MACS3 TypeError: an integer is required

[luised94]

Discussed in https://github.com/macs3-project/MACS/discussions/522

^{Originally posted by luised94 September 19, 2022} Wasnt sure if it should be on issue or discussion board.

Hello, I have been trying to use MACS3 from the command line to call peaks from a SAM file. I have been trying to adapt the protocol from https://www.biologie.ens.fr/~mthomas/other/chip-seq-training/#download, which uses bowtie to generate SAM files and macs1 to perform the analysis. I have been getting the following error:

INFO @ Mon, 19 Sep 2022 15:30:04:

Command line: callpeak -t SRR576933.sam -c SRR576938.sam -f SAM --gsize 4639675 --name macs3 --bw 400 --nomodel --keep-dup 1 --bdg

ARGUMENTS LIST:

name = macs3

format = SAM

ChIP-seq file = ['SRR576933.sam']

control file = ['SRR576938.sam']

effective genome size = 4.64e+06

band width = 400

model fold = [5, 50]

qvalue cutoff = 5.00e-02

The maximum gap between significant sites is assigned as the read length/tag size.

The minimum length of peaks is assigned as the predicted fragment length "d".

Larger dataset will be scaled towards smaller dataset.

Range for calculating regional lambda is: 1000 bps and 10000 bps

Broad region calling is off

Paired-End mode is off

INFO @ Mon, 19 Sep 2022 15:30:04: #1 read tag files... INFO @ Mon, 19 Sep 2022 15:30:04: #1 read treatment tags... Traceback (most recent call last): File "/home/lius/.local/bin/macs3", line 725, in main() File "/home/lius/.local/bin/macs3", line 48, in main run( args ) File "/home/lius/.local/lib/python3.8/site-packages/MACS3/Commands/callpeak_cmd.py", line 70, in run (treat, control) = load_tag_files_options (options) File "/home/lius/.local/lib/python3.8/site-packages/MACS3/Commands/callpeak_cmd.py", line 366, in load_tag_files_options treat = tp.build_fwtrack() File "MACS3/IO/Parser.pyx", line 398, in MACS3.IO.Parser.GenericParser.build_fwtrack File "MACS3/IO/Parser.pyx", line 420, in MACS3.IO.Parser.GenericParser.build_fwtrack File "MACS3/IO/Parser.pyx", line 1044, in MACS3.IO.Parser.SAMParser.__fw_parse_line TypeError: an integer is required