afterqc IS NOT FOUND!

[AlexGaithuma]

I have installed in conda as per the instructions but still get the error: afterqc IS NOT FOUND! my param.bowtie.yaml looks like this:

#       Specify the path to samtools
PATH SAMTOOLS : /data1/IxoSca/envs/testPrseq/depend/samtools/bin
#       Specify the root path. That means where the ProkSeq bundle is unpacked.
#       The location should have the following folders
#       1. depend - contains all the binaries of the external packages
#       2. scripts - contains all the modules required for ProkSeq, and pipeline-vx.x.sh
#       3. data - Contains Gene ontology files for pathway analysis.
PATH ROOT : /data1/IxoSca/envs/testPrseq
#       If the above environment (depend, scripts, data) is true, the following
#       line maye uncommented.
PATH DEFAULT : "TRUE"
#       Specify the path to geneBody_coverage
PATH geneBody_coverage : /data1/IxoSca/envs/testPrseq/depend/RSeQC-2.6.2/scripts/
#       Specify the path to FEATURECOUNTS
PATH FEATURECOUNTS : /data1/IxoSca/envs/testPrseq/depend/subread-1.4.6-p5-Linux-i386/bin/
#       Specify the path to fastqc
PATH FASTQC : /data1/IxoSca/envs/testPrseq/depend/FastQC
#       Specify the path to bowtie
PATH BOWTIE : /data1/IxoSca/envs/testPrseq/depend/bowtie2/bowtie2-2.3.5.1-linux-x86_64
#       Specify the path to salmon if salmon is required
PATH SALMON : /data1/IxoSca/envs/testPrseq/depend/salmon-latest_linux_x86_64/bin
#       Specify the path to pypy required for running afterqc
PATH PYPY : /data1/IxoSca/envs/testPrseq/depend/pypy2.7-v7.2.0-linux64/bin/
#       Specify the path to readfasta
PATH READFASTA : /data1/IxoSca/envs/testPrseq/depend
#
#       End of file "param.input"
#

command :

python scripts/prokseq.py -s samples.bowtie.PEsample -p param.bowtie.yaml -n 4

The error is:

Checking required tools or packages:
   samtools : Found
     salmon : Found
     fastqc : Found
     bowtie : Found
    afterqc : Not found
  readFasta : Found
          R : Found
    GnBdCov : Found
    FeatCnt : Found
Checking R packages:
DESeq2 : FALSE
ggplot2 : TRUE
edgeR : FALSE
NOISeq : TRUE
limma : FALSE
clusterProfiler : FALSE
apeglm : FALSE
RUVSeq : FALSE
RColorBrewer : TRUE
AFTERQC:
    afterqc IS NOT FOUND!
    Some of the packages are missing.
     Try to install these packages.

[snandiDS]

Please check if the folder afterqc is present in the depend folder. You should get the following. afterqc ├── AfterQC-master │ ├── after.py │ ├── barcodeprocesser.py │ ├── barcodeprocesser.pyc │ ├── bubbledetector.py │ ├── bubbleprocesser.py │ ├── circledetector.py │ ├── debubble.py │ ├── Dockerfile │ ├── editdistance │ ├── fastq.py │ ├── fastq.pyc │ ├── LICENSE │ ├── Makefile │ ├── preprocesser.py │ ├── preprocesser.pyc │ ├── pycache │ ├── qcreporter.py │ ├── qcreporter.pyc │ ├── qualitycontrol.py │ ├── qualitycontrol.pyc │ ├── README.md │ ├── report_sample │ ├── testdata │ ├── util.py │ └── util.pyc └── master.zip

On Sun, Jul 17, 2022 at 4:07 AM Alex Kiare Gaithuma < @.***> wrote:

I have installed in conda as per the instructions but still get the error: afterqc IS NOT FOUND! my param.bowtie.yaml looks like this:

Specify the path to samtools

PATH SAMTOOLS : /data1/IxoSca/envs/testPrseq/depend/samtools/bin

Specify the root path. That means where the ProkSeq bundle is unpacked.

The location should have the following folders

1. depend - contains all the binaries of the external packages

2. scripts - contains all the modules required for ProkSeq, and pipeline-vx.x.sh

3. data - Contains Gene ontology files for pathway analysis.

PATH ROOT : /data1/IxoSca/envs/testPrseq

If the above environment (depend, scripts, data) is true, the following

line maye uncommented.

PATH DEFAULT : "TRUE"

Specify the path to geneBody_coverage

PATH geneBody_coverage : /data1/IxoSca/envs/testPrseq/depend/RSeQC-2.6.2/scripts/

Specify the path to FEATURECOUNTS

PATH FEATURECOUNTS : /data1/IxoSca/envs/testPrseq/depend/subread-1.4.6-p5-Linux-i386/bin/

Specify the path to fastqc

PATH FASTQC : /data1/IxoSca/envs/testPrseq/depend/FastQC

Specify the path to bowtie

PATH BOWTIE : /data1/IxoSca/envs/testPrseq/depend/bowtie2/bowtie2-2.3.5.1-linux-x86_64

Specify the path to salmon if salmon is required

PATH SALMON : /data1/IxoSca/envs/testPrseq/depend/salmon-latest_linux_x86_64/bin

Specify the path to pypy required for running afterqc

PATH PYPY : /data1/IxoSca/envs/testPrseq/depend/pypy2.7-v7.2.0-linux64/bin/

Specify the path to readfasta

PATH READFASTA : /data1/IxoSca/envs/testPrseq/depend #

End of file "param.input"

#

command :

python scripts/prokseq.py -s samples.bowtie.PEsample -p param.bowtie.yaml -n 4

The error is:

Checking required tools or packages: samtools : Found salmon : Found fastqc : Found bowtie : Found afterqc : Not found readFasta : Found R : Found GnBdCov : Found FeatCnt : Found Checking R packages: DESeq2 : FALSE ggplot2 : TRUE edgeR : FALSE NOISeq : TRUE limma : FALSE clusterProfiler : FALSE apeglm : FALSE RUVSeq : FALSE RColorBrewer : TRUE AFTERQC: afterqc IS NOT FOUND! Some of the packages are missing. Try to install these packages.

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[AlexGaithuma]

Hi snandiDS, Thanks. All the files are there (apart from an extra file == .gitignore). I also made sure they have permissions. Still gives the same error.

[AMK06-1993]

If you go where the Pypy executable is and try to run it with ./pypy, do you get the same error? In my case it was the matter of downloading bzip2 package to run pypy. More about it here: https://www.biostars.org/p/266111/ Hope it helps