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Ólavur Mortensen olavurmortensen

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  • Tórshavn, Faroe Islands
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@olavurmortensen
olavurmortensen / hail_error
Created July 2, 2021 13:12
---------------------------------------------------------------------------
FatalError Traceback (most recent call last)
<ipython-input-80-accb05dc05de> in <module>
----> 1 hl.len(mt.AD).summarize()
/opt/conda/envs/fargen-1-exome/lib/python3.7/site-packages/hail/expr/expressions/base_expression.py in summarize(self, handler)
1102 if handler is None:
1103 handler = hl.utils.default_handler()
-> 1104 handler(self._summarize(name=prefix))
1105
@olavurmortensen
olavurmortensen / cypher_explain
Created September 16, 2020 13:51
{'args': {'Details': 'updates, executions, runtime, batches, failedBatches, '
'batchErrors, failedCommits, commitErrors, wasTerminated',
'EstimatedRows': 10000.0,
'planner': 'COST',
'planner-impl': 'IDP',
'planner-version': '4.1',
'runtime': 'INTERPRETED',
'runtime-impl': 'INTERPRETED',
'runtime-version': '4.1',
'version': 'CYPHER 4.1'},
@olavurmortensen
olavurmortensen / cypher_profile
Created September 16, 2020 13:51
{'args': {'DbHits': 0,
'Details': 'updates, executions, runtime, batches, failedBatches, '
'batchErrors, failedCommits, commitErrors, wasTerminated',
'EstimatedRows': 10000.0,
'GlobalMemory': 0,
'PageCacheHitRatio': 0.0,
'PageCacheHits': 0,
'PageCacheMisses': 0,
'Rows': 1,
'planner': 'COST',
@olavurmortensen
olavurmortensen / system_calls_template.py
Created August 18, 2020 11:32
Don't code in Bash, learn to use system calls in Python.
#!/usr/bin/env python3
import sys, os, shutil, subprocess, logging
# Set logging level; log everything.
logging.basicConfig(level=logging.INFO)
# Define some inputs.
input1 = sys.argv[1]
input2 = sys.argv[2]
@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 - - - - - - -
@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 / 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 / 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 / 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 / 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