Problem with Plot generation

[PiresAllanSilva]

During the run in docker this error occurs:

Traceback (most recent call last): File "scripts/prokseq.py", line 711, in main() File "scripts/prokseq.py", line 600, in main fn.createGeneBodyPlot(rList) File "/root/prokseq/scripts/libmod/pipeFunc.py", line 235, in createGeneBodyPlot VAL = AR[1].rstrip().split(",") IndexError: list index out of range

What should I do?

[snandiDS]

I doubt something's wrong with the input files. Please check them once again. Let us know if the problem persists.

On Thu, Sep 16, 2021 at 9:44 PM Állan Pires da Silva < @.***> wrote:

During the run in docker this error occurs:

Traceback (most recent call last): File "scripts/prokseq.py", line 711, in main() File "scripts/prokseq.py", line 600, in main fn.createGeneBodyPlot(rList) File "/root/prokseq/scripts/libmod/pipeFunc.py", line 235, in createGeneBodyPlot VAL = AR[1].rstrip().split(",") IndexError: list index out of range

What should I do?

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[PiresAllanSilva]

Hi, all I'd solve the problem by replacing the genome file. Now i'm having a new problem with DeSeq:

Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, : line 1 did not have 6 elements Calls: read.table -> scan Execution halted

Would you help me?

[PiresAllanSilva]

The problem is at DESeq2 script. cd1 <- read.table(sample, sep = " ", skip = 12) sep should be: "" But after the modifications on script the prokseq.py overwrite my modifications.

[snandiDS]

I think sep=" " is correct. The code looks for a sample file which is as follows.

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

File "sample" - sample description file

Specify the names of the sample files and tag them as "treat" and

"control". ###################################################################################

Specify the genome file, and specify the path where the

indexed file will be stored, and the prifex of the indexed genome.

Default is 'bowtie2_genome'.

GENOME SequenceChromosome.fasta bowtie2_genome/sequenceChr

Specify the fastq files

Specify the output name of the sam files.

Followed by the tag/class/condition of the sample (treated or

control)

List all the fastq files as bellow.

FASTQ sampleTreat_1.R1.fq sampleTreat_1.R2.fq sampleTreat_1.sam treat FASTQ sampleTreat_2.R1.fq sampleTreat_2.R2.fq sampleTreat_2.sam treat FASTQ sampleTreat_3.R1.fq sampleTreat_3.R2.fq sampleTreat_3.sam treat FASTQ sampleCtrl_1.R1.fq sampleCtrl_1.R2.fq sampleCtrl_1.sam control FASTQ sampleCtrl_2.R1.fq sampleCtrl_2.R2.fq sampleCtrl_2.sam control FASTQ sampleCtrl_3.R1.fq sampleCtrl_3.R2.fq sampleCtrl_3.sam control #

End of file "sample"

# Please check if you are providing single-end sample files while running paired-end. Hope this helps.

On Sat, Oct 30, 2021 at 3:36 AM Állan Pires da Silva < @.***> wrote:

The problem is at DESeq2 script. cd1 <- read.table(sample, sep = " ", skip = 12) sep should be: "" But after the modifications on script the prokseq.py overwrite my modifications.

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[kirkgrubbs1]

Hi, all I'd solve the problem by replacing the genome file. Now i'm having a new problem with DeSeq:

Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, : line 1 did not have 6 elements Calls: read.table -> scan Execution halted

Would you help me?

I'm having the same issue with the plot generation step. Did you figure out what was wrong with your genome file?

[plwalker12]

If you are unable to complete the GeneBodyPlot it's because the fasta, BED, and/or GTF files that you are using as the input do not match (leading to the index error). Make sure you are obtaining the FASTA and GTF from the same source (same version) and then convert that GTF to the BED file to assure they match.