Empty output from UMItools dedup after fastp processing

Empty output from UMItools dedup after fastp processing



I have been running into an interesting error during my sequencing analysis.
We have a paired-end library with UMIs on both ends of the fragments, 6 nts each, for a total of 12 nt.
Now, I have been using fastp for preprocessing of my reads, including adapter and quality trimming, base correction, PolyG trimming and also UMI extraction. Here one exemplary command:

fastp -i sample1_R1.fastq -I sample_R2.fastq --umi --umi_loc=per_read --umi_len=6 --trim_poly_g 10 --html sample1_fastp.html -w 32 -c -o sample1_R1_fastp.fastq -O sample1_R2_fastp.fastq  

After alignment (bowtie2) I wanted to use UMItools dedup on the .bam files, however then the resulting output .bam files are entirely empty. Here the command:

umi_tools dedup -I sample1.BAM --paired --umi-seperator=":" -S sample1_dedup.bam -L sample1_dedup.log

The seperator was of course specified, as fastp by default uses “:” as a seperator.

Has anyone run into a similar issue and if so, have you found a workaround?
I am thankful for any and all replies!






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