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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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ATAC macs14 peak calling #157

Open catch-minie opened 8 years ago

catch-minie commented 8 years ago

I am facing following error while using macs14 Command used : macs14 -t test.bam -c control.bam Error

ARGUMENTS LIST:

name = NA

format = AUTO

ChIP-seq file =text4.bam

control file = control.bam

effective genome size = 2.70e+09

band width = 300

model fold = 10,30

pvalue cutoff = 1.00e-05

Large dataset will be scaled towards smaller dataset.

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

INFO @ Thu, 20 Oct 2016 17:18:49: #1 read tag files... INFO @ Thu, 20 Oct 2016 17:18:49: #1 read treatment tags... INFO @ Thu, 20 Oct 2016 17:18:49: Detected format is: BAM INFO @ Thu, 20 Oct 2016 17:18:52: tag size: 50 INFO @ Thu, 20 Oct 2016 17:18:59: 1000000 INFO @ Thu, 20 Oct 2016 17:19:05: 2000000 INFO @ Thu, 20 Oct 2016 17:19:10: 3000000 INFO @ Thu, 20 Oct 2016 17:19:15: 4000000 INFO @ Thu, 20 Oct 2016 17:19:20: 5000000 INFO @ Thu, 20 Oct 2016 17:19:25: 6000000 INFO @ Thu, 20 Oct 2016 17:19:30: 7000000 INFO @ Thu, 20 Oct 2016 17:19:35: 8000000 INFO @ Thu, 20 Oct 2016 17:19:40: 9000000 INFO @ Thu, 20 Oct 2016 17:19:45: 10000000 INFO @ Thu, 20 Oct 2016 17:19:50: 11000000 INFO @ Thu, 20 Oct 2016 17:19:55: 12000000 INFO @ Thu, 20 Oct 2016 17:20:01: 13000000 INFO @ Thu, 20 Oct 2016 17:20:06: 14000000 INFO @ Thu, 20 Oct 2016 17:20:11: 15000000 INFO @ Thu, 20 Oct 2016 17:20:16: 16000000 Traceback (most recent call last): File "/usr/local/bin/macs14", line 366, in main() File "/usr/local/bin/macs14", line 60, in main (treat, control) = load_tag_files_options (options) File "/usr/local/bin/macs14", line 338, in load_tag_files_options treat = tp.build_fwtrack() File "/usr/local/lib/python2.7/dist-packages/MACS14/IO/Parser.py", line 812, in build_fwtrack (chrid,fpos,strand) = self.__fw_binary_parse(fread(entrylength))
File "/usr/lib/python2.7/gzip.py", line 268, in read self._read(readsize) File "/usr/lib/python2.7/gzip.py", line 332, in _read self._read_eof() File "/usr/lib/python2.7/gzip.py", line 354, in _read_eof hex(self.crc))) IOError: CRC check failed 0xbf9b068b != 0x7494add5L

Can any one help me to solve this, I have no ideas what is wrong , I have used the same command before and it worked fine

zhanxw commented 8 years ago

I guess your input file is broken? Please check your bam files are complete.

taoliu commented 8 years ago

Agree with @zhanxw . Also, I suggest you to use MACS2 to call ATAC-Seq peaks since MACS2 is capable of dealing with PE data.

philippadoherty commented 2 weeks ago

Closing this issue as stale, due to inactivity. Please feel free to re-open this with a comment.