Bismark2summary not working for output with hisat2

[JingranZhuo]

Hello Felix,

I ran bismark with hisat2 to align the reads. It seems the output files can be recognize by bismark2summary. The error message is as follows.

Command error: INFO: Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred INFO: Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred INFO: Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred No Bismark/Bowtie2 single-end BAM files detected No Bismark/Bowtie2 paired-end BAM files detected No Bismark/HISAT2 single-end BAM files detected No Bismark/HISAT2 paired-end BAM files detected

Thanks!

[FelixKrueger]

Hi Jingran,

I just simulated a few files for both single-end and paired-end scenarios, and it all worked just fine:

├── PE
│   ├── bismark_summary_report.html
│   ├── bismark_summary_report.txt
│   ├── sample1_R1_bismark_hisat2_pe.bam
│   ├── sample1_R1_bismark_hisat2_PE_report.txt
│   ├── sample1_R1.fastq.gz
│   ├── sample1_R2.fastq.gz
│   ├── test2_R1_bismark_hisat2_pe.bam
│   ├── test2_R1_bismark_hisat2_PE_report.txt
│   ├── test2_R1.fastq.gz
│   └── test2_R2.fastq.gz
└── SE
    ├── bismark_summary_report.html
    ├── bismark_summary_report.txt
    ├── SE_test1_bismark_hisat2.bam
    ├── SE_test1_bismark_hisat2_SE_report.txt
    ├── SE_test1.fastq.gz
    ├── SE_test2_bismark_hisat2.bam
    ├── SE_test2_bismark_hisat2_SE_report.txt
    ├── SE_test2.fastq.gz
    ├── SE_test3_bismark_hisat2.bam
    ├── SE_test3_bismark_hisat2_SE_report.txt
    ├── SE_test3.fastq.gz
    ├── simulated_bismark_hisat2.bam
    ├── simulated_bismark_hisat2_SE_report.txt
    └── simulated.fastq.gz

Which version are you running?

[JingranZhuo]

Hello Felix, I am using bismark/0.24.2. The error occurs both when I run it locally or via our nextflow pipelines. https://github.com/vonMeyennLab/nf_methylseq. Best regards, Jingran

…

________________________________ From: Felix Krueger ***@***.***> Sent: 06 August 2024 13:36:10 To: FelixKrueger/Bismark Cc: Zhuo Jingran; Author Subject: Re: [FelixKrueger/Bismark] Bismark2summary not working for output with hisat2 (Issue #693) Hi Jingran, I just simulated a few files for both single-end and paired-end scenarios, and it all worked just fine: ├── PE │ ├── bismark_summary_report.html │ ├── bismark_summary_report.txt │ ├── sample1_R1_bismark_hisat2_pe.bam │ ├── sample1_R1_bismark_hisat2_PE_report.txt │ ├── sample1_R1.fastq.gz │ ├── sample1_R2.fastq.gz │ ├── test2_R1_bismark_hisat2_pe.bam │ ├── test2_R1_bismark_hisat2_PE_report.txt │ ├── test2_R1.fastq.gz │ └── test2_R2.fastq.gz └── SE ├── bismark_summary_report.html ├── bismark_summary_report.txt ├── SE_test1_bismark_hisat2.bam ├── SE_test1_bismark_hisat2_SE_report.txt ├── SE_test1.fastq.gz ├── SE_test2_bismark_hisat2.bam ├── SE_test2_bismark_hisat2_SE_report.txt ├── SE_test2.fastq.gz ├── SE_test3_bismark_hisat2.bam ├── SE_test3_bismark_hisat2_SE_report.txt ├── SE_test3.fastq.gz ├── simulated_bismark_hisat2.bam ├── simulated_bismark_hisat2_SE_report.txt └── simulated.fastq.gz Which version are you running? — Reply to this email directly, view it on GitHub<#693 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/A4MGDTSIW3JPF6VCYRFJ3MLZQCYKVAVCNFSM6AAAAABMB33NWWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDENZRGA3TOMBYGA>. You are receiving this because you authored the thread.Message ID: ***@***.***> [ { ***@***.***": "http://schema.org", ***@***.***": "EmailMessage", "potentialAction": { ***@***.***": "ViewAction", "target": "#693 (comment)", "url": "#693 (comment)", "name": "View Issue" }, "description": "View this Issue on GitHub", "publisher": { ***@***.***": "Organization", "name": "GitHub", "url": "https://github.com" } } ]

[FelixKrueger]

We are in a bit of a pickle now, since v0.24.2 correctly identifies both SE and PE files generated by Bismark/HISAT2. Did you rename your files by any chance? Are they in a different format than the ones above?

[JingranZhuo]

Hello Felix,

Here I have the filenames like this:

(sample_name)_GRCm39_bismark_ht2_pe.bam

Best,
Jingran

[FelixKrueger]

Alright, it's the filenames resulting from your nextflow workflow then.

 @detected_files = <*bismark_hisat2.bam>;  # SE HISAT2
...
 @detected_files = <*bismark_hisat2_pe.bam>; # PE HISAT2

a simple rename s/_ht2_/_hisat2_/ in your results folder might do the trick.

By the way, MultiQC should also be a good option for capturing the output.

[JingranZhuo]

Thank you Felix