fastp - Empty result file
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0
Entering edit mode
2.4 years ago

I used fastp to trim my fastq files using the following command:

fastp -i sample_R1.fastq.gz -o sample_trimR1.fastq -I sample_R2.fastq.gz -O sample_trimR2.fastq -j sample.report.json -h sample.report.html

I got the following output in the json file:

{
    "summary": {
        "before_filtering": {
            "total_reads":79553254,
            "total_bases":12012541354,
            "q20_bases":7812456920,
            "q30_bases":6344706483,
            "q20_rate":0.650358,
            "q30_rate":0.528174,
            "read1_mean_length":151,
            "read2_mean_length":151,
            "gc_content":0.542021
        },
        "after_filtering": {
            "total_reads":25934168,
            "total_bases":3842951646,
            "q20_bases":3199589958,
            "q30_bases":2758122028,
            "q20_rate":0.832587,
            "q30_rate":0.717709,
            "read1_mean_length":148,
            "read2_mean_length":148,
            "gc_content":0.476687
        }
    },
    "filtering_result": {
        "passed_filter_reads": 25934168,

But the output files which were supposed to contain trimmed reads were empty files and the html report shows a blank page. I did not get any error message.

Please help me understand what is going wrong and how to solve this

fastp • 889 views
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What's the fastp version you're using? Are you completely sure they're empty files?

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Yes, the files are empty. I used fastp v0.20.0

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Entering edit mode
2.4 years ago
GenoMax 108k
"filtering_result": {
        "passed_filter_reads": 25934168,

That clearly says that you have data that survived. You must have write permissions to the destination if you did get zero byte files. Do you have enough space available?

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Yes, there was space. But I tried writing the output to a different disk and it worked! Thanks!

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