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bxlab / metaWRAP

MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis
MIT License
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error for metaWRAP read_qc after update to v0.7.7 #16

Open itiago opened 6 years ago

itiago commented 6 years ago

I did the up date to v0.7.7 as bellow, and then tried to run metaWRAP read_qc... Thanks for any help.

igor@ubuntu:~$ source activate metawrap-env
(metawrap-env) igor@ubuntu:~$ conda update -c ursky metawrap-mg
Solving environment: done

==> WARNING: A newer version of conda exists. <==
  current version: 4.4.10
  latest version: 4.4.11

Please update conda by running

    $ conda update -n base conda

## Package Plan ##

  environment location: /home/igor/miniconda2/envs/metawrap-env

  added / updated specs: 
    - metawrap-mg

The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    metawrap-mg-0.7.7          |        py27pl5_0         912 KB  ursky

The following packages will be UPDATED:

    metawrap-mg: 0.7.6-py27pl5_0 ursky --> 0.7.7-py27pl5_0 ursky

Proceed ([y]/n)? y

Downloading and Extracting Packages
metawrap-mg 0.7.7: ##################################################### | 100% 
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
(metawrap-env) igor@ubuntu:~$ metaWRAP read_qc --skip-bmtagger --skip-pre-qc-report --skip-post-qc-report -1 /home/igor/Metagenomes/AC3_2MetaGenMerged_R_1.fastq -2 /home/igor/Metagenomes/AC3_2MetaGenMerged_R_2.fastq -o /home/igor/metaWRAP/AC3_metagenome/READ_QC
metawrap /home/igor/miniconda2/envs/metawrap-env/bin/metawrap-modules/read_qc --skip-bmtagger --skip-pre-qc-report --skip-post-qc-report -1 /home/igor/Metagenomes/AC3_2MetaGenMerged_R_1.fastq -2 /home/igor/Metagenomes/AC3_2MetaGenMerged_R_2.fastq -o /home/igor/metaWRAP/AC3_metagenome/READ_QC

########################################################################################################################
#####                                              RUNNING TRIM-GALORE                                             #####
########################################################################################################################

/home/igor/miniconda2/envs/metawrap-env/bin/metawrap-modules/read_qc.sh: line 124: trim_galore: command not found
mv: cannot stat '/home/igor/metaWRAP/AC3_metagenome/READ_QC/AC3_2MetaGenMerged_R_1_val_1.fq': No such file or directory
mv: cannot stat '/home/igor/metaWRAP/AC3_metagenome/READ_QC/AC3_2MetaGenMerged_R_2_val_2.fq': No such file or directory

************************************************************************************************************************
*****                            Something went wrong with trimming the reads. Exiting.                            *****
************************************************************************************************************************

real    0m0.123s
user    0m0.052s
sys 0m0.028s
ursky commented 6 years ago

Wow, thank you. Looks like I forgot to include trim-galore as a dependency for metaWRAP in the conda installation! The issue has been fixed in metaWRAP v=0.7.8. Thank you for your patience, and let me know how it goes!