Issue running metaWRAP-Read_qc

[pedrovanzele]

Hi! I am with an issue during the read_qc step of the metaWRAP tutorial.

When I tried the command line as it is in the tutorial:

for F in RAW_READS/*_1.fastq; do R=${F%_*}_2.fastq; BASE=${F##*/}; SAMPLE=${BASE%_*}; metawrap read_qc -1 $F -2 $R -t 1 -o READ_QC/$SAMPLE  & done

I got those messages (for all samples):

metawrap read_qc -1 RAW_READS/8_1.fastq -2 RAW_READS/8_2.fastq -t 1 -o READ_QC/8

########################################################################################################################
#####                                             MAKING PRE-QC REPORT                                             #####
########################################################################################################################

/home/microbiota-lab/metaWRAP/bin/metawrap-modules/read_qc.sh: line 117: fastqc: command not found

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

I tried to run the line with the --skip-pre-qc-report --skip-post-qc-report arguments, but this time the error was briefly like:

/home/microbiota-lab/metaWRAP/bin/metawrap-modules/read_qc.sh: line 130: trim_galore: command not found

mv: mv: cannot stat 'READ_QC/7/7_1_val_1.fq'cannot stat 'READ_QC/8/8_1_val_1.fq'mv: cannot stat 'READ_QC/5/5_1_val_1.fq': No such file or directory

Something went wrong with trimming the reads. Exiting.

And then I tried also --skip-trimming, but I got (briefly):

/home/microbiota-lab/metaWRAP/bin/metawrap-modules/read_qc.sh: line 154: bmtagger.sh: command not found

Something went wrong with running Bmtagger! Exiting.

I already renamed my reads to F = name_1.fastq and R = name_2.fastq, and as the code shows the program can find them. I guess that its a problem in the modules to find their functions. But they appears to be successfully installed, as when I do metawrap read_qc -h, or simply metawrap -h it shows all the options.

Can someone help me, please? Thank you.

[pedrovanzele]

I forgot to mention that I installed the program using the Manual installation (this is best, if you are comfortable) option of the tutorial. But I guess that it this step not worked:

mamba install --only-deps -c ursky metawrap-mg

I got the following message:

warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY

Could not solve for environment specs

The following packages are incompatible
└─ metawrap-mg is not installable because there are no viable options
   ├─ metawrap-mg [0.8|0.8.2|0.8.3] would require
   │  └─ cairo 1.14.8 , which does not exist (perhaps a missing channel);
   ├─ metawrap-mg [0.8.4|0.8.5|...|1.1.3] would require
   │  └─ cairo 1.14.8.* , which does not exist (perhaps a missing channel);
   ├─ metawrap-mg [1.1.4|1.1.5|1.1.6|1.1.7] would require
   │  └─ openblas 0.3.5.* , which does not exist (perhaps a missing channel);
   ├─ metawrap-mg [1.1.8|1.2] would require
   │  └─ r-ggplot2 3.1.0.* , which conflicts with any installable versions previously reported;
   ├─ metawrap-mg [1.2.1|1.2.2|...|1.3.2] would require
   │  └─ maxbin2 2.2.6.* , which conflicts with any installable versions previously reported;
   └─ metawrap-mg 1.3.0 conflicts with any installable versions previously reported.

So, maybe the read_qc step is not working because the program was not installed? How can I correct and really install it?
Thank you.

[benyoung93]

also running into this problem, it seems the validated reads have been successfully trimmed and cleaned, but the next step of doing the fastqc is not working.

My files are P10_R1_val_1.fq.gz, and the error is mv: cannot stat P10_1_val_1.fq’: No such file or directory so I am assuming it may be the gunzipped part which is causing the error.

I am going to go into the read_qc script to see if this is the case.

[benyoung93]

So unzipping also did not seem to work. My work around is to run each of the steps in read_qc unless someone has a fix for this :).

Ben

[benyoung93]

Hi Hi, just a quick update. I still have not been able to trouble shoot or get this to work within metawrap.

As such, I took the read_qc steps (https://github.com/bxlab/metaWRAP/blob/master/bin/metawrap-modules/read_qc.sh) and generated conda environments for trim_galore and bmtagger and have successfully completed the same steps as in metawrap.

Happy to provide this script, and also if devs want to troubleshoot the errors and why its not working happy to provide log files and what not :).

[yqy6611]

You have to do a major revision of read_qc script manually as NCBI updated algorithms of BMTagger. Check the helper document: https://ftp.ncbi.nlm.nih.gov/pub/agarwala/bmtagger/README

Don't use metawrap-mg. Release the restrictions of python version and install dependencies manually.