User: DY Chen

gravatar for DY Chen
DY Chen10
Reputation:
10
Status:
New User
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Last seen:
21 hours ago
Joined:
1 year, 10 months ago
Email:
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 11 days 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 12 days 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 12 days 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 12 days 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 12 days 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 12 days 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 12 days 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 12 days ago by DY Chen10

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Scholar 11 days ago, created an answer that has been accepted. For A: snakemake: pipeline failed with MissingOutputException

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