MACS2 not working in paired end mode

Question

[Filago]

Hello guys, have paired fastq ATAC-seq data and generated a SAM file with bowtie2 and also chromap (my problem occurs for both). I want to conduct peak-calling with macs2 applying the following command:

macs2 callpeak -f SAM -t test.sam -n test -g hs -q 0.01 --keep-dup auto --call-summits

The command works without any errors but it says

# Paired-End mode is off

in the results.

Thus I converted my SAM to bam using

samtools view -b test.sam > test.bam

and again called peaks with

macs2 callpeak -f BAMPE -t test.bam -n test -g hs -q 0.01 --keep-dup auto --call-summits

Now it says:

# Paired-End mode is on

as it should be, but the following error occurs:

AssertionError: Lambda must > 0, however we got 0

Do you know why this error occurs / how to solve it?

Best,

Andreas