User: DY Chen

gravatar for DY Chen
DY Chen10
Reputation:
10
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New User
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Last seen:
7 months, 2 weeks ago
Joined:
2 years, 7 months ago
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4********@qq.com

Posts by DY Chen

<prev • 8 results • page 1 of 1 • next >
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Answer: A: snakemake: pipeline failed with MissingOutputException
... At least solved the problem but as totally new to `snakemake`, still need to spend time learining and figuring out the mechanism behind - After updating to `snakemake v5.7.3`, pipeline failed on a local machine because of `shell.prefix("source ~/.bash_profile")` in `Snakefile`. Actually I modify ...
written 9 months ago by DY Chen10
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Comment: C: snakemake: pipeline failed with MissingOutputException
... Yes I can. I can run STAR alone, I can run code generated by snakemake -np (create directory bam/ and quant/ manually ), and even I can run the same pipeline successfully at least on my local machine with snakemake v3.13.3. But now with v5.7.3, the pipeline fail even on local machine. ...
written 9 months ago by DY Chen10
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Comment: C: snakemake: pipeline failed with MissingOutputException
... Sorry to make confused. At the begining the pipeline worked well on a local machine but failed when submited to cluster. After posting the question I found the version of snakemake was 3.13.3...So I updated to 5.7.3 and then I found the pipeline failed on both of the local machine and cluster. Thus, ...
written 9 months ago by DY Chen10
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Comment: C: snakemake: pipeline failed when submit to cluster
... Yeah snakemake created the `bam/` directory but not the file `bam/A2_Aligned.toTranscriptome.out.bam`. I used `snakemake -np` to create shell command and ran it manually. The command ran successfully except I needed to create directory `bam/` and `quant/` manually, but I think snakemake can automati ...
written 9 months ago by DY Chen10
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Comment: C: snakemake: pipeline failed when submit to cluster
... I saw that and tried to add parameters `--latency-wait 180', but just spent more time to see the error message. The weird thing is that after upgrading snakemake, running it on a local machine also failed MissingOutputException in line 24 of /backup/home/xuheping_Group/chendianyu/project/ ...
written 9 months ago by DY Chen10
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Comment: C: snakemake: pipeline failed when submit to cluster
... The official one here: https://snakemake.readthedocs.io/en/stable/getting_started/installation.html (Seems forgot to use `-c conda-forge` at that time, anyway it works now) However, after upgrading to v5.7.4, still surfer the problem. As I have two pairs of raw paired-end fastq file, the error file ...
written 9 months ago by DY Chen10
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Comment: C: snakemake: pipeline failed when submit to cluster
... 3.13.3... I didn't realized it is such an old version. Follow the instructions of snakemake tutorial and do not know why it is not the latest. I will try the latest version to see whether the problem is solved. ...
written 9 months ago by DY Chen10
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8 follow
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snakemake: pipeline failed with MissingOutputException
... To make it easy I have to modify the post. The situation is that at the beginning I ran the pipeline well on a local machine but failed when submitted to cluster. After posting the question, I found the version of snakemake was 3.13.3, so I updated to v5.7.3, and then I found it failed on both of th ...
snakemake rna-seq written 9 months ago by DY Chen10

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Scholar 9 months ago, created an answer that has been accepted. For A: snakemake: pipeline failed with MissingOutputException

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