我正在尝试在两个配对文件(1.fq.gz 和 2.fq.gz)上运行 fastqc。跑步:
snakemake --use-conda -np newenv/1_fastqc.html
...产生看起来像明智的 DAG:
Building DAG of jobs...
Job stats:
job count min threads max threads
---------- ------- ------------- -------------
curlewtest 1 1 1
total 1 1 1
[Sat May 21 11:27:40 2022]
rule curlewtest:
input: 1.fq.gz, 2.fq.gz
output: newenv/1_fastqc.html, newenv/2_fastqc.html
jobid: 0
resources: tmpdir=/tmp
fastqc 1.fq.gz 2.fq.gz
Job stats:
job count min threads max threads
---------- ------- ------------- -------------
curlewtest 1 1 1
total 1 1 1
This was a dry-run (flag -n). The order of jobs does not reflect the order of execution.
当我运行作业时
snakemake --use-conda --cores all newenv/1_fastqc.html
,分析运行,但输出文件无法出现。 Snakemake 还会抛出以下错误:
Waiting at most 5 seconds for missing files.
MissingOutputException in line 2 of /mnt/data/kcollier/snakemake-workspace/snakefile:
Job Missing files after 5 seconds. This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait:
newenv/1_fastqc.html
newenv/2_fastqc.html completed successfully, but some output files are missing. 0
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
增加延迟并没有帮助。我之前创建的输出目录(
newenv
)也消失了。还有人知道这是为什么吗?
如果没有您的代码,就很难准确回答导致错误的原因。但是,如果您的 shell 命令(或脚本)没有完全按照规则的输出指令中所述生成输出,则可能会发生这种情况 - 它可能就像文件路径中的错误一样简单。
也许尝试运行 Snakemake 运行的 shell 命令,看看是否创建了您期望的输出文件。通过在您的snakemake命令中添加--verbose/-p标志或--debug标志,您可以轻松查看Snakemake运行的命令。
当您在输出中指定的文件之一实际上并未生成时,就会发生这种情况
请参阅“处理丢失文件错误”以获取更多详细信息: https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/03-chaining_rules/index.html