Mapping ChIP-seq paired end data with bowtie2

[erika_]

Hi!

Having some trouble with bowtie2 rn

Using public data from an encode entry for my course project and can get past this error:

readU: Success
(ERR): bowtie2-align exited with value 1

Here is my code:

bowtie2-build chm13v2.0.fa.qz chm13v2_bt2
bowtie2 -x chm13v2_bt2 -1 ENCFF025YQV.fastq.gz -2 ENCFF572GPA.fastq.gz | awk '$2 != 4 {print}' | samtools view -S -b '-' > NUFIP1_CHiPseq_PE_output.bam

Also tried running simplified version, but some error result:

bowtie2 -x chm13v2_bt2 -1 ENCFF025YQV.fastq.gz -2 ENCFF572GPA.fastq.gz -S NUFIP1_CHiPseq_PE_output.sam

Does anyone have any ideas?
Thank you