Error with filterbytile.sh from BBMap suite
HI dear friends
What is the meaning of this error ?
my command is
filterbytile.sh -Xmx10G threads=48 reads=-1 lowqualityonly=t in=SRR24564994_1.fastq.gz in2=SRR24564994_2.fastq.gz out1=SRR24564994_1_filter.fastq.gz out2=SRR24564994_2_filter.fastq.gz
Thank you so much
1 answer
Log in to answer this question.
More posts like this
-
Per tile sequence fails after trimming
written by ijarne •
-
Using BBtools to remove polyGs in Illumina data
written by hpapoli
-
PolyA and PolyG sequences in FastQC/MultiQC report
written by kenneditodd •
-
Help with the reads filtering process
written by valentinavan •
-
RNA-seq QC - adapter content and high duplication
written by Simon •
-
My alignment rate in Bowtie2 was too low
written by Liu Zijia •
-
ATAC-seq fragment size distribution - huge spike at 150 bp
written by Simon •
-
bbduk trimmed out too many sequences
written by AfinaM •
It is possible that you are assigning relatively less memory for the number of threads being run. Can you try increasing the memory (50 or 60g) or lowering the tread number (to say 12). 48 seems like an overkill.
If that does not help make sure you validate your fastq files to ensure that there is no corruption.
I had issues with tools interpreting the SRR24564994
.1as read-pair identifier instead of read-counter (as well as the second read's.2suffix). Try to skip the first reads. You also might want to tryallowidenticalnames=t.