Problem with Bowtie2

[Kanomble]

During the mapping step with bowtie2 the pipeline tries to execute following command: /depend/bowtie2/bowtie2-2.3.5.1-linux-x86_64/bowtie2 -x bowtie2_genome/sequenceChrAEP -1 good/G2_S12_L002_R1_001.fastq.gz -2 good/G2_S12_L002_R2_001.fastq.gz -I 0 -X 500 -k 1 -p 1 -S sampleFree_2_2.sam 2> sampleFree_2_2.sam.alignSummary which resulted into an error.

However, the files good/G2_S12_L002_R1_001.fastq.gz and good/G2_S12_L002_R2_001.fastq.gz are named wrong, therefore the program can't find the files and throws an error. The correct spelling of the files should be -1 good/G2_S12_L002_R1_001.good.fq.gz -2 good/G2_S12_L002_R2_001.good.fq.gz. I can do this step manually with changed file-names.

If you have any suggestion please write a mail to: lukas.becker@hhu.de

[snandiDS]

Thank you for the query. We will cross-check the code and will get back to you soon.

On Fri, Oct 15, 2021 at 2:43 PM Lukas Becker @.***> wrote:

During the mapping step with bowtie2 the pipeline tries to execute following command: /depend/bowtie2/bowtie2-2.3.5.1-linux-x86_64/bowtie2 -x bowtie2_genome/sequenceChrAEP -1 good/G2_S12_L002_R1_001.fastq.gz -2 good/G2_S12_L002_R2_001.fastq.gz -I 0 -X 500 -k 1 -p 1 -S sampleFree_2_2.sam 2> sampleFree_2_2.sam.alignSummary which resulted into an error.

However, the files good/G2_S12_L002_R1_001.fastq.gz and good/G2_S12_L002_R2_001.fastq.gz are named wrong, therefore the program can't find the files and throws an error. The correct spelling of the files should be `-1 good/G2_S12_L002_R1_001.good.fq.gz -2 good/G2_S12_L002_R2_001.good.fq.gz. I can do this step manually with changed file-names.

If you have any suggestion please write a mail to: @.***

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[Kanomble]

Any suggestions how to solve this problem?

[snandiDS]

Sorry for the delay. We will get back to you soon.

On Thu, Oct 28, 2021 at 6:24 PM Lukas Becker @.***> wrote:

Any suggestions how to solve this problem?

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[snandiDS]

Hi,

I just reran the program, and it is running okay. I changed the example sample fastq files to mimic your file names.

The output I get is as follows:

Running bowtie with G2_S123_ctrl_R1_001.good.fq and G2_S123_ctrl_R2_001.good.fq

/root/prokseq/depend/bowtie2/bowtie2-2.3.5.1-linux-x86_64/bowtie2 -x bowtie2_genome/sequenceChr -1 good/G2_S123_ctrl_R1_001.good.fq -2 good/G2_S123_ctrl_R2_001.good.fq -I 0 -X 500 -k 1 -p 1 -S sampleCtrl_3.sam 2> sampleCtrl_3.sam.alignSummary
starting thread <Thread(Thread-36, initial)>
Output: 

 Success.

While running the package, after afterQC, the program creates the good directory and picks up the file from there—for example, /root/prokseq/depend/bowtie2/bowtie2-2.3.5.1-linux-x86_64/bowtie2 -x bowtie2_genome/sequenceChr -1 good/G2_S123_ctrl_R1_001.good.fq -2 good/G2_S123_ctrl_R2_001.good.fq -I 0 -X 500 -k 1 -p 1 -S sampleCtrl_3.sam 2> sampleCtrl_3.sam.alignSummary

Later on, it dumps the files in "Output/QC_afterFilter/FilteredReads/".

However, I guess it will be worth running the pipeline once with expanded files to address your problem. Such as G2_S12_ctrl_R1_001.fastq.

[plwalker12]

I ran into issues with the "good" files and if your issue is then same then I suggest the following: If your sample files have a separate path then the "good" folder with those new files will be places in that path but will not get queued up when running bowtie. Bowtie will be using the path prokseq/good.

So make sure your sample files are in prokseq, or I have also worked around this by going into the script and just taking out the /good/ path to the files and replacing it with my own path.