Recursive input calling in Snakemake rule

up vote
0
down vote

favorite

I am writing rule to process some data:

data in directory will be something like:

myfirst.trim_1P, myfirst.trim_2P, mysecond.trim_1P, mysecond.trim_2P,...

rule trim_data:

        input:"{dataset}/{sample}.trim_{r}P"

        output:"{dataset}/{sample}.{r}.fastq"

        params:

            length=14

        shell:

            """

            reformat.sh forcetrimleft="{params.length}" in="{input}" out="{output}"

            """

I have this error:

WorkflowError:

RecursionError: maximum recursion depth exceeded

If building the DAG exceeds the recursion limit

myDir/myfirst.1.trimed.1.trimed.2.trimed.2.trimed.2....

Why it run in recursive way if the output different from the input? and how I can fix it?

edited Nov 22 at 18:22

asked Nov 21 at 21:50

Medhat Helmy

934820

add a comment |

up vote
0
down vote

favorite

I am writing rule to process some data:

data in directory will be something like:

myfirst.trim_1P, myfirst.trim_2P, mysecond.trim_1P, mysecond.trim_2P,...

rule trim_data:

        input:"{dataset}/{sample}.trim_{r}P"

        output:"{dataset}/{sample}.{r}.fastq"

        params:

            length=14

        shell:

            """

            reformat.sh forcetrimleft="{params.length}" in="{input}" out="{output}"

            """

I have this error:

WorkflowError:

RecursionError: maximum recursion depth exceeded

If building the DAG exceeds the recursion limit

myDir/myfirst.1.trimed.1.trimed.2.trimed.2.trimed.2....

Why it run in recursive way if the output different from the input? and how I can fix it?

edited Nov 22 at 18:22

asked Nov 21 at 21:50

Medhat Helmy

934820

add a comment |

up vote
0
down vote

favorite

I am writing rule to process some data:

data in directory will be something like:

myfirst.trim_1P, myfirst.trim_2P, mysecond.trim_1P, mysecond.trim_2P,...

rule trim_data:

        input:"{dataset}/{sample}.trim_{r}P"

        output:"{dataset}/{sample}.{r}.fastq"

        params:

            length=14

        shell:

            """

            reformat.sh forcetrimleft="{params.length}" in="{input}" out="{output}"

            """

I have this error:

WorkflowError:

RecursionError: maximum recursion depth exceeded

If building the DAG exceeds the recursion limit

myDir/myfirst.1.trimed.1.trimed.2.trimed.2.trimed.2....

Why it run in recursive way if the output different from the input? and how I can fix it?

edited Nov 22 at 18:22

asked Nov 21 at 21:50

Medhat Helmy

934820

I am writing rule to process some data:

data in directory will be something like:

myfirst.trim_1P, myfirst.trim_2P, mysecond.trim_1P, mysecond.trim_2P,...

rule trim_data:

        input:"{dataset}/{sample}.trim_{r}P"

        output:"{dataset}/{sample}.{r}.fastq"

        params:

            length=14

        shell:

            """

            reformat.sh forcetrimleft="{params.length}" in="{input}" out="{output}"

            """

I have this error:

WorkflowError:

RecursionError: maximum recursion depth exceeded

If building the DAG exceeds the recursion limit

myDir/myfirst.1.trimed.1.trimed.2.trimed.2.trimed.2....

Why it run in recursive way if the output different from the input? and how I can fix it?

snakemake

edited Nov 22 at 18:22

asked Nov 21 at 21:50

Medhat Helmy

934820

edited Nov 22 at 18:22

asked Nov 21 at 21:50

Medhat Helmy

934820

edited Nov 22 at 18:22

asked Nov 21 at 21:50

Medhat Helmy

934820

asked Nov 21 at 21:50

Medhat Helmy

934820

asked Nov 21 at 21:50

Medhat Helmy

934820

add a comment |

1 Answer
1

active

oldest

votes

up vote
0
down vote

This is a wild guess... Maybe the wildcards capture more then they should since they are interpreted as regular expression. If {dataset}, {sample} and {r} take a defined list of values, try constraining their scope with:

wildcard_constraints:

    dataset= '|'.join([re.escape(x) for x in DATASET]),

    sample= '|'.join([re.escape(x) for x in SAMPLE]),

    r= '|'.join([re.escape(x) for x in R]),

Where DATASET, SAMPLE and R are lists of values (e.g. R= ['1', '2'])

answered Nov 22 at 10:07

dariober

9061121

Thanks, this could be the case I will test it and give feedback.
– Medhat Helmy
Nov 22 at 18:33

unfortunately, it did not work. I will try to figure something else, Thanks.
– Medhat Helmy
Nov 26 at 16:00

So the error was in another downstream rule that could cause this recursion I fixed it and add some constraints on the name like this rule bam2fastq: input: datain="{dataset}/{sample}.{filter, ^[0-9]}.bam" output: dataout="{dataset}/{sample}.{filter}.reads.fastq" run: shell(""" bedtools bamtofastq -i "{input.datain}" -fq "{output.dataout}" """)
– Medhat Helmy
Nov 26 at 20:23

add a comment |

Your Answer

StackExchange.ifUsing("editor", function () {
StackExchange.using("externalEditor", function () {
StackExchange.using("snippets", function () {
StackExchange.snippets.init();
});
});
}, "code-snippets");

StackExchange.ready(function() {
var channelOptions = {
tags: "".split(" "),
id: "1"
};
initTagRenderer("".split(" "), "".split(" "), channelOptions);

StackExchange.using("externalEditor", function() {
// Have to fire editor after snippets, if snippets enabled
if (StackExchange.settings.snippets.snippetsEnabled) {
StackExchange.using("snippets", function() {
createEditor();
});
}
else {
createEditor();
}
});

function createEditor() {
StackExchange.prepareEditor({
heartbeatType: 'answer',
convertImagesToLinks: true,
noModals: true,
showLowRepImageUploadWarning: true,
reputationToPostImages: 10,
bindNavPrevention: true,
postfix: "",
imageUploader: {
brandingHtml: "Powered by u003ca class="icon-imgur-white" href="https://imgur.com/"u003eu003c/au003e",
contentPolicyHtml: "User contributions licensed under u003ca href="https://creativecommons.org/licenses/by-sa/3.0/"u003ecc by-sa 3.0 with attribution requiredu003c/au003e u003ca href="https://stackoverflow.com/legal/content-policy"u003e(content policy)u003c/au003e",
allowUrls: true
},
onDemand: true,
discardSelector: ".discard-answer"
,immediatelyShowMarkdownHelp:true
});

}
});

draft saved

draft discarded

Sign up or log in

StackExchange.ready(function () {
StackExchange.helpers.onClickDraftSave('#login-link');
});

Post as a guest

Name

Required, but never shown

StackExchange.ready(
function () {
StackExchange.openid.initPostLogin('.new-post-login', 'https%3a%2f%2fstackoverflow.com%2fquestions%2f53420956%2frecursive-input-calling-in-snakemake-rule%23new-answer', 'question_page');
}
);

Post as a guest

Name

Required, but never shown

1 Answer
1

active

oldest

votes

1 Answer
1

active

oldest

votes

up vote
0
down vote

wildcard_constraints:

    dataset= '|'.join([re.escape(x) for x in DATASET]),

    sample= '|'.join([re.escape(x) for x in SAMPLE]),

    r= '|'.join([re.escape(x) for x in R]),

Where DATASET, SAMPLE and R are lists of values (e.g. R= ['1', '2'])

answered Nov 22 at 10:07

dariober

9061121

Thanks, this could be the case I will test it and give feedback.
– Medhat Helmy
Nov 22 at 18:33

unfortunately, it did not work. I will try to figure something else, Thanks.
– Medhat Helmy
Nov 26 at 16:00

So the error was in another downstream rule that could cause this recursion I fixed it and add some constraints on the name like this rule bam2fastq: input: datain="{dataset}/{sample}.{filter, ^[0-9]}.bam" output: dataout="{dataset}/{sample}.{filter}.reads.fastq" run: shell(""" bedtools bamtofastq -i "{input.datain}" -fq "{output.dataout}" """)
– Medhat Helmy
Nov 26 at 20:23

add a comment |

up vote
0
down vote

wildcard_constraints:

    dataset= '|'.join([re.escape(x) for x in DATASET]),

    sample= '|'.join([re.escape(x) for x in SAMPLE]),

    r= '|'.join([re.escape(x) for x in R]),

Where DATASET, SAMPLE and R are lists of values (e.g. R= ['1', '2'])

answered Nov 22 at 10:07

dariober

9061121

Thanks, this could be the case I will test it and give feedback.
– Medhat Helmy
Nov 22 at 18:33

unfortunately, it did not work. I will try to figure something else, Thanks.
– Medhat Helmy
Nov 26 at 16:00

So the error was in another downstream rule that could cause this recursion I fixed it and add some constraints on the name like this rule bam2fastq: input: datain="{dataset}/{sample}.{filter, ^[0-9]}.bam" output: dataout="{dataset}/{sample}.{filter}.reads.fastq" run: shell(""" bedtools bamtofastq -i "{input.datain}" -fq "{output.dataout}" """)
– Medhat Helmy
Nov 26 at 20:23

add a comment |

up vote
0
down vote

wildcard_constraints:

    dataset= '|'.join([re.escape(x) for x in DATASET]),

    sample= '|'.join([re.escape(x) for x in SAMPLE]),

    r= '|'.join([re.escape(x) for x in R]),

Where DATASET, SAMPLE and R are lists of values (e.g. R= ['1', '2'])

answered Nov 22 at 10:07

dariober

9061121

wildcard_constraints:

    dataset= '|'.join([re.escape(x) for x in DATASET]),

    sample= '|'.join([re.escape(x) for x in SAMPLE]),

    r= '|'.join([re.escape(x) for x in R]),

Where DATASET, SAMPLE and R are lists of values (e.g. R= ['1', '2'])

answered Nov 22 at 10:07

dariober

9061121

answered Nov 22 at 10:07

dariober

9061121

answered Nov 22 at 10:07

dariober

9061121

answered Nov 22 at 10:07

dariober

9061121

Thanks, this could be the case I will test it and give feedback.
– Medhat Helmy
Nov 22 at 18:33

unfortunately, it did not work. I will try to figure something else, Thanks.
– Medhat Helmy
Nov 26 at 16:00

So the error was in another downstream rule that could cause this recursion I fixed it and add some constraints on the name like this rule bam2fastq: input: datain="{dataset}/{sample}.{filter, ^[0-9]}.bam" output: dataout="{dataset}/{sample}.{filter}.reads.fastq" run: shell(""" bedtools bamtofastq -i "{input.datain}" -fq "{output.dataout}" """)
– Medhat Helmy
Nov 26 at 20:23

add a comment |

Thanks, this could be the case I will test it and give feedback.
– Medhat Helmy
Nov 22 at 18:33

unfortunately, it did not work. I will try to figure something else, Thanks.
– Medhat Helmy
Nov 26 at 16:00

So the error was in another downstream rule that could cause this recursion I fixed it and add some constraints on the name like this rule bam2fastq: input: datain="{dataset}/{sample}.{filter, ^[0-9]}.bam" output: dataout="{dataset}/{sample}.{filter}.reads.fastq" run: shell(""" bedtools bamtofastq -i "{input.datain}" -fq "{output.dataout}" """)
– Medhat Helmy
Nov 26 at 20:23

Thanks, this could be the case I will test it and give feedback.
– Medhat Helmy
Nov 22 at 18:33

unfortunately, it did not work. I will try to figure something else, Thanks.
– Medhat Helmy
Nov 26 at 16:00

So the error was in another downstream rule that could cause this recursion I fixed it and add some constraints on the name like this

rule bam2fastq:     input:         datain="{dataset}/{sample}.{filter, ^[0-9]}.bam"     output:         dataout="{dataset}/{sample}.{filter}.reads.fastq"     run:         shell("""             bedtools bamtofastq -i "{input.datain}" -fq "{output.dataout}"              """)

– Medhat Helmy
Nov 26 at 20:23

So the error was in another downstream rule that could cause this recursion I fixed it and add some constraints on the name like this

rule bam2fastq:     input:         datain="{dataset}/{sample}.{filter, ^[0-9]}.bam"     output:         dataout="{dataset}/{sample}.{filter}.reads.fastq"     run:         shell("""             bedtools bamtofastq -i "{input.datain}" -fq "{output.dataout}"              """)

– Medhat Helmy
Nov 26 at 20:23

add a comment |

draft saved

draft discarded

Thanks for contributing an answer to Stack Overflow!

Please be sure to answer the question. Provide details and share your research!

But avoid …

Asking for help, clarification, or responding to other answers.

Making statements based on opinion; back them up with references or personal experience.

To learn more, see our tips on writing great answers.

Some of your past answers have not been well-received, and you're in danger of being blocked from answering.

Please pay close attention to the following guidance:

Please be sure to answer the question. Provide details and share your research!

But avoid …

Asking for help, clarification, or responding to other answers.

Making statements based on opinion; back them up with references or personal experience.

To learn more, see our tips on writing great answers.

draft saved

draft discarded

Sign up or log in

StackExchange.ready(function () {
StackExchange.helpers.onClickDraftSave('#login-link');
});

Post as a guest

Name

Required, but never shown

Post as a guest

Name

Required, but never shown

Sign up or log in

StackExchange.ready(function () {
StackExchange.helpers.onClickDraftSave('#login-link');
});

Post as a guest

Name

Required, but never shown

Sign up or log in

StackExchange.ready(function () {
StackExchange.helpers.onClickDraftSave('#login-link');
});

Post as a guest

Name

Required, but never shown

Sign up or log in

StackExchange.ready(function () {
StackExchange.helpers.onClickDraftSave('#login-link');
});

Post as a guest

Name

Required, but never shown

Name

Required, but never shown

Name

Required, but never shown

This page is only for reference, If you need detailed information, please check here

搜尋此網誌

Htykuut