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PacificBiosciences / FALCON_unzip

Making diploid assembly becomes common practice for genomic study
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FileNotExistError: "No such file:'/data/falcon/0-rawreads/raw_reads.db' on '......'" #40

Closed danshu closed 7 years ago

danshu commented 8 years ago

Hi,

I'm running falcon_unzip and I have this error:

FileNotExistError: "No such file:'/data/falcon/0-rawreads/raw_reads.db' on '......'"

Because I ran falcon using preads, so the "0-rawreads" is definitely almost empty. Do I need to copy those files from the "0-rawreads" directory of a previous run?

Best, Quan

pb-cdunn commented 7 years ago

How did you solve this? It is possible that a recent change broke the preads entry (which should skip the 0- tasks).

danshu commented 7 years ago

I failed again when I copied "0-rawreads" directory of a previous run, with this error message: "DBshow: Cannot open .../0-rawreads/.raw_reads.idx for 'r' No handlers could be found for logger "pypeflow.task" Since I can not find .raw_reads.idx under "0-rawreads", I just rerun falcon from the begining because I'm not sure whether I have deleted these files previously or not. Then I'm running falcon_unzip now.

pb-cdunn commented 7 years ago

I don't understand that at all. The .raw_reads.* files are still in 0-rawreads. Maybe you can run UNIX find . to look for it? It's hard to say remotely.

No handlers could be found for logger "pypeflow.task"

You need to initialize the logger. You can use a logging config from FALCON-examples/run/synth0/, or you can google "python logging config".

Since I can not find .raw_reads.idx under "0-rawreads", I just rerun falcon from the begining because I'm not sure whether I have deleted these files previously or not.

Please let us know if you identify and solve a bug. This is open-source software. We rely on user submissions for many things.

danshu commented 7 years ago

By "locate raw_reads.idx", I can find .raw_reads.* files in 0-rawreads of previous run using raw reads but not when I copied that directory to current run using preads. So is it due to that the command "cp" can not actually copy these .raw_reads.* files?

pb-cdunn commented 7 years ago

You probably needed to use something like cp -r or rsync to copy a directory tree recursively. If you copy sets of files using *, then you would need to set something like dotall (if using bash) in your shell.

danshu commented 7 years ago

@pb-cdunn Thanks!