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macs3-project / MACS

MACS -- Model-based Analysis of ChIP-Seq
https://macs3-project.github.io/MACS/
BSD 3-Clause "New" or "Revised" License
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struct.error: unpack requires a string argument of length 4 #260

Open Belsufu opened 5 years ago

Belsufu commented 5 years ago

I am having this issue but I do not know why exactly. Could you help me? Thank you in advance

INFO @ Fri, 28 Sep 2018 22:39:33:

Command line: callpeak -t AndrewCD38LowR1.BedUtils.bed -f BED --format BAMPE -n BAMPEAndrewCD38Low_ -g hs

ARGUMENTS LIST:

name = BAMPEAndrewCD38Low_

format = BAMPE

ChIP-seq file = ['AndrewCD38LowR1.BedUtils.bed']

control file = None

effective genome size = 2.70e+09

band width = 300

model fold = [5, 50]

qvalue cutoff = 5.00e-02

Larger dataset will be scaled towards smaller dataset.

Range for calculating regional lambda is: 10000 bps

Broad region calling is off

Paired-End mode is on

INFO @ Fri, 28 Sep 2018 22:39:33: #1 read fragment files... INFO @ Fri, 28 Sep 2018 22:39:33: #1 read treatment fragments... Traceback (most recent call last): File "/n/app/macs2/2.1.1.20160309/bin/macs2", line 4, in import('pkg_resources').run_script('MACS2==2.1.1.20160309', 'macs2') File "/n/app/python/2.7.12/lib/python2.7/site-packages/pkg_resources/init.py", line 719, in run_script self.require(requires)[0].run_script(script_name, ns) File "/n/app/python/2.7.12/lib/python2.7/site-packages/pkg_resources/init.py", line 1511, in run_script exec(script_code, namespace, namespace) File "/n/app/macs2/2.1.1.20160309/lib/python2.7/site-packages/MACS2-2.1.1.20160309-py2.7-linux-x86_64.egg/EGG-INFO/scripts/macs2", line 617, in

File "/n/app/macs2/2.1.1.20160309/lib/python2.7/site-packages/MACS2-2.1.1.20160309-py2.7-linux-x86_64.egg/EGG-INFO/scripts/macs2", line 57, in main

File "build/bdist.linux-x86_64/egg/MACS2/callpeak_cmd.py", line 72, in run File "build/bdist.linux-x86_64/egg/MACS2/callpeak_cmd.py", line 358, in load_frag_files_options File "MACS2/IO/Parser.pyx", line 1024, in MACS2.IO.Parser.BAMPEParser.build_petrack (MACS2/IO/Parser.c:15888) File "MACS2/IO/Parser.pyx", line 1041, in MACS2.IO.Parser.BAMPEParser.build_petrack (MACS2/IO/Parser.c:15269) File "MACS2/IO/Parser.pyx", line 869, in MACS2.IO.Parser.BAMParser.get_references (MACS2/IO/Parser.c:12733) struct.error: unpack requires a string argument of length 4

taoliu commented 5 years ago

Because you used this options: "-t AndrewCD38LowR1.BedUtils.bed -f BED --format BAMPE" You have a bed file but you asked MACS2 to read it as BAM file. Try to remove "--format BAMPE" part.

NishatTamana51 commented 3 years ago

Thanks. I did the same error. Your solution helped me.