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 11 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 11 months ago by lizhichao80 • updated 11 months ago by Michael R. Crusoe1.8k
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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 11 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 12 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 12 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 12 months ago by lizhichao80 • updated 12 months ago by ATpoint36k
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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 12 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 12 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 12 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 12 months ago by lizhichao80

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Scholar 12 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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