Fastp: not enough samples showing

MultiQC
1

after running fastp , i used json file as input to run multiqc. i have total 3 json file consist of read1, read2 data (like-SRR…R1, SRR…R2). multiqc showed a result, where only one result was showing.

Screenshot (4)
Screenshot (4)1920×821 61.7 KB

what would be solution? i want all json file result , as like ( SRR…R1, SRR…R2, DRR…R1, DRR…R2)
AND

multiqc json result was like that-

"report_data_sources": {
        "fastp": {
            "all_sections": {
                "SRR5442949_1": "/mnt/c/Users/mirpr/Downloads/fastp.json"
            }
        }
    },
    "report_general_stats_data": [
        {
            "SRR5442949_1": {
                "filtering_result_passed_filter_reads": 32504748.0,
                "filtering_result_low_quality_reads": 85855.0,
                "filtering_result_too_many_N_reads": 0.0,
                "filtering_result_too_short_reads": 8056.0,
                "pct_duplication": 70.2493,
                "after_filtering_total_reads": 32504748.0,
                "after_filtering_total_bases": 1657613973.0,
                "after_filtering_q20_bases": 1634869178.0,
                "after_filtering_q30_bases": 1607077595.0,
                "after_filtering_q20_rate": 0.986279,
                "after_filtering_q30_rate": 0.969513,
                "after_filtering_gc_content": 0.497543,
                "before_filtering_total_reads": 32598659.0,
                "pct_surviving": 99.71191759759196
            }
        }
2

Hi @prabir,

Sorry you’re having problems. I moved your reply to a new thread, hope that’s ok.

Did you check the docs on this topic and try the suggested things there already?

If you’re still stuck, please attach the verbose MultiQC log. Or better still, the fastp result files themselves.

Thanks!

Phil

3

i visited common problems, but there is nothing related info.
so i attached google drive into this, where all muliqc & fastqp file log files are present google drive of all log files

4

Hi @prabir,

The problem is that you’ve renamed one of your Fastp output filenames to fastp1.json. MultiQC finds these by looking for the pattern *fastp.json (see docs) and so ignores this.

If you use a custom prefix instead of suffix, everything works as expected:

$ mv fastp1.mv fastp1.json 1fastp.json

$ multiqc .

  /// MultiQC 🔍 | v1.18

|           multiqc | Search path : /Users/ewels/Downloads/not enough samples
|         searching | ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100% 6/6
|             fastp | Found 2 reports
|           multiqc | Report      : multiqc_report.html
|           multiqc | Data        : multiqc_data
|           multiqc | MultiQC complete

Alternatively, if renaming the files like this is not an option, you can customise the MultiQC search pattern for Fastp (see docs).

I hope this helps!

Phil

5

Note that we may change this behaviour in the next release, meaning that MultiQC will work with any Fastp outputs regardless of the filenames: