User: lizhichao

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lizhichao80
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Posts by lizhichao

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Comment: C: cwl glob all the output files in a directory
... In fact,when I try to be more specific ,It worked. In addition ,I will try the writting format:`items: [ File, Directory ]` Thank you! ...
written 3 months ago by lizhichao80
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cwl glob all the output files in a directory
... iI try to capture all the output files in the directory 【./fpfn】by `glob ./fpfn/*` . But It failed, the error is :`Error validating output record. the `output` field is not valid \n because item is invalid \n because Expected class 'File' but this is 'Directory' ` So my grammar wrong? and How can ...
cwl written 3 months ago by lizhichao80 • updated 3 months ago by Michael R. Crusoe1.7k
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Comment: C: samtools sort: failed to create temporary file: No space left on device
... Tank you very much! I believe this can solve my problem. I will try it as soon as poosible ...
written 3 months ago by lizhichao80
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Comment: C: samtools sort: failed to create temporary file "/BOredq/NA12878.sorted.bam.tmp.0
... I dont think it could work,because the running environment is virtual after staging files. If i try to specify the external path such as /Bigdata/... in command,I believe it will failed because of not finding the path. ...
written 3 months ago by lizhichao80
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Comment: C: samtools sort: failed to create temporary file "/BOredq/NA12878.sorted.bam.tmp.0
... Thank you. my error is : `samtools sort: failed to create temporary file "/BOredq/NA12878.sorted.bam.tmp.0000.bam": No space left on device ` And samtools sort module's "-T" option just specify the prefix instead of output dir. `$samtools sort Usage: samtools sort [options...] [in.bam] Options: ...
written 3 months ago by lizhichao80
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samtools sort: failed to create temporary file: No space left on device
... Hi,I run the cwl workflow in the local machine. I write the cwl and run in [/Bigdata], but the running work seems to fill the /dev and reports that No space left on device. I want to konw why? my fastq is about 70G Filesystem Size Used Avail Use% Mounted on udev 32G 4 ...
samtools cwl written 3 months ago by lizhichao80 • updated 3 months ago by ATpoint24k
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Answer: C: cwl: Source 'outputtbi' of type ["null", "File"] may be incompatible
... I have solve the problem .the reason is cwl workflow Strictly requires the file types of the nodes before and after to be consistent. Thank you anyway! ...
written 3 months ago by lizhichao80
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Comment: C: cwl: Source 'outputtbi' of type ["null", "File"] may be incompatible
... OK. I will pay attention to it . I have solve the problem .the reason is cwl workflow Strictly requires the file types of the nodes before and after to be consistent ...
written 3 months ago by lizhichao80
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Comment: A: cwl: Source 'outputtbi' of type ["null", "File"] may be incompatible
... my cwl :`class: Workflow cwlVersion: v1.0 id: olympus doc: basic olympus wgs pipeline label: olympus $namespaces: sbg: 'https://www.sevenbridges.com/' inputs: - id: fastq1 type: File 'sbg:x': -552.9009399414062 'sbg:y': 181.4827117919922 - id: ref type: 'File[]' 'sbg:x': -3 ...
written 3 months ago by lizhichao80
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Comment: A: cwl: Source 'outputtbi' of type ["null", "File"] may be incompatible
... errors:`Workflow checker warning: olympus.cwl:173:9: Source 'outputtbi' of type ["null", "File"] may be incompatible olympus.cwl:262:9: with sink 'intbi' of type ["null", {"items": "File", "type": "array"}] olympus.cwl:214:9: Source 'outputbam' of type ["null", "File"] may be incompatible olympus. ...
written 3 months ago by lizhichao80

Latest awards to lizhichao

Scholar 3 months ago, created an answer that has been accepted. For C: cwl: Source 'outputtbi' of type ["null", "File"] may be incompatible

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