Yes, there was space. But I tried writing the output to a different disk and it worked! Thanks!
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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
"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?
Yes, there was space. But I tried writing the output to a different disk and it worked! Thanks!
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What's the fastp version you're using? Are you completely sure they're empty files?
Yes, the files are empty. I used fastp v0.20.0