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healthyPlant / PhytoPipe

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After upgrading Trinity to v2.15.1, assembly failed. The file contigs.fasta size is 0. How can I do? #5

Open xhu556 opened 10 months ago

xhu556 commented 10 months ago

My PhytoPipe exited and showed the following error message after I upgraded Trinity to v2.15.1,

Writing $project/annotation/$sample.blastn.krona.html...
MissingOutputException in line 147 of /software/PhytoPipe/rules/assemble.smk:
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:

When I checked the assembly log file, 

 cat logs/assemble/$sample.trinity.log

I found the following error message:

Can't locate DB_File.pm in @INC (you may need to install the DB_File module)  .......

How can I do?

xhu556 commented 10 months ago

It seems that the perl module DB::File is missed in the PERL5LIB. Please install it using CPAN. 

sudo cpanm install DB_File

If you see an error "fatal error: db.h: No such file or directory" in the log file, please install libdb-dev.
Here is the command for Ubuntu. 

sudo apt-get install libdb-dev

If you use Conda, you can install it using conda install,

conda install -c bioconda perl-db-file

When Trinity is ready, you can rerun your PhytoPipe,

nohup snakemake  --configfile /software/PhytoPipe/config.yaml -s /software/PhytoPipe/Snakefile --config workDir=/$project --cores 32 -R run_trinity &