November 19, 2021 [reading notes] a summary of common problems of sneakemake (Part 2)

Abstract

As you continue to learn , There are too many processes ,snakemake There are many problems , The previous one snakemake FAQ summary （ On ） A part has been summarized , Today, I would like to add some other problems encountered .

Problem summary

(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

rule That's all right. , But an error is reported after the command is executed , The command needs to be tested separately .
shell Special symbols in （’’/{} etc. ） Yes shell Executing a command has an impact , Especially in use awk perhaps sed On command , There are always problems , Some require backslashes in front of special symbols , Comment out the meaning of special symbols .

NameError: The name ‘XXX’ is unknown in this context. Please make sure that you defined that variable. Also note that braces not used for variable access have to be escaped by repeating them, i.e. { {XXX}}

shell The curly brackets in mainly refer to input and output Content , If it is shell The command reference , Double curly braces are required .

EOL while scanning string literal

There are too many or too few double quotation marks

The flag ‘directory’ used in rule merge_anno is only valid for outputs, not inputs.Building DAG of jobs… ChildIOException:File/directory is a child to another output:(’./10_1_CGPDDS210602_20210713/04.Annotation/pSM620’, dfast)(’./10_1_CGPDDS210602_20210713/04.Annotation/pSM620/all_anno_upset.png’, plot)

In front of the process rule Generated Output folder Can not be used as the back rule The output file The path of .

Error: Directory cannot be locked. Please make sure that no other Snakemake process is trying to create the same files in the following directory:

The previous execution was interrupted suddenly （ctrl+z）, Need to use --unlock Parameter to release folder restrictions

summary

About snakemake Most of these two questions cover , There may be some snakemake Advanced skills presentation , such as if Application , Of course, we should learn it well before we can sort it out for everyone , Welcome to join the group , Scan code or add vx：bbplayer2021, Invite in