linux/bin/intel64:/shared/ucl/sysops/lquota/bin:/ shared/ucl/apps/cluster-bin:/shared/ucl/apps/cluster- scripts:/shared/ucl/apps/mrxvt/0.5.4/bin:/shared/ucl/ apps/tmux/2.2/gnu-4.9.2/bin:/shared/ucl/apps/emacs/24.5/ gnu-4.9.2/bin:/shared/ucl/apps/giflib/5.1.1/gnu-4.9.2/ bin:/shared/ucl/apps/dos2unix/7.3/gnu-4.9.2/bin:/shared/ucl/ apps/NEdit/5.6-Aug15/bin:/shared/ucl/apps/nano/2.4.2/ gnu-4.9.2//bin:/shared/ucl/apps/GERun:/shared/ucl/apps/ screen/4.2.1/bin:/shared/ucl/apps/subversion/1.8.13/bin:/ shared/ucl/apps/apr-util/1.5.4/bin:/shared/ucl/apps/apr/1. 5.2/bin:/shared/ucl/apps/git/2.10.2/gnu-4.9.2/bin:/shared/ ucl/apps/flex/2.5.39/gnu-4.9.2/bin:/shared/ucl/apps/cmake/ 3.2.1/gnu-4.9.2/bin:/shared/ucl/apps/gcc/4.9.2/bin:/opt/ sge/bin:/opt/sge/bin/lx-amd64:/usr/local/bin:/usr/bin:/usr/ local/sbin:/usr/sbin:/home/sejjhwi/bin)

check_chr_v_nochr_search_1 ran in 0 sec with 1/0 lines to STDERR/OUT FAIL "11" != "0" (LINE 55) ./giggle_tests.sh: line 56: ../../bin/giggle: No such file or directory PASS "0" == "0" (LINE 56)

check_chr_v_nochr_search_2 ran in 0 sec with 1/0 lines to STDERR/OUT FAIL "11" != "0" (LINE 55) ./giggle_tests.sh: line 56: ../../bin/giggle: No such file or directory PASS "0" == "0" (LINE 56)

check_chr_v_nochr_search_3 ran in 0 sec with 1/0 lines to STDERR/OUT FAIL "11" != "0" (LINE 55) ./giggle_tests.sh: line 56: ../../bin/giggle: No such file or directory PASS "0" == "0" (LINE 56)

check_chr_v_nochr_search_4 ran in 0 sec with 1/0 lines to STDERR/OUT FAIL "11" != "0" (LINE 55) ./giggle_tests.sh: line 56: ../../bin/giggle: No such file or directory PASS "0" == "0" (LINE 56)

check_chr_v_nochr_search_5 ran in 0 sec with 1/0 lines to STDERR/OUT FAIL "11" != "0" (LINE 55) ./giggle_tests.sh: line 56: ../../bin/giggle: No such file or directory PASS "0" == "0" (LINE 56)

check_chr_v_nochr_search_6 ran in 0 sec with 1/0 lines to STDERR/OUT FAIL "11" != "0" (LINE 55) ./giggle_tests.sh: line 56: ../../bin/giggle: No such file or directory PASS "0" == "0" (LINE 56)

check_chr_v_nochr_search_7 ran in 0 sec with 1/0 lines to STDERR/OUT FAIL "11" != "0" (LINE 55) ./giggle_tests.sh: line 56: ../../bin/giggle: No such file or directory PASS "0" == "0" (LINE 56)

check_chr_v_nochr_search_8 ran in 0 sec with 1/0 lines to STDERR/OUT FAIL "11" != "0" (LINE 55) ./giggle_tests.sh: line 56: ../../bin/giggle: No such file or directory PASS "0" == "0" (LINE 56)

check_chr_v_nochr_search_9 ran in 0 sec with 1/0 lines to STDERR/OUT FAIL "11" != "0" (LINE 55) ./giggle_tests.sh: line 56: ../../bin/giggle: No such file or directory PASS "0" == "0" (LINE 56)

check_chr_v_nochr_search_10 ran in 0 sec with 1/0 lines to STDERR/OUT FAIL "11" != "0" (LINE 55) ./giggle_tests.sh: line 56: ../../bin/giggle: No such file or directory PASS "0" == "0" (LINE 56)

check_bulk_insert ran in 0 sec with 1/0 lines to STDERR/OUT FAIL "23" != "0" (LINE 79) ./giggle_tests.sh: line 80: ../../bin/giggle: No such file or directory PASS "0" == "0" (LINE 80)

check_offset_additional_data ran in 0 sec with 1/0 lines to STDERR/OUT FAIL "72" != "0" (LINE 87) PASS "0" == "0" (LINE 88)

check_dense_index ran in 0 sec with 1/0 lines to STDERR/OUT FAIL EXIT CODE (LINE 102) --> expected EX_OK, observed Unknown code: 127

sshtest v0.1.5

25 Tests 13 Failures 12 Successes

I assume there shouldn’t be any failures? I then ran the next command:

[sejjhwi@login08 func]$ cd ../unit/ [sejjhwi@login08 unit]$ make rm -f test_hash_list test_cache test_bulk_insert test_leaf_data test_genetic_offset_index test_lists test_offset_index test_giggle test_bpt test_disk_store test_ll test_file_read rm -f _Runner.c rm -rf dSYM/

ruby ./unity/auto/generate_test_runner.rb test_hash_list.c

ruby ./unity/generate_test_runner.rb test_hash_list.c gcc -Werror -g -o test_hash_list \ -I./unity \ -I../../src/ \ -I../../lib/htslib/ \ -DTEST ./unity/unity.c \ -DSAMTOOLS=1 \ -pthread \ ../../src/disk_store.c ../../src/cache.c ../../src/giggle_index.c ../../src/lists.c ../../src/util.c ../../src/ll.c ../../src/timer.c ../../src/file_read.c ../../src/bpt.c ../../src/wah.c ../../src/leaf.c ../../src/jsw_avltree.c ../../src/pq.c ../../src/offset_index.c ../../src/fastlz.c \ test_hash_list.c test_hash_list_Runner.c \ ../../lib/htslib//libhts.a \ -lz -lm -lcurl -lcrypto -lssl ../../lib/htslib//libhts.a(bgzf.o): In function bgzf_open': /home/sejjhwi/GIGGLE/giggle/lib/htslib/bgzf.c:290: undefined reference to __intel_sse2_strchr' /home/sejjhwi/GIGGLE/giggle/lib/htslib/bgzf.c:74: undefined reference to `_intel_fast_memset'

There are basically hundreds of lines that give the same error message relating to intel….. I am running my scripts on a HPC cluster and I’m not sure if I need to change any of my settings or download supporting programs to overcome this problem?

Any help will be much appreciated, best wishes

Hywel

From: Ryan Layer [mailto:notifications@github.com] Sent: 12 July 2017 15:05 To: ryanlayer/giggle Cc: Williams, Hywel; Author Subject: Re: [ryanlayer/giggle] gargs command? (#24)

It looks like the gargs download step was the last entry in the "Get source code" section of that examples.

ls *.bed | ../gargs -p 30 "bgzip {}" uses 30 threads to compress bed files.

gargs takes input from STDIN, and for every line maps fields in the line to arguments in a command. In this case ls *bed give a list of bed files, and gargs maps each line to the command bgzip FILE. -p 30 says use up to 30 threads.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/ ryanlayer/giggle/issues/24#issuecomment-314779650, or mute the thread< https://github.com/notifications/unsubscribe-auth/ AMWdj2sR2cpHdudSIPUyh7V9QSAO65TZks5sNNKjgaJpZM4OVct0>.

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-- Ryan Layer

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[ryanlayer]

Are you using an intel compiler?

On Thu, Jul 13, 2017 at 9:17 AM, Hywel Williams notifications@github.com wrote:

Thanks for the help.

Here is a list of some of my settings: BASH_VERSINFO=([0]="4" [1]="2" [2]="46" [3]="1" [4]="release" [5]="x86_64-redhat-linux-gnu") BASH_VERSION='4.2.46(1)-release' COMPILER_TAG=intel-2017 CPATH=/shared/ucl/apps/python/bundles/python2-2.0.0/venv/ include:/shared/ucl/apps/openblas/0.2.14/gnu-4.9.2/ include:/shared/ucl/apps/python/2.7.12/gnu-4.9.2/include:/shared/ucl/apps/ intel/2017.Update1/impi/2017.1.132/intel64/include:/shared/ ucl/apps/intel/2017.Update1/compilers_and_libraries_2017. 1.132/linux/daal/include:/shared/ucl/apps/intel/2017. Update1/compilers_and_libraries2017.1.132/linux/ tbb/include:/shared/ucl/apps/intel/2017.Update1/compilers and_libraries_2017.1.132/linux/mkl/include:/shared/ucl/ apps/intel/2017.Update1/compilers_and_libraries_2017. 1.132/linux/ipp/include:/shared/ucl/apps/giflib/5.1.1/ gnu-4.9.2/include:/shared/ucl/apps/apr-util/1.5.4/include:/ shared/ucl/apps/apr/1.5.2/include:/shared/ucl/apps/flex/2.5.39/gnu-4.9.2/include

LOADEDMODULES=gcc-libs/4.9.2:cmake/3.2.1:flex/2.5.39:git/2. 10.2:apr/1.5.2:apr-util/1.5.4:subversion/1.8.13:screen/4.2. 1:gerun:nano/2.4.2:nedit/5.6-aug15:dos2unix/7.3:giflib/5.1. 1:emacs/24.5:tmux/2.2:mrxvt/0.5.4:userscripts/1.3.0:rcps- core/1.0.0:compilers/intel/2017/update1:mpi/intel/2017/ update1/intel:default-modules/2017:python/2.7.12:openblas/0. 2.14/gnu-4.9.2:python2/recommended

If this doesn’t include any particular piece of information please let me know and I will find it for you. For reference I simply used the ‘set’ command to extract this info.

Best wishes

Hywel

From: Ryan Layer [mailto:notifications@github.com] Sent: 13 July 2017 16:06 To: ryanlayer/giggle Cc: Williams, Hywel; Author Subject: Re: [ryanlayer/giggle] gargs command? (#24)

There are 2 issues here:

1. You need bedtools in your path to run the tests. I will update the README to make this clear.
2. There is a problem compiling htslib. What environment are you using (OS version, gcc version etc.)? I want to try and replicate that error. I think the issue is the order in which libraries are linked, but I cannot be sure without testing.

On Thu, Jul 13, 2017 at 8:54 AM, Hywel Williams notifications@github.com

wrote:

Hi Ryan,

I have managed to download all the rme data as described in your giggle examples section. However, when I ran the test (./giggle_tests.sh) I received the following:

[sejjhwi@login08 func]$ ./giggle_tests.sh which: no bedtools in (/home/sejjhwi/.python2local/ bin:/shared/ucl/apps/python/bundles/python2-2.0.0/venv/ bin:/shared/ucl/apps/openblas/0.2.14/gnu-4.9.2/bin:/shared/ ucl/apps/python/2.7.12/gnu-4.9.2/bin:/shared/ucl/apps/ intel-mpi/ucl-wrapper/bin:/shared/ucl/apps/intel/2017. Update1/impi/2017.1.132/intel64/bin:/shared/ucl/apps/ intel/2017.Update1/debugger_2017/gdb/intel64_mic/bin:/ shared/ucl/apps/intel/2017.Update1/compilersand libraries_2017.1.132/linux/mpi/intel64/bin:/shared/ucl/ apps/intel/2017.Update1/compilers_and_libraries_2017. 1.132/linux/bin/intel64:/shared/ucl/sysops/lquota/bin:/ shared/ucl/apps/cluster-bin:/shared/ucl/apps/cluster- scripts:/shared/ucl/apps/mrxvt/0.5.4/bin:/shared/ucl/ apps/tmux/2.2/gnu-4.9.2/bin:/shared/ucl/apps/emacs/24.5/ gnu-4.9.2/bin:/shared/ucl/apps/giflib/5.1.1/gnu-4.9.2/ bin:/shared/ucl/apps/dos2unix/7.3/gnu-4.9.2/bin:/shared/ucl/ apps/NEdit/5.6-Aug15/bin:/shared/ucl/apps/nano/2.4.2/ gnu-4.9.2//bin:/shared/ucl/apps/GERun:/shared/ucl/apps/ screen/4.2.1/bin:/shared/ucl/apps/subversion/1.8.13/bin:/ shared/ucl/apps/apr-util/1.5.4/bin:/shared/ucl/apps/apr/1. 5.2/bin:/shared/ucl/apps/git/2.10.2/gnu-4.9.2/bin:/shared/ ucl/apps/flex/2.5.39/gnu-4.9.2/bin:/shared/ucl/apps/cmake/ 3.2.1/gnu-4.9.2/bin:/shared/ucl/apps/gcc/4.9.2/bin:/opt/ sge/bin:/opt/sge/bin/lx-amd64:/usr/local/bin:/usr/bin:/usr/ local/sbin:/usr/sbin:/home/sejjhwi/bin)

check_chr_v_nochr_search_1 ran in 0 sec with 1/0 lines to STDERR/OUT FAIL "11" != "0" (LINE 55) ./giggle_tests.sh: line 56: ../../bin/giggle: No such file or directory PASS "0" == "0" (LINE 56)

check_chr_v_nochr_search_2 ran in 0 sec with 1/0 lines to STDERR/OUT FAIL "11" != "0" (LINE 55) ./giggle_tests.sh: line 56: ../../bin/giggle: No such file or directory PASS "0" == "0" (LINE 56)

check_chr_v_nochr_search_3 ran in 0 sec with 1/0 lines to STDERR/OUT FAIL "11" != "0" (LINE 55) ./giggle_tests.sh: line 56: ../../bin/giggle: No such file or directory PASS "0" == "0" (LINE 56)

check_chr_v_nochr_search_4 ran in 0 sec with 1/0 lines to STDERR/OUT FAIL "11" != "0" (LINE 55) ./giggle_tests.sh: line 56: ../../bin/giggle: No such file or directory PASS "0" == "0" (LINE 56)

check_chr_v_nochr_search_5 ran in 0 sec with 1/0 lines to STDERR/OUT FAIL "11" != "0" (LINE 55) ./giggle_tests.sh: line 56: ../../bin/giggle: No such file or directory PASS "0" == "0" (LINE 56)

check_chr_v_nochr_search_6 ran in 0 sec with 1/0 lines to STDERR/OUT FAIL "11" != "0" (LINE 55) ./giggle_tests.sh: line 56: ../../bin/giggle: No such file or directory PASS "0" == "0" (LINE 56)

check_chr_v_nochr_search_7 ran in 0 sec with 1/0 lines to STDERR/OUT FAIL "11" != "0" (LINE 55) ./giggle_tests.sh: line 56: ../../bin/giggle: No such file or directory PASS "0" == "0" (LINE 56)

check_chr_v_nochr_search_8 ran in 0 sec with 1/0 lines to STDERR/OUT FAIL "11" != "0" (LINE 55) ./giggle_tests.sh: line 56: ../../bin/giggle: No such file or directory PASS "0" == "0" (LINE 56)

check_chr_v_nochr_search_9 ran in 0 sec with 1/0 lines to STDERR/OUT FAIL "11" != "0" (LINE 55) ./giggle_tests.sh: line 56: ../../bin/giggle: No such file or directory PASS "0" == "0" (LINE 56)

check_chr_v_nochr_search_10 ran in 0 sec with 1/0 lines to STDERR/OUT FAIL "11" != "0" (LINE 55) ./giggle_tests.sh: line 56: ../../bin/giggle: No such file or directory PASS "0" == "0" (LINE 56)

check_bulk_insert ran in 0 sec with 1/0 lines to STDERR/OUT FAIL "23" != "0" (LINE 79) ./giggle_tests.sh: line 80: ../../bin/giggle: No such file or directory PASS "0" == "0" (LINE 80)

check_offset_additional_data ran in 0 sec with 1/0 lines to STDERR/OUT FAIL "72" != "0" (LINE 87) PASS "0" == "0" (LINE 88)

check_dense_index ran in 0 sec with 1/0 lines to STDERR/OUT FAIL EXIT CODE (LINE 102) --> expected EX_OK, observed Unknown code: 127

sshtest v0.1.5

25 Tests 13 Failures 12 Successes

I assume there shouldn’t be any failures? I then ran the next command:

[sejjhwi@login08 func]$ cd ../unit/ [sejjhwi@login08 unit]$ make rm -f test_hash_list test_cache test_bulk_insert test_leaf_data test_genetic_offset_index test_lists test_offset_index test_giggle test_bpt test_disk_store test_ll test_file_read rm -f _Runner.c rm -rf dSYM/

ruby ./unity/auto/generate_test_runner.rb test_hash_list.c

ruby ./unity/generate_test_runner.rb test_hash_list.c gcc -Werror -g -o test_hash_list \ -I./unity \ -I../../src/ \ -I../../lib/htslib/ \ -DTEST ./unity/unity.c \ -DSAMTOOLS=1 \ -pthread \ ../../src/disk_store.c ../../src/cache.c ../../src/giggle_index.c ../../src/lists.c ../../src/util.c ../../src/ll.c ../../src/timer.c ../../src/file_read.c ../../src/bpt.c ../../src/wah.c ../../src/leaf.c ../../src/jsw_avltree.c ../../src/pq.c ../../src/offset_index.c ../../src/fastlz.c \ test_hash_list.c test_hash_list_Runner.c \ ../../lib/htslib//libhts.a \ -lz -lm -lcurl -lcrypto -lssl ../../lib/htslib//libhts.a(bgzf.o): In function bgzf_open': /home/sejjhwi/GIGGLE/giggle/lib/htslib/bgzf.c:290: undefined reference to __intel_sse2_strchr' /home/sejjhwi/GIGGLE/giggle/lib/htslib/bgzf.c:74: undefined reference to `_intel_fast_memset'

There are basically hundreds of lines that give the same error message relating to intel….. I am running my scripts on a HPC cluster and I’m not sure if I need to change any of my settings or download supporting programs to overcome this problem?

Any help will be much appreciated, best wishes

Hywel

From: Ryan Layer [mailto:notifications@github.com] Sent: 12 July 2017 15:05 To: ryanlayer/giggle Cc: Williams, Hywel; Author Subject: Re: [ryanlayer/giggle] gargs command? (#24)

It looks like the gargs download step was the last entry in the "Get source code" section of that examples.

ls *.bed | ../gargs -p 30 "bgzip {}" uses 30 threads to compress bed files.

gargs takes input from STDIN, and for every line maps fields in the line to arguments in a command. In this case ls *bed give a list of bed files, and gargs maps each line to the command bgzip FILE. -p 30 says use up to 30 threads.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/ ryanlayer/giggle/issues/24#issuecomment-314779650, or mute the thread< https://github.com/notifications/unsubscribe-auth/ AMWdj2sR2cpHdudSIPUyh7V9QSAO65TZks5sNNKjgaJpZM4OVct0>.

— You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub https://github.com/ryanlayer/giggle/issues/24#issuecomment-315102542, or mute the thread https://github.com/notifications/unsubscribe-auth/ AAlDUddxEqJLtRHZ8SMp2iO4hEt7gux7ks5sNi-mgaJpZM4OVct0 .

-- Ryan Layer

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/ ryanlayer/giggle/issues/24#issuecomment-315106197, or mute the thread< https://github.com/notifications/unsubscribe-auth/ AMWdj0qM8HdQ49dkebpyk43odFowOWBvks5sNjJSgaJpZM4OVct0>.

— You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub https://github.com/ryanlayer/giggle/issues/24#issuecomment-315109720, or mute the thread https://github.com/notifications/unsubscribe-auth/AAlDUeNhc2D3OWWYaGXtKoQ8Osvb2UGvks5sNjUKgaJpZM4OVct0 .

-- Ryan Layer

[HGENETIC]

I believe it’s GCC but the following (from our computer science wiki page) suggests I may be able to switch?

Set compiler module The Python versions on Legion were built with GCC. You can run them with the default Intel compilers loaded because everything depends on the gcc-libs/4.9.2 module. When you are building your own Python packages you should have the GCC compiler module loaded however, to avoid the situation where you build a package with the Intel compiler and then try to run it with GCC, in which case it will be unable to find Intel-specific instructions. module unload compilers module load compilers/gnu/4.9.2 Would you suggest running this command and trying again?

From: Ryan Layer [mailto:notifications@github.com] Sent: 13 July 2017 16:54 To: ryanlayer/giggle Cc: Williams, Hywel; Author Subject: Re: [ryanlayer/giggle] gargs command? (#24)

Are you using an intel compiler?

On Thu, Jul 13, 2017 at 9:17 AM, Hywel Williams notifications@github.com wrote:

Thanks for the help.

Here is a list of some of my settings: BASH_VERSINFO=([0]="4" [1]="2" [2]="46" [3]="1" [4]="release" [5]="x86_64-redhat-linux-gnu") BASH_VERSION='4.2.46(1)-release' COMPILER_TAG=intel-2017 CPATH=/shared/ucl/apps/python/bundles/python2-2.0.0/venv/ include:/shared/ucl/apps/openblas/0.2.14/gnu-4.9.2/ include:/shared/ucl/apps/python/2.7.12/gnu-4.9.2/include:/shared/ucl/apps/ intel/2017.Update1/impi/2017.1.132/intel64/include:/shared/ ucl/apps/intel/2017.Update1/compilers_and_libraries_2017. 1.132/linux/daal/include:/shared/ucl/apps/intel/2017. Update1/compilers_and_libraries2017.1.132/linux/ tbb/include:/shared/ucl/apps/intel/2017.Update1/compilers and_libraries_2017.1.132/linux/mkl/include:/shared/ucl/ apps/intel/2017.Update1/compilers_and_libraries_2017. 1.132/linux/ipp/include:/shared/ucl/apps/giflib/5.1.1/ gnu-4.9.2/include:/shared/ucl/apps/apr-util/1.5.4/include:/ shared/ucl/apps/apr/1.5.2/include:/shared/ucl/apps/flex/2.5.39/gnu-4.9.2/include

LOADEDMODULES=gcc-libs/4.9.2:cmake/3.2.1:flex/2.5.39:git/2. 10.2:apr/1.5.2:apr-util/1.5.4:subversion/1.8.13:screen/4.2. 1:gerun:nano/2.4.2:nedit/5.6-aug15:dos2unix/7.3:giflib/5.1. 1:emacs/24.5:tmux/2.2:mrxvt/0.5.4:userscripts/1.3.0:rcps- core/1.0.0:compilers/intel/2017/update1:mpi/intel/2017/ update1/intel:default-modules/2017:python/2.7.12:openblas/0. 2.14/gnu-4.9.2:python2/recommended

If this doesn’t include any particular piece of information please let me know and I will find it for you. For reference I simply used the ‘set’ command to extract this info.

Best wishes

Hywel

From: Ryan Layer [mailto:notifications@github.com] Sent: 13 July 2017 16:06 To: ryanlayer/giggle Cc: Williams, Hywel; Author Subject: Re: [ryanlayer/giggle] gargs command? (#24)

There are 2 issues here:

1. You need bedtools in your path to run the tests. I will update the README to make this clear.
2. There is a problem compiling htslib. What environment are you using (OS version, gcc version etc.)? I want to try and replicate that error. I think the issue is the order in which libraries are linked, but I cannot be sure without testing.

On Thu, Jul 13, 2017 at 8:54 AM, Hywel Williams notifications@github.com

wrote:

Hi Ryan,

I have managed to download all the rme data as described in your giggle examples section. However, when I ran the test (./giggle_tests.sh) I received the following:

[sejjhwi@login08 func]$ ./giggle_tests.sh which: no bedtools in (/home/sejjhwi/.python2local/ bin:/shared/ucl/apps/python/bundles/python2-2.0.0/venv/ bin:/shared/ucl/apps/openblas/0.2.14/gnu-4.9.2/bin:/shared/ ucl/apps/python/2.7.12/gnu-4.9.2/bin:/shared/ucl/apps/ intel-mpi/ucl-wrapper/bin:/shared/ucl/apps/intel/2017. Update1/impi/2017.1.132/intel64/bin:/shared/ucl/apps/ intel/2017.Update1/debugger_2017/gdb/intel64_mic/bin:/ shared/ucl/apps/intel/2017.Update1/compilersand libraries_2017.1.132/linux/mpi/intel64/bin:/shared/ucl/ apps/intel/2017.Update1/compilers_and_libraries_2017. 1.132/linux/bin/intel64:/shared/ucl/sysops/lquota/bin:/ shared/ucl/apps/cluster-bin:/shared/ucl/apps/cluster- scripts:/shared/ucl/apps/mrxvt/0.5.4/bin:/shared/ucl/ apps/tmux/2.2/gnu-4.9.2/bin:/shared/ucl/apps/emacs/24.5/ gnu-4.9.2/bin:/shared/ucl/apps/giflib/5.1.1/gnu-4.9.2/ bin:/shared/ucl/apps/dos2unix/7.3/gnu-4.9.2/bin:/shared/ucl/ apps/NEdit/5.6-Aug15/bin:/shared/ucl/apps/nano/2.4.2/ gnu-4.9.2//bin:/shared/ucl/apps/GERun:/shared/ucl/apps/ screen/4.2.1/bin:/shared/ucl/apps/subversion/1.8.13/bin:/ shared/ucl/apps/apr-util/1.5.4/bin:/shared/ucl/apps/apr/1. 5.2/bin:/shared/ucl/apps/git/2.10.2/gnu-4.9.2/bin:/shared/ ucl/apps/flex/2.5.39/gnu-4.9.2/bin:/shared/ucl/apps/cmake/ 3.2.1/gnu-4.9.2/bin:/shared/ucl/apps/gcc/4.9.2/bin:/opt/ sge/bin:/opt/sge/bin/lx-amd64:/usr/local/bin:/usr/bin:/usr/ local/sbin:/usr/sbin:/home/sejjhwi/bin)

check_chr_v_nochr_search_1 ran in 0 sec with 1/0 lines to STDERR/OUT FAIL "11" != "0" (LINE 55) ./giggle_tests.sh: line 56: ../../bin/giggle: No such file or directory PASS "0" == "0" (LINE 56)

check_chr_v_nochr_search_2 ran in 0 sec with 1/0 lines to STDERR/OUT FAIL "11" != "0" (LINE 55) ./giggle_tests.sh: line 56: ../../bin/giggle: No such file or directory PASS "0" == "0" (LINE 56)

check_chr_v_nochr_search_3 ran in 0 sec with 1/0 lines to STDERR/OUT FAIL "11" != "0" (LINE 55) ./giggle_tests.sh: line 56: ../../bin/giggle: No such file or directory PASS "0" == "0" (LINE 56)

check_chr_v_nochr_search_4 ran in 0 sec with 1/0 lines to STDERR/OUT FAIL "11" != "0" (LINE 55) ./giggle_tests.sh: line 56: ../../bin/giggle: No such file or directory PASS "0" == "0" (LINE 56)

check_chr_v_nochr_search_5 ran in 0 sec with 1/0 lines to STDERR/OUT FAIL "11" != "0" (LINE 55) ./giggle_tests.sh: line 56: ../../bin/giggle: No such file or directory PASS "0" == "0" (LINE 56)

check_chr_v_nochr_search_6 ran in 0 sec with 1/0 lines to STDERR/OUT FAIL "11" != "0" (LINE 55) ./giggle_tests.sh: line 56: ../../bin/giggle: No such file or directory PASS "0" == "0" (LINE 56)

check_chr_v_nochr_search_7 ran in 0 sec with 1/0 lines to STDERR/OUT FAIL "11" != "0" (LINE 55) ./giggle_tests.sh: line 56: ../../bin/giggle: No such file or directory PASS "0" == "0" (LINE 56)

check_chr_v_nochr_search_8 ran in 0 sec with 1/0 lines to STDERR/OUT FAIL "11" != "0" (LINE 55) ./giggle_tests.sh: line 56: ../../bin/giggle: No such file or directory PASS "0" == "0" (LINE 56)

check_chr_v_nochr_search_9 ran in 0 sec with 1/0 lines to STDERR/OUT FAIL "11" != "0" (LINE 55) ./giggle_tests.sh: line 56: ../../bin/giggle: No such file or directory PASS "0" == "0" (LINE 56)

check_chr_v_nochr_search_10 ran in 0 sec with 1/0 lines to STDERR/OUT FAIL "11" != "0" (LINE 55) ./giggle_tests.sh: line 56: ../../bin/giggle: No such file or directory PASS "0" == "0" (LINE 56)

check_bulk_insert ran in 0 sec with 1/0 lines to STDERR/OUT FAIL "23" != "0" (LINE 79) ./giggle_tests.sh: line 80: ../../bin/giggle: No such file or directory PASS "0" == "0" (LINE 80)

check_offset_additional_data ran in 0 sec with 1/0 lines to STDERR/OUT FAIL "72" != "0" (LINE 87) PASS "0" == "0" (LINE 88)

check_dense_index ran in 0 sec with 1/0 lines to STDERR/OUT FAIL EXIT CODE (LINE 102) --> expected EX_OK, observed Unknown code: 127

sshtest v0.1.5

25 Tests 13 Failures 12 Successes

I assume there shouldn’t be any failures? I then ran the next command:

[sejjhwi@login08 func]$ cd ../unit/ [sejjhwi@login08 unit]$ make rm -f test_hash_list test_cache test_bulk_insert test_leaf_data test_genetic_offset_index test_lists test_offset_index test_giggle test_bpt test_disk_store test_ll test_file_read rm -f _Runner.c rm -rf dSYM/

ruby ./unity/auto/generate_test_runner.rb test_hash_list.c

ruby ./unity/generate_test_runner.rb test_hash_list.c gcc -Werror -g -o test_hash_list \ -I./unity \ -I../../src/ \ -I../../lib/htslib/ \ -DTEST ./unity/unity.c \ -DSAMTOOLS=1 \ -pthread \ ../../src/disk_store.c ../../src/cache.c ../../src/giggle_index.c ../../src/lists.c ../../src/util.c ../../src/ll.c ../../src/timer.c ../../src/file_read.c ../../src/bpt.c ../../src/wah.c ../../src/leaf.c ../../src/jsw_avltree.c ../../src/pq.c ../../src/offset_index.c ../../src/fastlz.c \ test_hash_list.c test_hash_list_Runner.c \ ../../lib/htslib//libhts.a \ -lz -lm -lcurl -lcrypto -lssl ../../lib/htslib//libhts.a(bgzf.o): In function bgzf_open': /home/sejjhwi/GIGGLE/giggle/lib/htslib/bgzf.c:290: undefined reference to __intel_sse2_strchr' /home/sejjhwi/GIGGLE/giggle/lib/htslib/bgzf.c:74: undefined reference to `_intel_fast_memset'

There are basically hundreds of lines that give the same error message relating to intel….. I am running my scripts on a HPC cluster and I’m not sure if I need to change any of my settings or download supporting programs to overcome this problem?

Any help will be much appreciated, best wishes

Hywel

From: Ryan Layer [mailto:notifications@github.com] Sent: 12 July 2017 15:05 To: ryanlayer/giggle Cc: Williams, Hywel; Author Subject: Re: [ryanlayer/giggle] gargs command? (#24)

It looks like the gargs download step was the last entry in the "Get source code" section of that examples.

ls *.bed | ../gargs -p 30 "bgzip {}" uses 30 threads to compress bed files.

gargs takes input from STDIN, and for every line maps fields in the line to arguments in a command. In this case ls *bed give a list of bed files, and gargs maps each line to the command bgzip FILE. -p 30 says use up to 30 threads.

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[ryanlayer]

Yes, please. Completely remove the giggle folder, re-clone, run

module unload compilers module load compilers/gnu/4.9.2

, and then make.

On Thu, Jul 13, 2017 at 10:00 AM, Hywel Williams notifications@github.com wrote:

I believe it’s GCC but the following (from our computer science wiki page) suggests I may be able to switch?

Set compiler module The Python versions on Legion were built with GCC. You can run them with the default Intel compilers loaded because everything depends on the gcc-libs/4.9.2 module. When you are building your own Python packages you should have the GCC compiler module loaded however, to avoid the situation where you build a package with the Intel compiler and then try to run it with GCC, in which case it will be unable to find Intel-specific instructions. module unload compilers module load compilers/gnu/4.9.2 Would you suggest running this command and trying again?

From: Ryan Layer [mailto:notifications@github.com] Sent: 13 July 2017 16:54 To: ryanlayer/giggle Cc: Williams, Hywel; Author Subject: Re: [ryanlayer/giggle] gargs command? (#24)

Are you using an intel compiler?

On Thu, Jul 13, 2017 at 9:17 AM, Hywel Williams notifications@github.com

wrote:

Thanks for the help.

Here is a list of some of my settings: BASH_VERSINFO=([0]="4" [1]="2" [2]="46" [3]="1" [4]="release" [5]="x86_64-redhat-linux-gnu") BASH_VERSION='4.2.46(1)-release' COMPILER_TAG=intel-2017 CPATH=/shared/ucl/apps/python/bundles/python2-2.0.0/venv/ include:/shared/ucl/apps/openblas/0.2.14/gnu-4.9.2/ include:/shared/ucl/apps/python/2.7.12/gnu-4.9.2/include:/shared/ucl/apps/

intel/2017.Update1/impi/2017.1.132/intel64/include:/shared/ ucl/apps/intel/2017.Update1/compilers_and_libraries_2017. 1.132/linux/daal/include:/shared/ucl/apps/intel/2017. Update1/compilers_and_libraries2017.1.132/linux/ tbb/include:/shared/ucl/apps/intel/2017.Update1/compilers and_libraries_2017.1.132/linux/mkl/include:/shared/ucl/ apps/intel/2017.Update1/compilers_and_libraries_2017. 1.132/linux/ipp/include:/shared/ucl/apps/giflib/5.1.1/ gnu-4.9.2/include:/shared/ucl/apps/apr-util/1.5.4/include:/ shared/ucl/apps/apr/1.5.2/include:/shared/ucl/apps/flex/2.5.39/gnu-4.9.2/include

LOADEDMODULES=gcc-libs/4.9.2:cmake/3.2.1:flex/2.5.39:git/2. 10.2:apr/1.5.2:apr-util/1.5.4:subversion/1.8.13:screen/4.2. 1:gerun:nano/2.4.2:nedit/5.6-aug15:dos2unix/7.3:giflib/5.1. 1:emacs/24.5:tmux/2.2:mrxvt/0.5.4:userscripts/1.3.0:rcps- core/1.0.0:compilers/intel/2017/update1:mpi/intel/2017/ update1/intel:default-modules/2017:python/2.7.12:openblas/0. 2.14/gnu-4.9.2:python2/recommended

If this doesn’t include any particular piece of information please let me know and I will find it for you. For reference I simply used the ‘set’ command to extract this info.

Best wishes

Hywel

From: Ryan Layer [mailto:notifications@github.com] Sent: 13 July 2017 16:06 To: ryanlayer/giggle Cc: Williams, Hywel; Author Subject: Re: [ryanlayer/giggle] gargs command? (#24)

There are 2 issues here:

1. You need bedtools in your path to run the tests. I will update the README to make this clear.
2. There is a problem compiling htslib. What environment are you using (OS version, gcc version etc.)? I want to try and replicate that error. I think the issue is the order in which libraries are linked, but I cannot be sure without testing.

On Thu, Jul 13, 2017 at 8:54 AM, Hywel Williams < notifications@github.com>

wrote:

Hi Ryan,

I have managed to download all the rme data as described in your giggle examples section. However, when I ran the test (./giggle_tests.sh) I received the following:

[sejjhwi@login08 func]$ ./giggle_tests.sh which: no bedtools in (/home/sejjhwi/.python2local/ bin:/shared/ucl/apps/python/bundles/python2-2.0.0/venv/ bin:/shared/ucl/apps/openblas/0.2.14/gnu-4.9.2/bin:/shared/ ucl/apps/python/2.7.12/gnu-4.9.2/bin:/shared/ucl/apps/ intel-mpi/ucl-wrapper/bin:/shared/ucl/apps/intel/2017. Update1/impi/2017.1.132/intel64/bin:/shared/ucl/apps/ intel/2017.Update1/debugger_2017/gdb/intel64_mic/bin:/ shared/ucl/apps/intel/2017.Update1/compilersand libraries_2017.1.132/linux/mpi/intel64/bin:/shared/ucl/ apps/intel/2017.Update1/compilers_and_libraries_2017. 1.132/linux/bin/intel64:/shared/ucl/sysops/lquota/bin:/ shared/ucl/apps/cluster-bin:/shared/ucl/apps/cluster- scripts:/shared/ucl/apps/mrxvt/0.5.4/bin:/shared/ucl/ apps/tmux/2.2/gnu-4.9.2/bin:/shared/ucl/apps/emacs/24.5/ gnu-4.9.2/bin:/shared/ucl/apps/giflib/5.1.1/gnu-4.9.2/ bin:/shared/ucl/apps/dos2unix/7.3/gnu-4.9.2/bin:/shared/ucl/ apps/NEdit/5.6-Aug15/bin:/shared/ucl/apps/nano/2.4.2/ gnu-4.9.2//bin:/shared/ucl/apps/GERun:/shared/ucl/apps/ screen/4.2.1/bin:/shared/ucl/apps/subversion/1.8.13/bin:/ shared/ucl/apps/apr-util/1.5.4/bin:/shared/ucl/apps/apr/1. 5.2/bin:/shared/ucl/apps/git/2.10.2/gnu-4.9.2/bin:/shared/ ucl/apps/flex/2.5.39/gnu-4.9.2/bin:/shared/ucl/apps/cmake/ 3.2.1/gnu-4.9.2/bin:/shared/ucl/apps/gcc/4.9.2/bin:/opt/ sge/bin:/opt/sge/bin/lx-amd64:/usr/local/bin:/usr/bin:/usr/ local/sbin:/usr/sbin:/home/sejjhwi/bin)

check_chr_v_nochr_search_1 ran in 0 sec with 1/0 lines to STDERR/OUT FAIL "11" != "0" (LINE 55) ./giggle_tests.sh: line 56: ../../bin/giggle: No such file or directory PASS "0" == "0" (LINE 56)

check_chr_v_nochr_search_2 ran in 0 sec with 1/0 lines to STDERR/OUT FAIL "11" != "0" (LINE 55) ./giggle_tests.sh: line 56: ../../bin/giggle: No such file or directory PASS "0" == "0" (LINE 56)

check_chr_v_nochr_search_3 ran in 0 sec with 1/0 lines to STDERR/OUT FAIL "11" != "0" (LINE 55) ./giggle_tests.sh: line 56: ../../bin/giggle: No such file or directory PASS "0" == "0" (LINE 56)

check_chr_v_nochr_search_4 ran in 0 sec with 1/0 lines to STDERR/OUT FAIL "11" != "0" (LINE 55) ./giggle_tests.sh: line 56: ../../bin/giggle: No such file or directory PASS "0" == "0" (LINE 56)

check_chr_v_nochr_search_5 ran in 0 sec with 1/0 lines to STDERR/OUT FAIL "11" != "0" (LINE 55) ./giggle_tests.sh: line 56: ../../bin/giggle: No such file or directory PASS "0" == "0" (LINE 56)

check_chr_v_nochr_search_6 ran in 0 sec with 1/0 lines to STDERR/OUT FAIL "11" != "0" (LINE 55) ./giggle_tests.sh: line 56: ../../bin/giggle: No such file or directory PASS "0" == "0" (LINE 56)

check_chr_v_nochr_search_7 ran in 0 sec with 1/0 lines to STDERR/OUT FAIL "11" != "0" (LINE 55) ./giggle_tests.sh: line 56: ../../bin/giggle: No such file or directory PASS "0" == "0" (LINE 56)

check_chr_v_nochr_search_8 ran in 0 sec with 1/0 lines to STDERR/OUT FAIL "11" != "0" (LINE 55) ./giggle_tests.sh: line 56: ../../bin/giggle: No such file or directory PASS "0" == "0" (LINE 56)

check_chr_v_nochr_search_9 ran in 0 sec with 1/0 lines to STDERR/OUT FAIL "11" != "0" (LINE 55) ./giggle_tests.sh: line 56: ../../bin/giggle: No such file or directory PASS "0" == "0" (LINE 56)

check_chr_v_nochr_search_10 ran in 0 sec with 1/0 lines to STDERR/OUT FAIL "11" != "0" (LINE 55) ./giggle_tests.sh: line 56: ../../bin/giggle: No such file or directory PASS "0" == "0" (LINE 56)

check_bulk_insert ran in 0 sec with 1/0 lines to STDERR/OUT FAIL "23" != "0" (LINE 79) ./giggle_tests.sh: line 80: ../../bin/giggle: No such file or directory PASS "0" == "0" (LINE 80)

check_offset_additional_data ran in 0 sec with 1/0 lines to STDERR/OUT FAIL "72" != "0" (LINE 87) PASS "0" == "0" (LINE 88)

check_dense_index ran in 0 sec with 1/0 lines to STDERR/OUT FAIL EXIT CODE (LINE 102) --> expected EX_OK, observed Unknown code: 127

sshtest v0.1.5

25 Tests 13 Failures 12 Successes

I assume there shouldn’t be any failures? I then ran the next command:

[sejjhwi@login08 func]$ cd ../unit/ [sejjhwi@login08 unit]$ make rm -f test_hash_list test_cache test_bulk_insert test_leaf_data test_genetic_offset_index test_lists test_offset_index test_giggle test_bpt test_disk_store test_ll test_file_read rm -f _Runner.c rm -rf dSYM/

ruby ./unity/auto/generate_test_runner.rb test_hash_list.c

ruby ./unity/generate_test_runner.rb test_hash_list.c gcc -Werror -g -o test_hash_list \ -I./unity \ -I../../src/ \ -I../../lib/htslib/ \ -DTEST ./unity/unity.c \ -DSAMTOOLS=1 \ -pthread \ ../../src/disk_store.c ../../src/cache.c ../../src/giggle_index.c ../../src/lists.c ../../src/util.c ../../src/ll.c ../../src/timer.c ../../src/file_read.c ../../src/bpt.c ../../src/wah.c ../../src/leaf.c ../../src/jsw_avltree.c ../../src/pq.c ../../src/offset_index.c ../../src/fastlz.c \ test_hash_list.c test_hash_list_Runner.c \ ../../lib/htslib//libhts.a \ -lz -lm -lcurl -lcrypto -lssl ../../lib/htslib//libhts.a(bgzf.o): In function bgzf_open': /home/sejjhwi/GIGGLE/giggle/lib/htslib/bgzf.c:290: undefined reference to __intel_sse2_strchr' /home/sejjhwi/GIGGLE/giggle/lib/htslib/bgzf.c:74: undefined reference to `_intel_fast_memset'

There are basically hundreds of lines that give the same error message relating to intel….. I am running my scripts on a HPC cluster and I’m not sure if I need to change any of my settings or download supporting programs to overcome this problem?

Any help will be much appreciated, best wishes

Hywel

From: Ryan Layer [mailto:notifications@github.com] Sent: 12 July 2017 15:05 To: ryanlayer/giggle Cc: Williams, Hywel; Author Subject: Re: [ryanlayer/giggle] gargs command? (#24)

It looks like the gargs download step was the last entry in the "Get source code" section of that examples.

ls *.bed | ../gargs -p 30 "bgzip {}" uses 30 threads to compress bed files.

gargs takes input from STDIN, and for every line maps fields in the line to arguments in a command. In this case ls *bed give a list of bed files, and gargs maps each line to the command bgzip FILE. -p 30 says use up to 30 threads.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/ ryanlayer/giggle/issues/24#issuecomment-314779650, or mute the thread< https://github.com/notifications/unsubscribe-auth/ AMWdj2sR2cpHdudSIPUyh7V9QSAO65TZks5sNNKjgaJpZM4OVct0>.

— You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub https://github.com/ryanlayer/giggle/issues/24#issuecomment-315102542,

or mute the thread https://github.com/notifications/unsubscribe-auth/ AAlDUddxEqJLtRHZ8SMp2iO4hEt7gux7ks5sNi-mgaJpZM4OVct0 .

-- Ryan Layer

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-- Ryan Layer

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-- Ryan Layer

[HGENETIC]

Dear Ryan,

Many thanks for your help so far, I have today just run my first query so I know the software is up and running which is fantastic. However, in my results file the data is in the format:

[cid:image001.png@01D30226.12E4BE70]

And there is no related P-value with any of the results. I have looked in your readme files but I cant decipher the code that calculates the p-value for each genomic interval, could you please direct me to the correct location.

Many thanks again for your help

Hywel

From: Ryan Layer [mailto:notifications@github.com] Sent: 12 July 2017 15:05 To: ryanlayer/giggle Cc: Williams, Hywel; Author Subject: Re: [ryanlayer/giggle] gargs command? (#24)

It looks like the gargs download step was the last entry in the "Get source code" section of that examples.

ls *.bed | ../gargs -p 30 "bgzip {}" uses 30 threads to compress bed files.

gargs takes input from STDIN, and for every line maps fields in the line to arguments in a command. In this case ls *bed give a list of bed files, and gargs maps each line to the command bgzip FILE. -p 30 says use up to 30 threads.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/ryanlayer/giggle/issues/24#issuecomment-314779650, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AMWdj2sR2cpHdudSIPUyh7V9QSAO65TZks5sNNKjgaJpZM4OVct0.

[ryanlayer]

That image didn't come through, but I bet you need to add the "-s" stats option. I will update the readme with that info. Thanks.

On Fri, Jul 21, 2017 at 6:34 AM, Hywel Williams notifications@github.com wrote:

Dear Ryan,

Many thanks for your help so far, I have today just run my first query so I know the software is up and running which is fantastic. However, in my results file the data is in the format:

[cid:image001.png@01D30226.12E4BE70]

And there is no related P-value with any of the results. I have looked in your readme files but I cant decipher the code that calculates the p-value for each genomic interval, could you please direct me to the correct location.

Many thanks again for your help

Hywel

From: Ryan Layer [mailto:notifications@github.com] Sent: 12 July 2017 15:05 To: ryanlayer/giggle Cc: Williams, Hywel; Author Subject: Re: [ryanlayer/giggle] gargs command? (#24)

It looks like the gargs download step was the last entry in the "Get source code" section of that examples.

ls *.bed | ../gargs -p 30 "bgzip {}" uses 30 threads to compress bed files.

gargs takes input from STDIN, and for every line maps fields in the line to arguments in a command. In this case ls *bed give a list of bed files, and gargs maps each line to the command bgzip FILE. -p 30 says use up to 30 threads.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/ ryanlayer/giggle/issues/24#issuecomment-314779650, or mute the thread< https://github.com/notifications/unsubscribe-auth/ AMWdj2sR2cpHdudSIPUyh7V9QSAO65TZks5sNNKjgaJpZM4OVct0>.

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-- Ryan Layer

[HGENETIC]

Yes that does sound like the solution, thanks again.

Sent from my iPhone

On 21 Jul 2017, at 14:31, Ryan Layer notifications@github.com<mailto:notifications@github.com> wrote:

That image didn't come through, but I bet you need to add the "-s" stats option. I will update the readme with that info. Thanks.

On Fri, Jul 21, 2017 at 6:34 AM, Hywel Williams notifications@github.com<mailto:notifications@github.com> wrote:

Dear Ryan,

Many thanks for your help so far, I have today just run my first query so I know the software is up and running which is fantastic. However, in my results file the data is in the format:

[cid:image001.png@01D30226.12E4BE70]

And there is no related P-value with any of the results. I have looked in your readme files but I cant decipher the code that calculates the p-value for each genomic interval, could you please direct me to the correct location.

Many thanks again for your help

Hywel

From: Ryan Layer [mailto:notifications@github.com] Sent: 12 July 2017 15:05 To: ryanlayer/giggle Cc: Williams, Hywel; Author Subject: Re: [ryanlayer/giggle] gargs command? (#24)

It looks like the gargs download step was the last entry in the "Get source code" section of that examples.

ls *.bed | ../gargs -p 30 "bgzip {}" uses 30 threads to compress bed files.

gargs takes input from STDIN, and for every line maps fields in the line to arguments in a command. In this case ls *bed give a list of bed files, and gargs maps each line to the command bgzip FILE. -p 30 says use up to 30 threads.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/ ryanlayer/giggle/issues/24#issuecomment-314779650, or mute the thread< https://github.com/notifications/unsubscribe-auth/ AMWdj2sR2cpHdudSIPUyh7V9QSAO65TZks5sNNKjgaJpZM4OVct0>.

— You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub https://github.com/ryanlayer/giggle/issues/24#issuecomment-316989270, or mute the thread https://github.com/notifications/unsubscribe-auth/AAlDUYK7qs7QmKMyPGFEWhr7lF0iFPyyks5sQJrcgaJpZM4OVct0 .

-- Ryan Layer

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/ryanlayer/giggle/issues/24#issuecomment-317001558, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AMWdjxWkxDSYn07NDjczsOnVmwmNT9KEks5sQKhDgaJpZM4OVct0.

[ryanlayer]

Great. Please let me know of any bugs you find or features that would be helpful.

On Fri, Jul 21, 2017 at 7:52 AM, Hywel Williams notifications@github.com wrote:

Yes that does sound like the solution, thanks again.

Sent from my iPhone

On 21 Jul 2017, at 14:31, Ryan Layer <notifications@github.com<mailto: notifications@github.com>> wrote:

That image didn't come through, but I bet you need to add the "-s" stats option. I will update the readme with that info. Thanks.

On Fri, Jul 21, 2017 at 6:34 AM, Hywel Williams <notifications@github.com< mailto:notifications@github.com>> wrote:

Dear Ryan,

Many thanks for your help so far, I have today just run my first query so I know the software is up and running which is fantastic. However, in my results file the data is in the format:

[cid:image001.png@01D30226.12E4BE70]

And there is no related P-value with any of the results. I have looked in your readme files but I cant decipher the code that calculates the p-value for each genomic interval, could you please direct me to the correct location.

Many thanks again for your help

Hywel

From: Ryan Layer [mailto:notifications@github.com] Sent: 12 July 2017 15:05 To: ryanlayer/giggle Cc: Williams, Hywel; Author Subject: Re: [ryanlayer/giggle] gargs command? (#24)

It looks like the gargs download step was the last entry in the "Get source code" section of that examples.

ls *.bed | ../gargs -p 30 "bgzip {}" uses 30 threads to compress bed files.

gargs takes input from STDIN, and for every line maps fields in the line to arguments in a command. In this case ls *bed give a list of bed files, and gargs maps each line to the command bgzip FILE. -p 30 says use up to 30 threads.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/ ryanlayer/giggle/issues/24#issuecomment-314779650, or mute the thread< https://github.com/notifications/unsubscribe-auth/ AMWdj2sR2cpHdudSIPUyh7V9QSAO65TZks5sNNKjgaJpZM4OVct0>.

— You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub https://github.com/ryanlayer/giggle/issues/24#issuecomment-316989270, or mute the thread https://github.com/notifications/unsubscribe-auth/ AAlDUYK7qs7QmKMyPGFEWhr7lF0iFPyyks5sQJrcgaJpZM4OVct0 .

-- Ryan Layer

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/ ryanlayer/giggle/issues/24#issuecomment-317001558, or mute the thread< https://github.com/notifications/unsubscribe-auth/ AMWdjxWkxDSYn07NDjczsOnVmwmNT9KEks5sQKhDgaJpZM4OVct0>.

— You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub https://github.com/ryanlayer/giggle/issues/24#issuecomment-317006771, or mute the thread https://github.com/notifications/unsubscribe-auth/AAlDUQp6vZGFjkaz1fJ3A7WU8mOGqUktks5sQK0cgaJpZM4OVct0 .

-- Ryan Layer

[HGENETIC]

Hi Ryan,

I have successfully run the giggle search through the rme dataset and am trying to interpret the data as I have a very large number of significant results that I need to prioritise. However, I thought I’d also like to repeat my analyses through some of the other datasets you highlight in the paper and so have started on the fantom data. I have downloaded the dataset with no problems but when I get to this line of the script:

$GIGGLE_ROOT/scripts/sort_bed "split/*" split_sort/

I keep getting the following error message:

bash: line 5: split_sort//xeroderma_pigentosum_b_cell_line-XPL_17.bed.gz: No such file or directory

which is repeated for every bed file in that directory. Do you have an idea as to what is causing this error?

Thanks

Hywel

From: Ryan Layer [mailto:notifications@github.com] Sent: 21 July 2017 14:53 To: ryanlayer/giggle Cc: Williams, Hywel; Author Subject: Re: [ryanlayer/giggle] gargs command? (#24)

Great. Please let me know of any bugs you find or features that would be helpful.

On Fri, Jul 21, 2017 at 7:52 AM, Hywel Williams notifications@github.com wrote:

Yes that does sound like the solution, thanks again.

Sent from my iPhone

On 21 Jul 2017, at 14:31, Ryan Layer <notifications@github.com<mailto: notifications@github.com>> wrote:

That image didn't come through, but I bet you need to add the "-s" stats option. I will update the readme with that info. Thanks.

On Fri, Jul 21, 2017 at 6:34 AM, Hywel Williams <notifications@github.com< mailto:notifications@github.com>> wrote:

Dear Ryan,

Many thanks for your help so far, I have today just run my first query so I know the software is up and running which is fantastic. However, in my results file the data is in the format:

[cid:image001.png@01D30226.12E4BE70]

And there is no related P-value with any of the results. I have looked in your readme files but I cant decipher the code that calculates the p-value for each genomic interval, could you please direct me to the correct location.

Many thanks again for your help

Hywel

From: Ryan Layer [mailto:notifications@github.com] Sent: 12 July 2017 15:05 To: ryanlayer/giggle Cc: Williams, Hywel; Author Subject: Re: [ryanlayer/giggle] gargs command? (#24)

It looks like the gargs download step was the last entry in the "Get source code" section of that examples.

ls *.bed | ../gargs -p 30 "bgzip {}" uses 30 threads to compress bed files.

gargs takes input from STDIN, and for every line maps fields in the line to arguments in a command. In this case ls *bed give a list of bed files, and gargs maps each line to the command bgzip FILE. -p 30 says use up to 30 threads.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/ ryanlayer/giggle/issues/24#issuecomment-314779650, or mute the thread< https://github.com/notifications/unsubscribe-auth/ AMWdj2sR2cpHdudSIPUyh7V9QSAO65TZks5sNNKjgaJpZM4OVct0>.

— You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub https://github.com/ryanlayer/giggle/issues/24#issuecomment-316989270, or mute the thread https://github.com/notifications/unsubscribe-auth/ AAlDUYK7qs7QmKMyPGFEWhr7lF0iFPyyks5sQJrcgaJpZM4OVct0 .

-- Ryan Layer

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/ ryanlayer/giggle/issues/24#issuecomment-317001558, or mute the thread< https://github.com/notifications/unsubscribe-auth/ AMWdjxWkxDSYn07NDjczsOnVmwmNT9KEks5sQKhDgaJpZM4OVct0>.

— You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub https://github.com/ryanlayer/giggle/issues/24#issuecomment-317006771, or mute the thread https://github.com/notifications/unsubscribe-auth/AAlDUQp6vZGFjkaz1fJ3A7WU8mOGqUktks5sQK0cgaJpZM4OVct0 .

-- Ryan Layer

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/ryanlayer/giggle/issues/24#issuecomment-317007005, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AMWdj7HdvrfRzcHVOYrd-y2bDrpFWHpGks5sQK1OgaJpZM4OVct0.

[ryanlayer]

Did you create the directory split_sort?

On Jul 27, 2017, at 2:31 AM, Hywel Williams notifications@github.com wrote:

Hi Ryan,

I have successfully run the giggle search through the rme dataset and am trying to interpret the data as I have a very large number of significant results that I need to prioritise. However, I thought I’d also like to repeat my analyses through some of the other datasets you highlight in the paper and so have started on the fantom data. I have downloaded the dataset with no problems but when I get to this line of the script:

$GIGGLE_ROOT/scripts/sort_bed "split/*" split_sort/

I keep getting the following error message:

bash: line 5: split_sort//xeroderma_pigentosum_b_cell_line-XPL_17.bed.gz: No such file or directory

which is repeated for every bed file in that directory. Do you have an idea as to what is causing this error?

Thanks

Hywel

From: Ryan Layer [mailto:notifications@github.com] Sent: 21 July 2017 14:53 To: ryanlayer/giggle Cc: Williams, Hywel; Author Subject: Re: [ryanlayer/giggle] gargs command? (#24)

Great. Please let me know of any bugs you find or features that would be helpful.

On Fri, Jul 21, 2017 at 7:52 AM, Hywel Williams notifications@github.com wrote:

Yes that does sound like the solution, thanks again.

Sent from my iPhone

On 21 Jul 2017, at 14:31, Ryan Layer <notifications@github.com<mailto: notifications@github.com>> wrote:

That image didn't come through, but I bet you need to add the "-s" stats option. I will update the readme with that info. Thanks.

On Fri, Jul 21, 2017 at 6:34 AM, Hywel Williams <notifications@github.com< mailto:notifications@github.com>> wrote:

Dear Ryan,

Many thanks for your help so far, I have today just run my first query so I know the software is up and running which is fantastic. However, in my results file the data is in the format:

[cid:image001.png@01D30226.12E4BE70]

And there is no related P-value with any of the results. I have looked in your readme files but I cant decipher the code that calculates the p-value for each genomic interval, could you please direct me to the correct location.

Many thanks again for your help

Hywel

From: Ryan Layer [mailto:notifications@github.com] Sent: 12 July 2017 15:05 To: ryanlayer/giggle Cc: Williams, Hywel; Author Subject: Re: [ryanlayer/giggle] gargs command? (#24)

It looks like the gargs download step was the last entry in the "Get source code" section of that examples.

ls *.bed | ../gargs -p 30 "bgzip {}" uses 30 threads to compress bed files.

gargs takes input from STDIN, and for every line maps fields in the line to arguments in a command. In this case ls *bed give a list of bed files, and gargs maps each line to the command bgzip FILE. -p 30 says use up to 30 threads.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<https://github.com/ ryanlayer/giggle/issues/24#issuecomment-314779650>, or mute the thread< https://github.com/notifications/unsubscribe-auth/ AMWdj2sR2cpHdudSIPUyh7V9QSAO65TZks5sNNKjgaJpZM4OVct0>.

— You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub https://github.com/ryanlayer/giggle/issues/24#issuecomment-316989270, or mute the thread <https://github.com/notifications/unsubscribe-auth/ AAlDUYK7qs7QmKMyPGFEWhr7lF0iFPyyks5sQJrcgaJpZM4OVct0> .

-- Ryan Layer

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<https://github.com/ ryanlayer/giggle/issues/24#issuecomment-317001558>, or mute the thread< https://github.com/notifications/unsubscribe-auth/ AMWdjxWkxDSYn07NDjczsOnVmwmNT9KEks5sQKhDgaJpZM4OVct0>.

— You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub https://github.com/ryanlayer/giggle/issues/24#issuecomment-317006771, or mute the thread https://github.com/notifications/unsubscribe-auth/AAlDUQp6vZGFjkaz1fJ3A7WU8mOGqUktks5sQK0cgaJpZM4OVct0 .

-- Ryan Layer

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/ryanlayer/giggle/issues/24#issuecomment-317007005, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AMWdj7HdvrfRzcHVOYrd-y2bDrpFWHpGks5sQK1OgaJpZM4OVct0. — You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub, or mute the thread.

[HGENETIC]

The directory was made but it was empty. I think the problem was that the bgzip command isn’t in my root path and so I had to edit the sort_bed script which was causing me a number of problems but is now resolved and the data has just been indexed!

Thanks

Hywel

From: Ryan Layer [mailto:notifications@github.com] Sent: 27 July 2017 14:25 To: ryanlayer/giggle Cc: Williams, Hywel; Author Subject: Re: [ryanlayer/giggle] gargs command? (#24)

Did you create the directory split_sort?

On Jul 27, 2017, at 2:31 AM, Hywel Williams notifications@github.com wrote:

Hi Ryan,

I have successfully run the giggle search through the rme dataset and am trying to interpret the data as I have a very large number of significant results that I need to prioritise. However, I thought I’d also like to repeat my analyses through some of the other datasets you highlight in the paper and so have started on the fantom data. I have downloaded the dataset with no problems but when I get to this line of the script:

$GIGGLE_ROOT/scripts/sort_bed "split/*" split_sort/

I keep getting the following error message:

bash: line 5: split_sort//xeroderma_pigentosum_b_cell_line-XPL_17.bed.gz: No such file or directory

which is repeated for every bed file in that directory. Do you have an idea as to what is causing this error?

Thanks

Hywel

From: Ryan Layer [mailto:notifications@github.com] Sent: 21 July 2017 14:53 To: ryanlayer/giggle Cc: Williams, Hywel; Author Subject: Re: [ryanlayer/giggle] gargs command? (#24)

Great. Please let me know of any bugs you find or features that would be helpful.

On Fri, Jul 21, 2017 at 7:52 AM, Hywel Williams notifications@github.com wrote:

Yes that does sound like the solution, thanks again.

Sent from my iPhone

On 21 Jul 2017, at 14:31, Ryan Layer <notifications@github.com<mailto: notifications@github.com>> wrote:

That image didn't come through, but I bet you need to add the "-s" stats option. I will update the readme with that info. Thanks.

On Fri, Jul 21, 2017 at 6:34 AM, Hywel Williams <notifications@github.com< mailto:notifications@github.com>> wrote:

Dear Ryan,

Many thanks for your help so far, I have today just run my first query so I know the software is up and running which is fantastic. However, in my results file the data is in the format:

[cid:image001.png@01D30226.12E4BE70]

And there is no related P-value with any of the results. I have looked in your readme files but I cant decipher the code that calculates the p-value for each genomic interval, could you please direct me to the correct location.

Many thanks again for your help

Hywel

From: Ryan Layer [mailto:notifications@github.com] Sent: 12 July 2017 15:05 To: ryanlayer/giggle Cc: Williams, Hywel; Author Subject: Re: [ryanlayer/giggle] gargs command? (#24)

It looks like the gargs download step was the last entry in the "Get source code" section of that examples.

ls *.bed | ../gargs -p 30 "bgzip {}" uses 30 threads to compress bed files.

gargs takes input from STDIN, and for every line maps fields in the line to arguments in a command. In this case ls *bed give a list of bed files, and gargs maps each line to the command bgzip FILE. -p 30 says use up to 30 threads.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/ ryanlayer/giggle/issues/24#issuecomment-314779650, or mute the thread< https://github.com/notifications/unsubscribe-auth/ AMWdj2sR2cpHdudSIPUyh7V9QSAO65TZks5sNNKjgaJpZM4OVct0>.

— You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub https://github.com/ryanlayer/giggle/issues/24#issuecomment-316989270, or mute the thread https://github.com/notifications/unsubscribe-auth/ AAlDUYK7qs7QmKMyPGFEWhr7lF0iFPyyks5sQJrcgaJpZM4OVct0 .

-- Ryan Layer

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/ ryanlayer/giggle/issues/24#issuecomment-317001558, or mute the thread< https://github.com/notifications/unsubscribe-auth/ AMWdjxWkxDSYn07NDjczsOnVmwmNT9KEks5sQKhDgaJpZM4OVct0>.

— You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub https://github.com/ryanlayer/giggle/issues/24#issuecomment-317006771, or mute the thread https://github.com/notifications/unsubscribe-auth/AAlDUQp6vZGFjkaz1fJ3A7WU8mOGqUktks5sQK0cgaJpZM4OVct0 .

-- Ryan Layer

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/ryanlayer/giggle/issues/24#issuecomment-317007005, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AMWdj7HdvrfRzcHVOYrd-y2bDrpFWHpGks5sQK1OgaJpZM4OVct0. — You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub, or mute the thread.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/ryanlayer/giggle/issues/24#issuecomment-318360830, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AMWdj6JguiodPoc8E31Rlb8D5Pvcu_Mtks5sSI-hgaJpZM4OVct0.

[ryanlayer]

Great. Let me know if there are any other issues.

On Thu, Jul 27, 2017 at 8:18 AM, Hywel Williams notifications@github.com wrote:

The directory was made but it was empty. I think the problem was that the bgzip command isn’t in my root path and so I had to edit the sort_bed script which was causing me a number of problems but is now resolved and the data has just been indexed!

Thanks

Hywel

From: Ryan Layer [mailto:notifications@github.com] Sent: 27 July 2017 14:25 To: ryanlayer/giggle Cc: Williams, Hywel; Author Subject: Re: [ryanlayer/giggle] gargs command? (#24)

Did you create the directory split_sort?

On Jul 27, 2017, at 2:31 AM, Hywel Williams notifications@github.com wrote:

Hi Ryan,

I have successfully run the giggle search through the rme dataset and am trying to interpret the data as I have a very large number of significant results that I need to prioritise. However, I thought I’d also like to repeat my analyses through some of the other datasets you highlight in the paper and so have started on the fantom data. I have downloaded the dataset with no problems but when I get to this line of the script:

$GIGGLE_ROOT/scripts/sort_bed "split/*" split_sort/

I keep getting the following error message:

bash: line 5: split_sort//xeroderma_pigentosum_b_cell_line-XPL_17.bed.gz: No such file or directory

which is repeated for every bed file in that directory. Do you have an idea as to what is causing this error?

Thanks

Hywel

From: Ryan Layer [mailto:notifications@github.com] Sent: 21 July 2017 14:53 To: ryanlayer/giggle Cc: Williams, Hywel; Author Subject: Re: [ryanlayer/giggle] gargs command? (#24)

Great. Please let me know of any bugs you find or features that would be helpful.

On Fri, Jul 21, 2017 at 7:52 AM, Hywel Williams < notifications@github.com> wrote:

Yes that does sound like the solution, thanks again.

Sent from my iPhone

On 21 Jul 2017, at 14:31, Ryan Layer <notifications@github.com<mailto: notifications@github.com>> wrote:

That image didn't come through, but I bet you need to add the "-s" stats option. I will update the readme with that info. Thanks.

On Fri, Jul 21, 2017 at 6:34 AM, Hywel Williams < notifications@github.com< mailto:notifications@github.com>> wrote:

Dear Ryan,

Many thanks for your help so far, I have today just run my first query so I know the software is up and running which is fantastic. However, in my results file the data is in the format:

[cid:image001.png@01D30226.12E4BE70]

And there is no related P-value with any of the results. I have looked in your readme files but I cant decipher the code that calculates the p-value for each genomic interval, could you please direct me to the correct location.

Many thanks again for your help

Hywel

From: Ryan Layer [mailto:notifications@github.com] Sent: 12 July 2017 15:05 To: ryanlayer/giggle Cc: Williams, Hywel; Author Subject: Re: [ryanlayer/giggle] gargs command? (#24)

It looks like the gargs download step was the last entry in the "Get source code" section of that examples.

ls *.bed | ../gargs -p 30 "bgzip {}" uses 30 threads to compress bed files.

gargs takes input from STDIN, and for every line maps fields in the line to arguments in a command. In this case ls *bed give a list of bed files, and gargs maps each line to the command bgzip FILE. -p 30 says use up to 30 threads.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/ ryanlayer/giggle/issues/24#issuecomment-314779650, or mute the thread< https://github.com/notifications/unsubscribe-auth/ AMWdj2sR2cpHdudSIPUyh7V9QSAO65TZks5sNNKjgaJpZM4OVct0>.

— You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub https://github.com/ryanlayer/giggle/issues/24#issuecomment- 316989270, or mute the thread https://github.com/notifications/unsubscribe-auth/ AAlDUYK7qs7QmKMyPGFEWhr7lF0iFPyyks5sQJrcgaJpZM4OVct0 .

-- Ryan Layer

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/ ryanlayer/giggle/issues/24#issuecomment-317001558, or mute the thread< https://github.com/notifications/unsubscribe-auth/ AMWdjxWkxDSYn07NDjczsOnVmwmNT9KEks5sQKhDgaJpZM4OVct0>.

— You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub https://github.com/ryanlayer/giggle/issues/24#issuecomment-317006771,

or mute the thread https://github.com/notifications/unsubscribe-auth/ AAlDUQp6vZGFjkaz1fJ3A7WU8mOGqUktks5sQK0cgaJpZM4OVct0 .

-- Ryan Layer

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/ ryanlayer/giggle/issues/24#issuecomment-317007005, or mute the thread< https://github.com/notifications/unsubscribe-auth/AMWdj7HdvrfRzcHVOYrd- y2bDrpFWHpGks5sQK1OgaJpZM4OVct0>. — You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub, or mute the thread.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/ ryanlayer/giggle/issues/24#issuecomment-318360830, or mute the thread< https://github.com/notifications/unsubscribe-auth/ AMWdj6JguiodPoc8E31Rlb8D5Pvcu_Mtks5sSI-hgaJpZM4OVct0>.

— You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub https://github.com/ryanlayer/giggle/issues/24#issuecomment-318375981, or mute the thread https://github.com/notifications/unsubscribe-auth/AAlDUVTBun4CJFiIfQ9bYR6nHNdsKiXoks5sSJxDgaJpZM4OVct0 .

-- Ryan Layer