Incomplete Bowtie2Mapping

[hariiyer16]

I am trying out esATAC by starting with the Quick Start approach (https://wzthu.github.io/esATAC/doc/vignettes.html#1_quick_start).

Basically trying out a single paired end read from my dataset using the following script:

conclusion <- atacPipe( # MODIFY: Change these paths to your own case files! fastqInput1 = file.path(dataDir, "RawData/S1_R1_001.fastq.gz"), fastqInput2 = file.path(dataDir, "RawData/S1_R2_001.fastq.gz"), refdir = file.path(dataDir, "esATAC_pipeline/refdir"), tmpdir = file.path(dataDir, "esATAC_pipeline/intermediate_results"), genome = "mm10")

The script produces output data in folders from Step_00 to Step_05.

However, in Step_05_pipe_Bowtie2Mapping, I see sam file for only the 1st mate ( "S1_R1_001.sam"), and the S1_R1_001.report file is empty.

The log file for Bowtie mapping (ntermediate_results/pipe/Step_05_pipe_Bowtie2Mapping/pipeFrame.obj.log) is as below:

Step Name:pipe_Bowtie2Mapping All Parameters for This Step: |Input: | fastqInput1: | "~/esATAC_pipeline/intermediate_results/pipe/Step_04_pipe_RemoveAdapter/S1_R1_001.fq" | fastqInput2: | "~/esATAC_pipeline/intermediate_results/pipe/Step_04_pipe_RemoveAdapter/S1_R2_001.fq" | bt2Idxs: | "~/esATAC_pipeline/refdir/mm10/genome.1.bt2" | "~/esATAC_pipeline/refdir/mm10/genome.2.bt2" | "~/esATAC_pipeline/refdir/mm10/genome.3.bt2" | "~/esATAC_pipeline/refdir/mm10/genome.4.bt2" | "~/esATAC_pipeline/refdir/mm10/genome.rev.1.bt2" | "~/esATAC_pipeline/refdir/mm10/genome.rev.2.bt2" |Output: | samOutput: | "~/esATAC_pipeline/intermediate_results/pipe/Step_05_pipe_Bowtie2Mapping/S1_R1_001.sam" | reportOutput: | "~/esATAC_pipeline/intermediate_results/pipe/Step_05_pipe_Bowtie2Mapping/S1_R1_001.report" |Other Parameters: | interleave: | FALSE | singleEnd: | FALSE | bt2Idx: | "~/esATAC_pipeline/refdir/mm10/genome" | paramList: | "a vector started with --no-discordant" | threads: | 2

---

Begin to check if it is finished... 2021-07-07 00:13:03 New step. Start processing data: start mapping with parameters: bowtie2 index:~/esATAC_pipeline/refdir/mm10/genome samOutput:~/esATAC_pipeline/intermediate_results/pipe/Step_05_pipe_Bowtie2Mapping/S1_R1_001.sam report:~/esATAC_pipeline/intermediate_results/pipe/Step_05_pipe_Bowtie2Mapping/S1_R1_001.report fastqInput1:~/esATAC_pipeline/intermediate_results/pipe/Step_04_pipe_RemoveAdapter/S1_R1_001.fq fastqInput2:~/esATAC_pipeline/intermediate_results/pipe/Step_04_pipe_RemoveAdapter/S1_R2_001.fq other parameters:-p 2 --no-discordant --no-unal --no-mixed -X 2000 2021-07-07 02:50:00 processing finished

ems everything is running fine but I don't get an output for read-2 (R2) and no html report. Will appreciate any suggestions of where I am going wrong.

Thank you.