Read_qc module error

[eertekin]

When I run the read_qc module

metawrap /home-2/eerteki2@jhu.edu/scratch/miniconda2/envs/metawrap-env/bin/metawrap-modules/read_qc -1 /home-2/eerteki2@jhu.edu/data/Emine_gypsum_metagenomes/RAW_READS/SAG-NEG-2_1.fastq -2 /home-2/eerteki2@jhu.edu/data/Emine_gypsum_metagenomes/RAW_READS/SAG-NEG-2_2.fastq -o SAG-NEG-2

I get the error:

########################################################################################################################

MAKING PRE-QC REPORT

########################################################################################################################

Error occurred during initialization of VM Unable to load native library: libverify.so: cannot open shared object file: No such file or directory

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Something went wrong with making pre-QC fastqc report. Exiting.

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[ursky]

Looks like your fastqc isnt working because of some Java library issue. I suspect you can't even run fastqc -h. Is it possible you have another java-jdk installation in a higher priority than the conda one?

[eertekin]

I think the problem was related with gcc. I updated it, and it seems resolved for now.

[ursky]

Can you tell me exactly how/what did you update to fix it?

[eertekin]

I ran : "conda update gcc" on the commandline. Its now version 4.8.5

[ursky]

Glad it worked. I'll try to add GCC as a dependency for next release (metaWRAP v=0.9). Thanks for the feedback!

[ursky]

For future reference, I had to remove the gcc dependancy from the metawrap-mg conda package as of metawrap v=0.9.1. This is because adding it causes some nasty conflicts between some gcc library packages. It is assumed that you have an up-to-date gcc on your system. Sorry for the inconvenience.