Error with filterbytile.sh from BBMap suite

Question

[SHIRUI]

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

[GenoMax]

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.

[michael.ante]

I had issues with tools interpreting the SRR24564994.1 as read-pair identifier instead of read-counter (as well as the second read's .2 suffix). Try to skip the first reads. You also might want to try allowidenticalnames=t.

Answer 1

[SHIRUI]

I have solved this problem. Because my data was downloaded from GEO database , After I converted SRR format of fastq to Illumina fastq, then, this problem was vanished

Thank you