I am really lost what exactly I can do to fix this error.
I am running snakemake to perform some post alignment quality checks.
My code looks like this:
SAMPLES = ["Exome_Tumor_sorted_mrkdup_bqsr", "Exome_Norm_sorted_mrkdup_bqsr",
"WGS_Tumor_merged_sorted_mrkdup_bqsr", "WGS_Norm_merged_sorted_mrkdup_bqsr"]
rule all:
input:
expand("post-alignment-qc/flagstat/{sample}.txt", sample=SAMPLES),
expand("post-alignment-qc/CollectInsertSizeMetics/{sample}.txt", sample=SAMPLES),
expand("post-alignment-qc/CollectAlignmentSummaryMetrics/{sample}.txt", sample=SAMPLES),
expand("post-alignment-qc/CollectGcBiasMetrics/{sample}_summary.txt", samples=SAMPLES) # this is the problem causing line
rule flagstat:
input:
bam = "align/{sample}.bam"
output:
"post-alignment-qc/flagstat/{sample}.txt"
log:
err='post-alignment-qc/logs/flagstat/{sample}_stderr.err'
shell:
"samtools flagstat {input} > {output} 2> {log.err}"
rule CollectInsertSizeMetics:
input:
bam = "align/{sample}.bam"
output:
txt="post-alignment-qc/CollectInsertSizeMetics/{sample}.txt",
pdf="post-alignment-qc/CollectInsertSizeMetics/{sample}.pdf"
log:
err='post-alignment-qc/logs/CollectInsertSizeMetics/{sample}_stderr.err',
out='post-alignment-qc/logs/CollectInsertSizeMetics/{sample}_stdout.txt'
shell:
"gatk CollectInsertSizeMetrics -I {input} -O {output.txt} -H {output.pdf} 2> {log.err}"
rule CollectAlignmentSummaryMetrics:
input:
bam = "align/{sample}.bam",
genome= "references/genome/ref_genome.fa"
output:
txt="post-alignment-qc/CollectAlignmentSummaryMetrics/{sample}.txt",
log:
err='post-alignment-qc/logs/CollectAlignmentSummaryMetrics/{sample}_stderr.err',
out='post-alignment-qc/logs/CollectAlignmentSummaryMetrics/{sample}_stdout.txt'
shell:
"gatk CollectAlignmentSummaryMetrics -I {input.bam} -O {output.txt} -R {input.genome} 2> {log.err}"
rule CollectGcBiasMetrics:
input:
bam = "align/{sample}.bam",
genome= "references/genome/ref_genome.fa"
output:
txt="post-alignment-qc/CollectGcBiasMetrics/{sample}_metrics.txt",
CHART="post-alignment-qc/CollectGcBiasMetrics/{sample}_metrics.pdf",
S="post-alignment-qc/CollectGcBiasMetrics/{sample}_summary.txt"
log:
err='post-alignment-qc/logs/CollectGcBiasMetrics/{sample}_stderr.err',
out='post-alignment-qc/logs/CollectGcBiasMetrics/{sample}_stdout.txt'
shell:
"gatk CollectGcBiasMetrics -I {input.bam} -O {output.txt} -R {input.genome} -CHART = {output.CHART} "
"-S {output.S} 2> {log.err}"
The error message says the following:
WildcardError in line 9 of Snakefile:
No values given for wildcard 'sample'.
File "Snakefile", line 9, in <module>
In my code above I have indicated the problem causing line. When I simply remove this line everything runs perfekt. I am really confused, because I pretty much copy and pasted each rule, and this is the only rule that causes any problems.
If someone could point out what I did wrong, I would be very thankful!
Cheers!
Seems like it could be a spelling mistake - in the highlighted line, you write samples=SAMPLES, but the wildcard is called {sample} without the "s".
In my makefile there is a variable that contains all source files:
SOURCES := $(shell find $(SRCDIR) -type f -name *.$(SRCEXT))
I now want to create a DEPFILES that contains the same files as SOURCES with two main differences:
Each file ends with ".d" instead of ".c"
Each file contains a "." before its basename, such that the resulting file is hidden.
I came up with this expression, which works well:
DEPFILES := $(foreach s,$(SOURCES:.$(SRCEXT)=.$(DEPSEXT)),$(shell echo $(s) | sed -e 's/^\(.*\/\)/\1./')))
Initially, I split SOURCES into the following lists:
PRE := $(dir $(SOURCES))
SUF := $(addprefix ".", $(notdir $(SOURCES)))
Question: How do you join those two lists in a makefile, such that the results equals DEPFILES? In other words: How do you pairwisely concat the strings from both lists?
Here is a simpler approach using makefile only and no shell - if I understood your requirement ok:
SRCS += bob/src1.c fred/src2.c src3.c
DEPS=$(join $(addsuffix ., $(dir $(SRCS))), $(notdir $(SRCS:.c=.d)))
# Some debug:
$(info 1. $(SRCS))
$(info 2. $(SRCS:.c=.d))
$(info 3. $(notdir $(SRCS:.c=.d)))
$(info 4. $(dir $(SRCS)))
.PHONY: all
all:
#echo SRCS: $(SRCS)
#echo DEPS: $(DEPS)
I broke the output down into steps so you can see what each part does - saves me to explain it!
outputs:
1. bob/src1.c fred/src2.c src3.c
2. bob/src1.d fred/src2.d src3.d
3. src1.d src2.d src3.d
4. bob/ fred/ ./
SRCS: bob/src1.c fred/src2.c src3.c
DEPS: bob/.src1.d fred/.src2.d ./.src3.d
There is Swift compiler option -target:
$ swiftc -h
...
-target <value> Generate code for the given target
...
Where from can I get all possible values for compiler option -target (i.e: x86_64-apple-ios11.0, x86_64-apple-macosx10.12, ...) ?
Thanks!
Look at https://github.com/apple/swift/blob/master/utils/build-script-impl
Search the build script for terms like SWIFT_HOST_VARIANT, SWIFT_HOST_VARIANT_SDK, SWIFT_HOST_VARIANT_ARCH and SWIFT_HOST_TRIPLE
#!/usr/bin/env bash
#===--- build-script-impl - Implementation details of build-script ---------===#
#
## This source file is part of the Swift.org open source project
# Each variable name is re-exported into this script in uppercase, where dashes
# are substituted by underscores. For example, `swift-install-components` is
# referred to as `SWIFT_INSTALL_COMPONENTS` in the remainder of this script.
KNOWN_SETTINGS=(
# name default description
# ... snip ...
darwin-deployment-version-osx "10.9" "minimum deployment target version for OS X"
darwin-deployment-version-ios "7.0" "minimum deployment target version for iOS"
# ... snip ...
function set_build_options_for_host() {
llvm_cmake_options=()
swift_cmake_options=()
cmark_cmake_options=()
lldb_cmake_options=()
swiftpm_bootstrap_options=()
SWIFT_HOST_VARIANT=
SWIFT_HOST_VARIANT_SDK=
SWIFT_HOST_VARIANT_ARCH=
SWIFT_HOST_TRIPLE=
local host="$1"
# Hosts which can be cross-compiled must specify:
# SWIFT_HOST_TRIPLE and llvm_target_arch (as well as usual HOST_VARIANT flags)
case ${host} in
freebsd-x86_64)
SWIFT_HOST_VARIANT="freebsd"
SWIFT_HOST_VARIANT_SDK="FREEBSD"
SWIFT_HOST_VARIANT_ARCH="x86_64"
;;
cygwin-x86_64)
SWIFT_HOST_VARIANT="cygwin"
SWIFT_HOST_VARIANT_SDK="CYGWIN"
SWIFT_HOST_VARIANT_ARCH="x86_64"
;;
# ... snip ...
linux-*)
SWIFT_HOST_VARIANT="linux"
SWIFT_HOST_VARIANT_SDK="LINUX"
case ${host} in
linux-x86_64)
SWIFT_HOST_VARIANT_ARCH="x86_64"
;;
# ... snip ...
linux-aarch64)
SWIFT_HOST_VARIANT_ARCH="aarch64"
;;
# ... snip ...
;;
macosx-* | iphoneos-* | iphonesimulator-* | \
appletvos-* | appletvsimulator-* | \
watchos-* | watchsimulator-*)
case ${host} in
macosx-x86_64)
xcrun_sdk_name="macosx"
llvm_target_arch=""
SWIFT_HOST_TRIPLE="x86_64-apple-macosx${DARWIN_DEPLOYMENT_VERSION_OSX}"
SWIFT_HOST_VARIANT="macosx"
SWIFT_HOST_VARIANT_SDK="OSX"
SWIFT_HOST_VARIANT_ARCH="x86_64"
I have a file which contains many sub-sections each starting with [begin] and ending with [end]:
[begin li1_1378184738754_91]
header=7075|lime|0|0|109582|0|1|2700073||0|0|0|[355]|1|0|ssb-li1-1378184738754-90||0||LIME |0|saved=true|0.002406508312038836|0|[ser=zu1:mtu=model_other_20120806calibex.csv:mu=model_other_20120806calibex.csv:scorerClassUsed=LinearPersonalizedProductSearchScorer][ser=uzu6:mtu=model_other_20120806calibex.csv:mu=model_other_20120806calibex.csv:scorerClassUsed=LinearPersonalizedProductSearchScorer][ser=xzs5:mtu=model_other_20120806calibex.csv:mu=model_other_20120806calibex.csv:scorerClassUsed=LinearPersonalizedProductSearchScorer][ser=sv-stda-zu3:mtu=model_other_20120806calibex.csv:mu=model_other_20120806calibex.csv:scorerClassUsed=LinearPersonalizedProductSearchScorer][ser=hzu8:mtu=model_other_20120806calibex.csv:mu=model_other_20120806calibex.csv:scorerClassUsed=LinearPersonalizedProductSearchScorer][ser=lzu3:mtu=model_other_20120806calibex.csv:mu=model_other_20120806calibex.csv:scorerClassUsed=LinearPersonalizedProductSearchScorer][ser=yzu2:mtu=model_other_20120806calibex.csv:mu=model_other_20120806calibex.csv:scorerClassUsed=LinearPersonalizedProductSearchScorer][ser=xzu7:mtu=model_other_20120806calibex.csv:mu=model_other_20120806calibex.csv:scorerClassUsed=LinearPersonalizedProductSearchScorer]|0|null|false|40||false|
attrs=0|0|0||0|
ptitle=690751404|1|1|1|Rest:1998636||||||2700401|175619|900.5636134725806|0.985486|39.166666666666664|$9.99|100.0|1|||
seller=1998636|1|9.99|1|-1||0|||||true||4.7937584|10412|false|
ptitle=5543369186|2|1|1|Rest:1533891||||||2700211|19615|886.8211044369053|0.776121|34.0|$119.99|100.0|1|||
seller=1533891|1|119.99|3|-1|1.0:text,In+size+6.0%2C7.0%2C8.0%2C8.5%2C9.0%2C9.5%2C10.0%2C...,0.0,,,,0,0,|2|||||true||2.95|20|true|
ptitle=622529158|3|1|1|||||||2700408|67402|796.5289827432475|0.893899|63.0|$5.27|100.0|1|||
seller=4281413|1|5.27|1|-1||0|||||true||4.695052|1769|true|
ptitle=5507199621|4|1|1|||||||2700220|56412|706.9031281251306|0.791171|45.0|$99.99|100.0|1|||
seller=4806107|1|-1.0|1|-1|1.0:sale,$,30.000000000000014,0.0,,,,0,0,:text,In+size+6.0%2C6.5%2C7.0%2C7.5%2C8.0%2C8.5%2C9.0%2C9...,0.0,,,,0,0,|2||||$130 $30.00 off|false||5.0|1|false|
ptitle=5502728013|5|1|1|||||||900000|0|698.7772340643119|0.836740|75.0|$40.95|100.0|1|||
seller=955448|1|40.95|1|-1||0|||||false||4.142857|7|false|
ptitle=840662011|6|1|1|Rest:265238||||||300233|62718|683.2927820751431|0.995513|52.0|$22.95|100.0|1|||
seller=265238|1|22.95|1|-1||0|||||false||4.478261|23|false|
ptitle=848084980|8|1|1|||||||2700073|145653|670.4809846773688|0.880587|60.0|$24.99|100.0|1|||
seller=5267046|1|24.99|1|-1||0|||||true||0.0|0|false|
ptitle=891200492|9|1|1|Rest:1030132||||||2701003|17215|668.8437575254773|0.825491|32.0|$519.99|100.0|1|||
seller=1030132|1|519.99|1|-1||0|||||false||4.7391305|23|false|
ptitle=641974054|10|1|1|||||||900000|69433|667.6678790058678|0.752129|57.0|$4.19|100.0|1|||
seller=3365158|1|4.19|1|-1||0|||||true||4.70907|4410|true|
ptitle=517591869|12|1|1|Rest:4802895||||||2700408|127644|643.0972570735605|0.893899|17.25|$23.95|100.0|1|||
seller=4318776|1|-1.0|3|-1||0|||||false||0.0|0|false|
ptitle=541549480|13|1|1|Rest:1180414||||||2702000|105832|597.4904572011968|0.752129|24.666666666666664|$8.27|100.0|1|||
seller=4636561|1|8.27|1|-1||0|||||false||4.8283377|734|true|
ptitle=1020561900|14|1|1|||||||2700063|159813|594.4717491579845|0.934869|75.0|$5.39|100.0|1|||
seller=4722645|1|5.39|1|-1|1.0:sale,$,0.6000000000000005,0.0,,,,0,0,:text,Free+Shipping+on+All+Orders%21,0.0,201301010000/,,,0,0,|2||||$5.99 $0.60 off|true||4.3942246|1593|true|
ptitle=507792308|15|1|1|Rest:4683455||||||2702000|105832|591.7739184402442|0.768311|22.5|$9.48|100.0|1|||
seller=4910651|1|-1.0|2|-1||0|||||false||5.0|1|false|
ptitle=1090571346|16|1|1|Rest:4452919||||||2700211|20824|776.4814913363535|0.776121|35.0|$59.99|100.0|1|||
seller=1533891|1|59.99|1|-1|1.0:sale,$,49.99999999999999,0.0,,,,0,0,:text,In+size+7.5%2C8.0%2C8.5%2C9.0%2C9.5%2C10.0%2C10.5...,0.0,,,,0,0,|2||||$110 $50.00 off|true||2.95|20|true|
ptitle=573017390|17|1|1|||||||2700073|91937|679.695660577044|0.880587|33.5|$14.85|100.0|1|||
seller=4281413|1|14.85|1|-1||0|||||true||4.695052|1769|true|
ptitle=5502723300|18|1|1|||||||900000|0|639.3095640940136|0.836740|75.0|$50.95|100.0|1|||
seller=955448|1|50.95|1|-1||0|||||false||4.142857|7|false|
ptitle=940022974|20|1|1|||||||2700600|58701|569.9503499778303|0.875839|59.0|$14.40|100.0|1|||
seller=4825227|1|14.4|1|12||0|||||true||4.0289855|276|true|
ptitle=5513277553|21|1|1|||||||2700220|56412|565.2712749001105|0.776121|44.33333333333333|$129.95|100.0|1|||
seller=4825252|1|129.95|1|23||0|||||true||4.0289855|276|true|
ptitle=890329961|22|1|1|||||||2700408|133796|564.7642425785796|0.837916|34.75|$61.95|100.0|1|||
seller=4825235|1|61.95|4|19||0|||||true||4.0289855|276|true|
ptitle=753852910|24|1|1|||||||2700073|146738|557.7419123688652|0.934869|47.69230769230769|$26.99|100.0|1|||
seller=4722645|1|26.99|10|-1|1.0:sale,$,3.0,0.0,,,,0,0,:text,Free+Shipping+on+All+Orders%21,0.0,201301010000/,,,0,0,|2||||$29.99 $3.00 off|true||4.3942246|1593|true|
ptitle=654738989|26|1|1|||||||900000|84012|554.7756559595525|0.752129|57.0|$3.19|100.0|1|||
seller=3365158|1|3.19|1|-1||0|||||true||4.70907|4410|true|
ptitle=707747307|27|1|1|Rest:4736009||||||2700063|76249|552.234395428327|0.889614|19.857142857142854|$6.39|100.0|1|||
seller=4736009|1|6.39|1|-1||0|||||false||4.8071113|15356|true|
ptitle=63531001|28|1|1|||||||2700408|82712|625.0421885589608|0.893899|47.166666666666664|$7.69|100.0|1|||
seller=4281413|1|7.69|3|-1||0|||||true||4.695052|1769|true|
ptitle=5502728016|29|1|1|||||||900000|0|605.9895507237038|0.836740|75.0|$503.00|100.0|1|||
seller=955448|1|503.0|1|-1||0|||||false||4.142857|7|false|
ptitle=507792308|31|1|1|Rest:4683455||||||2702000|105832|559.6902659046442|0.752129|22.5|$8.99|100.0|1|||
seller=5105812|1|-1.0|1|-1||0|||||false||0.0|0|false|
ptitle=753852910|32|1|1|||||||2700073|146738|545.9987095658629|0.870929|47.69230769230769|$22.49|100.0|1|||
seller=4143386|1|22.49|6|-1|1.0:sale,$,7.5,0.0,,,,0,0,:text,Free+Shipping+on+Orders+Over+%24100,0.0,201109010000/201409302359,,,0,0,|2||||$29.99 $7.50 off|false||4.7316346|2355|true|
ptitle=5513277553|33|1|1|Rest:1533891||||||2700220|56412|653.3133907916089|0.825491|44.33333333333333|$149.99|100.0|1|||
seller=1533891|1|149.99|3|-1|1.0:text,In+size+5.0%2C5.5%2C6.0%2C6.5%2C7.0%2C7.5%2C8.0%2C8...,0.0,,,,0,0,|2|||||true||2.95|20|true|
ptitle=63531001|34|1|1|||||||2700408|82712|541.8233547780552|0.893899|47.166666666666664|$7.72|100.0|1|||
seller=2370155|1|7.72|4|-1||0|||||false||4.85|40|false|
ptitle=1018957017|35|1|1|||||||2700073|145653|540.6093714604533|0.860614|56.0|$25.95|100.0|1|||
seller=5036683|1|25.95|1|-1||0|||||false||4.8405056|366|false|
ptitle=743682867|36|1|1|||||||2700073|63437|539.5985846455641|0.870929|58.0|$46.99|100.0|1|||
seller=193176|1|46.99|1|-1||0|||||true||4.8511987|1418|true|
ptitle=679858288|37|1|1|||||||2700063|188669|535.1360632897284|0.902031|30.0|$12.41|100.0|1|||
seller=4143386|1|12.41|2|-1|1.0:sale,$,1.379999999999999,0.0,,,,0,0,:text,Free+Shipping+on+Orders+Over+%24100,0.0,201109010000/201409302359,,,0,0,|2||||$13.79 $1.38 off|false||4.7316346|2355|true|
ptitle=994328713|38|1|1|||||||2700073|71463|534.7715925279717|0.870929|58.0|$1.29|100.0|1|||
seller=1787388|1|1.29|1|-1||0|||||false||4.680464|3624|false|
ptitle=886915818|40|1|1|||||||2700444|201835|529.7519801432289|0.934869|65.5|$44.99|100.0|1|||
seller=4561883|1|44.99|2|-1||0|||||true||4.7913384|508|false|
seller_hidden=227502|990765963|1147436601|-1
seller_hidden=5310958|622529158|5645627277|-1
seller_hidden=4825254|5543369186|5651114316|23
seller_hidden=5289138|5548930281|5653769481|-1
[end li1_1378184738754_91]
I am trying to run the command cat /home/nextag/logs/OutpdirImpressions.log.2013-09-02 | awk -F "$begin" '{print $0}' | awk '$0 ~ "header=7075" {print $0}'
As per this command i want to split the entire file into sub-sections beginning with the word 'begin'. Now in that i want those sub-sections which contains 'header=7075'
Expected output is that it will print the entire sub-section(those which contain that string), but i am getting only this portion as output:
header=7075|lime|0|0|109582|0|1|2700073||0|0|0|[355]|1|0|ssb-li1-1378184738754-90||0||LIME
|0|saved=true|0.002406508312038836|0|[ser=zu1:mtu=model_other_20120806calibex.csv:mu=model_other_20120806calibex.csv:scorerClassUsed=LinearPersonalizedProductSearchScorer][ser=uzu6:mtu=model_other_20120806calibex.csv:mu=model_other_20120806calibex.csv:scorerClassUsed=LinearPersonalizedProductSearchScorer][ser=xzs5:mtu=model_other_20120806calibex.csv:mu=model_other_20120806calibex.csv:scorerClassUsed=LinearPersonalizedProductSearchScorer][ser=sv-stda-zu3:mtu=model_other_20120806calibex.csv:mu=model_other_20120806calibex.csv:scorerClassUsed=LinearPersonalizedProductSearchScorer][ser=hzu8:mtu=model_other_20120806calibex.csv:mu=model_other_20120806calibex.csv:scorerClassUsed=LinearPersonalizedProductSearchScorer][ser=lzu3:mtu=model_other_20120806calibex.csv:mu=model_other_20120806calibex.csv:scorerClassUsed=LinearPersonalizedProductSearchScorer][ser=yzu2:mtu=model_other_20120806calibex.csv:mu=model_other_20120806calibex.csv:scorerClassUsed=LinearPersonalizedProductSearchScorer][ser=xzu7:mtu=model_other_20120806calibex.csv:mu=model_other_20120806calibex.csv:scorerClassUsed=LinearPersonalizedProductSearchScorer]|0|null|false|40||false|
I have tried using if in various ways, but it doesn't works. Can somebody please help me.
I tried awk -F "$begin" '{if($0 ~ "header=7075") {print $0}}' /home/nextag/logs/OutpdirImpressions.log.2013-09-02. It gave the same result
Can somebody please suggest that how do i get the complete sub-section in the result
Try this awk one-liner:
awk '$1=="[end"{p=0}/^header=7075/{p=1}p' file
In parts:
$1=="[end"{p=0} if you reach a line, with the first word "[end", then set the flag to zero
/^header=7075/{p=1} If you reach a line, which begins with "header=7075", set set the flag to one
p if the flag is non-zero, print the current line (equivalent to p{print} or p{print $0} or p!=0{print $0}
I'm working with the following script, run_test:
#!/bin/sh
temp=$1;
cat <<EOF | matlab
[status name] = unix('echo $temp');
disp(name);
% some Matlab code
test_complete = 1;
save(name)
exit
EOF
I want to pass a name to the script, run some code then save a .mat file with the name that was passed. However, there is a curious piece of behavior:
[energon2] ~ $ ./run_test 'run1'
Warning: No display specified. You will not be able to display graphics on the screen.
< M A T L A B (R) >
Copyright 1984-2010 The MathWorks, Inc.
Version 7.12.0.635 (R2011a) 64-bit (glnxa64)
March 18, 2011
To get started, type one of these: helpwin, helpdesk, or demo.
For product information, visit www.mathworks.com.
>> >> >> >> run1
>> >> >> >> >>
[energon2] ~ $ ls *.mat
run1?.mat
There is a "?" at the end of the file name when it's saved, but not when displayed on command line. This is acceptable for my needs, but a bit irritating to not know why it's occurring. Any explanation would be appreciated.
Edits, solution:
Yuk was correct below in the underlying cause and the use of save('$temp'). I'm now using the following script
#!/bin/sh
temp=$1;
cat <<EOF | matlab
% some Matlab code
test_complete = 1;
save('$temp')
exit
EOF
Thanks for the help.
You name variable has end-of-line as the last character. When you run echo run1 in unix this command display run1 and then "hit enter". In your script all the output of echo are saved to the name variable.
You can confirm it with the following:
>> format compact
>> [status, name] = unix('echo run1')
status =
0
name =
run1
>> numel(name)
ans =
5
>> int8(name(end))
ans =
10
>> int8(sprintf('\n'))
ans =
10
Apparently this character can be a part of a file name in unix, but shell displays it as ?.
Can't you do save($temp) instead?
EDIT: See my comments below for correction and more explanation.