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Ólavur Mortensen olavurmortensen

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olavurmortensen / keybase.md
Created February 26, 2015 20:28

Keybase proof

I hereby claim:

  • I am olavurmortensen on github.
  • I am olavurmortensen (https://keybase.io/olavurmortensen) on keybase.
  • I have a public key whose fingerprint is 097A 2A4A B7C9 2EAF ADA2 9F57 604D 0E0A AE81 0017

To claim this, I am signing this object:

@olavurmortensen
olavurmortensen / notes.md
Last active August 29, 2016 19:49

Notes

TODO:

  1. Stuff
  2. Other stuff
  3. More stuff

@olavurmortensen
olavurmortensen / Xorg.0.log
Created June 29, 2017 07:24
/var/log/Xorg.0.log
[ 16.354]
X.Org X Server 1.18.4
Release Date: 2016-07-19
[ 16.354] X Protocol Version 11, Revision 0
[ 16.354] Build Operating System: Linux 4.4.0-45-generic x86_64 Ubuntu
[ 16.354] Current Operating System: Linux telda 4.8.0-56-generic #61~16.04.1-Ubuntu SMP Wed Jun 14 11:58:22 UTC 2017 x86_64
[ 16.354] Kernel command line: BOOT_IMAGE=/vmlinuz-4.8.0-56-generic.efi.signed root=/dev/mapper/ubuntu--vg-root ro quiet splash vt.handoff=7
[ 16.354] Build Date: 02 November 2016 10:06:10PM
[ 16.354] xorg-server 2:1.18.4-0ubuntu0.2 (For technical support please see http://www.ubuntu.com/support)
[ 16.354] Current version of pixman: 0.33.6
@olavurmortensen
olavurmortensen / _invoke_snpindel_phaser_nocall.mro
Last active April 19, 2018 13:19
# Define phasing pipeline.
@include "_snpindel_phaser_nocall.mro"
# TODO:
# Zipped VCF or not?
# can the phased_possorted_bam.bam be used as "input", even though a different one is supposed to be supplied (_LINKED_READS_ALIGNER/MERGE_POS_BAM/fork0/files/pos_sorted_bam.bam)?
call _SNPINDEL_PHASER_NOCALL(
variants = "/mnt/fargen/experiments/freebayes_call_phased_bam/FN000518.vcf.gz",
sex = "male",
@olavurmortensen
olavurmortensen / nextflow.log
Last active November 29, 2018 09:42
Nov-28 13:04:44.499 [main] DEBUG nextflow.cli.Launcher - $> ./nextflow run exoseq/PairedSingleSampleWF.nf -with-docker nfcore/exoseq:gatkfix --reads /mnt/fargen/150123_NS500347_0004_AH2CKVAFXX/Data/Intensities/BaseCalls/318616*_L00*_R{1,2}_*.fastq.gz -c custom_docker.config
Nov-28 13:04:44.773 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 18.10.1
Nov-28 13:04:44.810 [main] INFO nextflow.cli.CmdRun - Launching `exoseq/PairedSingleSampleWF.nf` [adoring_murdock] - revision: b8629886d3
Nov-28 13:04:44.838 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /mnt/fargen/experiments/30-10-2018_linked_read_pipeline/wes2015/exoseq/nextflow.config
Nov-28 13:04:44.845 [main] DEBUG nextflow.config.ConfigBuilder - User config file: /mnt/fargen/experiments/30-10-2018_linked_read_pipeline/wes2015/custom_docker.config
Nov-28 13:04:44.846 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /mnt/fargen/experiments/30-10-2018_linked_read_pipeline/wes2015/exoseq/nextflow.config
Nov-28
@olavurmortensen
olavurmortensen / Perl configuration
Last active June 21, 2019 11:05
Perl setup info
Summary of my perl5 (revision 5 version 22 subversion 1) configuration:
Platform:
osname=linux, osvers=3.16.0, archname=x86_64-linux-gnu-thread-multi
uname='linux localhost 3.16.0 #1 smp debian 3.16.0 x86_64 gnulinux '
config_args='-Dusethreads -Duselargefiles -Dcc=x86_64-linux-gnu-gcc -Dcpp=x86_64-linux-gnu-cpp -Dld=x86_64-linux-gnu-gcc -Dccflags=-DDEBIAN -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Dldflags= -Wl,-Bsymbolic-functions -Wl,-z,relro -Dlddlflags=-shared -Wl,-Bsymbolic-functions -Wl,-z,relro -Dcccdlflags=-fPIC -Darchname=x86_64-linux-gnu -Dprefix=/usr -Dprivlib=/usr/share/perl/5.22 -Darchlib=/usr/lib/x86_64-linux-gnu/perl/5.22 -Dvendorprefix=/usr -Dvendorlib=/usr/share/perl5 -Dvendorarch=/usr/lib/x86_64-linux-gnu/perl5/5.22 -Dsiteprefix=/usr/local -Dsitelib=/usr/local/share/perl/5.22.1 -Dsitearch=/usr/local/lib/x86_64-linux-gnu/perl/5.22.1 -Dman1dir=/usr/share/man/man1 -Dman3dir=/usr/share/man/man3 -Dsiteman1dir=/usr/local/man
@olavurmortensen
olavurmortensen / Perl trace
Last active June 21, 2019 11:51
This file has been truncated, but you can view the full file.
1267 execve("/usr/bin/perl", ["perl", "LRSIM/simulateLinkedReads.pl"], [/* 95 vars */]) = 0
1267 brk(NULL) = 0x20fc000
1267 access("/etc/ld.so.nohwcap", F_OK) = -1 ENOENT (No such file or directory)
1267 mmap(NULL, 8192, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1, 0) = 0x7faf7958a000
1267 access("/etc/ld.so.preload", R_OK) = -1 ENOENT (No such file or directory)
1267 open("/etc/ld.so.cache", O_RDONLY|O_CLOEXEC) = 4
1267 fstat(4, {st_mode=S_IFREG|0644, st_size=126864, ...}) = 0
1267 mmap(NULL, 126864, PROT_READ, MAP_PRIVATE, 4, 0) = 0x7faf7956b000
1267 close(4) = 0
1267 access("/etc/ld.so.nohwcap", F_OK) = -1 ENOENT (No such file or directory)
@olavurmortensen
olavurmortensen / jupyter_troubleshoot.log
Created December 13, 2019 09:34
$PATH:
/home/olavur/miniconda3/envs/pypopgen/bin
/home/olavur/bin
/home/olavur/.local/bin
/home/olavur/Documents/goworkdir/bin
/usr/local/go/bin
/usr/local/GenomeBrowse
/home/olavur/bin
/home/olavur/.local/bin
/home/olavur/Documents/goworkdir/bin
@olavurmortensen
olavurmortensen / nextflow.log
Created March 5, 2020 14:13
Mar-05 13:00:04.013 [main] DEBUG nextflow.cli.Launcher - $> nextflow ../../../exolink/demux.nf -resume -ansi-log false
Mar-05 13:00:04.391 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 19.04.0
Mar-05 13:00:04.416 [main] INFO nextflow.cli.CmdRun - Launching `../../../exolink/demux.nf` [exotic_stonebraker] - revision: dbdd264a27
Mar-05 13:00:04.455 [main] DEBUG nextflow.config.ConfigBuilder - Found config local: /home/olavur/experiments/06-11-2019_exolink/tests/demux/181213_NS500347_0048_AHCMT3BGX5/nextflow.config
Mar-05 13:00:04.456 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/olavur/experiments/06-11-2019_exolink/tests/demux/181213_NS500347_0048_AHCMT3BGX5/nextflow.config
Mar-05 13:00:04.544 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `standard`
Mar-05 13:00:06.014 [main] DEBUG nextflow.Session - Session uuid: 1b801422-dc67-4975-9662-61fc90bef576
Mar-05 13:00:06.015 [main] DEBUG nextflow.Session - Run name: exotic_stonebraker
Mar-05 13:00:
@olavurmortensen
olavurmortensen / trace.txt
Last active March 5, 2020 14:30
task_id hash native_id name status exit submit duration realtime %cpu peak_rss peak_vmem rchar wchar
2 23/2da0e3 14443 extract_adapter CACHED 0 2020-03-05 11:05:36.054 161ms 2ms - - - - -
1 b9/c161f8 1509 bcl2fastq CACHED - 2020-03-05 14:10:35.864 - - - - - - -