No output files

[kchen96]

I ran the MACS 3 command. There seems to be no error in the log. However, no output files are saved. I checked all required packages, and they are installed and satisfy the requirements for MACS3. The output file directory is also writable. Could you help me fix it?

Command line: callpeak -t Renamed_Bam_files/HS766T_treatment_rep2.bam -c Renamed_Bam_files/HS766T_control_rep2.bam -n Peaks_files/HS766T_treatment_rep2_vs_control --outdir Peaks_files -g hs -s 37 --qvalue 0.01 --bdg --nomodel

# ARGUMENTS LIST:
# name = Peaks_files/HS766T_treatment_rep2_vs_control
# format = AUTO
# ChIP-seq file = ['Renamed_Bam_files/HS766T_treatment_rep2.bam']
# control file = ['Renamed_Bam_files/HS766T_control_rep2.bam']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# qvalue cutoff = 1.00e-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 @ Fri, 17 Feb 2023 23:02:31: #1 read tag files...
INFO @ Fri, 17 Feb 2023 23:02:31: #1 read treatment tags...
INFO @ Fri, 17 Feb 2023 23:02:31: Detected format is: BAM
INFO @ Fri, 17 Feb 2023 23:02:31: * Input file is gzipped.
INFO @ Fri, 17 Feb 2023 23:02:34: 736555 reads have been read.
INFO @ Fri, 17 Feb 2023 23:02:34: #1.2 read input tags...
INFO @ Fri, 17 Feb 2023 23:02:34: Detected format is: BAM
INFO @ Fri, 17 Feb 2023 23:02:34: * Input file is gzipped.
INFO @ Fri, 17 Feb 2023 23:02:36: 433633 reads have been read.
INFO @ Fri, 17 Feb 2023 23:02:36: #1 tag size is determined as 37 bps
INFO @ Fri, 17 Feb 2023 23:02:36: #1 tag size = 37.0
INFO @ Fri, 17 Feb 2023 23:02:36: #1 total tags in treatment: 736555
INFO @ Fri, 17 Feb 2023 23:02:36: #1 user defined the maximum tags...
INFO @ Fri, 17 Feb 2023 23:02:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s)
INFO @ Fri, 17 Feb 2023 23:02:36: #1 tags after filtering in treatment: 727574
INFO @ Fri, 17 Feb 2023 23:02:36: #1 Redundant rate of treatment: 0.01
INFO @ Fri, 17 Feb 2023 23:02:36: #1 total tags in control: 433633
INFO @ Fri, 17 Feb 2023 23:02:36: #1 user defined the maximum tags...
INFO @ Fri, 17 Feb 2023 23:02:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s)
INFO @ Fri, 17 Feb 2023 23:02:36: #1 tags after filtering in control: 428281
INFO @ Fri, 17 Feb 2023 23:02:36: #1 Redundant rate of control: 0.01
INFO @ Fri, 17 Feb 2023 23:02:36: #1 finished!
INFO @ Fri, 17 Feb 2023 23:02:36: #2 Build Peak Model...
INFO @ Fri, 17 Feb 2023 23:02:36: #2 Skipped...
INFO @ Fri, 17 Feb 2023 23:02:36: #2 Use 200 as fragment length
INFO @ Fri, 17 Feb 2023 23:02:36: #3 Call peaks...
INFO @ Fri, 17 Feb 2023 23:02:36: #3 Pre-compute pvalue-qvalue table...
INFO @ Fri, 17 Feb 2023 23:02:39: #3 In the peak calling step, the following will be performed simultaneously:
INFO @ Fri, 17 Feb 2023 23:02:39: #3 Write bedGraph files for treatment pileup (after scaling if necessary)... Peaks_files/HS766T_treatment_rep2_vs_control_treat_pileup.bdg
INFO @ Fri, 17 Feb 2023 23:02:39: #3 Write bedGraph files for control lambda (after scaling if necessary)... Peaks_files/HS766T_treatment_rep2_vs_control_control_lambda.bdg
INFO @ Fri, 17 Feb 2023 23:02:39: #3 Pileup will be based on sequencing depth in control.
INFO @ Fri, 17 Feb 2023 23:02:39: #3 Call peaks for each chromosome...
macs_script.sh: line 15: 25962 Segmentation fault (core dumped) macs3 callpeak -t "${treatment_bam}" -c "${control_bam}" -n "${output_prefix}" --outdir "${peaks_dir}" -g hs -s 37 --qvalue 0.01 --bdg --nomodel