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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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macs2 callpeak : ValueError: max() arg is an empty sequence #213

Open juliechevalier opened 7 years ago

juliechevalier commented 7 years ago

Hi,

I have an intermitent problem with Macs2 callpeak when I use build model. It seems a problem with building model because I have no problem when I use --nomodel and a fixed extend size in the same sample So I ran this command with MACS2 2.1.0.20151222 : callpeak --name MACS2 -t treat.bam --format=BAM --gsize 2451960000 --bw=300 --ratio 1.0 --slocal 1000 --llocal 10000 --keep-dup 2 --bdg --pvalue 0.01

ARGUMENTS LIST:

name = MACS2

format = BAM

ChIP-seq file = ['treat.bam']

control file = None

effective genome size = 2.45e+09

band width = 300

model fold = [5, 50]

pvalue cutoff = 1.00e-02

qvalue will not be calculated and reported as -1 in the final output.

Larger dataset will be scaled towards smaller dataset.

Range for calculating regional lambda is: 10000 bps

Broad region calling is off

INFO @ Fri, 15 Sep 2017 11:11:27: #1 read tag files... INFO @ Fri, 15 Sep 2017 11:11:27: #1 read treatment tags... INFO @ Fri, 15 Sep 2017 11:11:29: 1000000 INFO @ Fri, 15 Sep 2017 11:11:31: 2000000 INFO @ Fri, 15 Sep 2017 11:11:33: 3000000 ... ... ... INFO @ Fri, 15 Sep 2017 11:13:00: 48000000 INFO @ Fri, 15 Sep 2017 11:13:02: 49000000 INFO @ Fri, 15 Sep 2017 11:13:03: 50000000 INFO @ Fri, 15 Sep 2017 11:13:04: #1 tag size is determined as 16 bps INFO @ Fri, 15 Sep 2017 11:13:04: #1 tag size = 16 INFO @ Fri, 15 Sep 2017 11:13:04: #1 total tags in treatment: 50000000 INFO @ Fri, 15 Sep 2017 11:13:04: #1 user defined the maximum tags... INFO @ Fri, 15 Sep 2017 11:13:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 2 tag(s) INFO @ Fri, 15 Sep 2017 11:13:10: #1 tags after filtering in treatment: 50000000 INFO @ Fri, 15 Sep 2017 11:13:10: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Sep 2017 11:13:10: #1 finished! INFO @ Fri, 15 Sep 2017 11:13:10: #2 Build Peak Model... INFO @ Fri, 15 Sep 2017 11:13:18: #2 number of paired peaks: 9006 INFO @ Fri, 15 Sep 2017 11:13:18: start model_add_line... INFO @ Fri, 15 Sep 2017 11:13:31: start X-correlation...

Traceback (most recent call last): File "/data/galaxy-dist/tool_dependency/macs2/2.1.0.20151222/iuc/package_macs2_2_1_0_20151222/e1370f7d5e2f/bin/macs2", line 4, in import('pkg_resources').run_script('MACS2==2.1.0.20151222', 'macs2') File "/data/galaxy-dist/.venv/local/lib/python2.7/site-packages/pkg_resources/init.py", line 748, in run_script self.require(requires)[0].run_script(script_name, ns) File "/data/galaxy-dist/.venv/local/lib/python2.7/site-packages/pkg_resources/init.py", line 1524, in run_script exec(script_code, namespace, namespace) File "/data/galaxy-dist/tool_dependency/macs2/2.1.0.20151222/iuc/package_macs2_2_1_0_20151222/e1370f7d5e2f/lib/python/MACS2-2.1.0.20151222-py2.7-linux-x86_64.egg/EGG-INFO/scripts/macs2", line 614, in

File "/data/galaxy-dist/tool_dependency/macs2/2.1.0.20151222/iuc/package_macs2_2_1_0_20151222/e1370f7d5e2f/lib/python/MACS2-2.1.0.20151222-py2.7-linux-x86_64.egg/EGG-INFO/scripts/macs2", line 56, in main

File "build/bdist.linux-x86_64/egg/MACS2/callpeak_cmd.py", line 175, in run File "MACS2/PeakModel.pyx", line 108, in MACS2.PeakModel.PeakModel.init (MACS2/PeakModel.c:2385) File "MACS2/PeakModel.pyx", line 150, in MACS2.PeakModel.PeakModel.build (MACS2/PeakModel.c:2953) File "MACS2/PeakModel.pyx", line 230, in MACS2.PeakModel.PeakModel.__paired_peak_model (MACS2/PeakModel.c:4209) ValueError: max() arg is an empty sequence

Any idea ?

Thanks Julie

visze commented 5 years ago

Hi,

I have a (I guess) the same problem with the actual version (2.1.2) installed via conda..

This is the error. Any suggestions? I can share the BAM if you like

INFO  @ Tue, 22 Jan 2019 16:16:40:  203000000 
INFO  @ Tue, 22 Jan 2019 16:16:46:  204000000 
INFO  @ Tue, 22 Jan 2019 16:16:54: #1 tag size is determined as 20 bps 
INFO  @ Tue, 22 Jan 2019 16:16:54: #1 tag size = 20.0 
INFO  @ Tue, 22 Jan 2019 16:16:54: #1  total tags in treatment: 204782922 
INFO  @ Tue, 22 Jan 2019 16:16:54: #1 user defined the maximum tags... 
INFO  @ Tue, 22 Jan 2019 16:16:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) 
INFO  @ Tue, 22 Jan 2019 16:16:59: #1  tags after filtering in treatment: 171842001 
INFO  @ Tue, 22 Jan 2019 16:16:59: #1  Redundant rate of treatment: 0.16 
INFO  @ Tue, 22 Jan 2019 16:16:59: #1 finished! 
INFO  @ Tue, 22 Jan 2019 16:16:59: #2 Build Peak Model... 
INFO  @ Tue, 22 Jan 2019 16:16:59: #2 looking for paired plus/minus strand peaks... 
INFO  @ Tue, 22 Jan 2019 16:17:15: #2 number of paired peaks: 18187 
INFO  @ Tue, 22 Jan 2019 16:17:15: start model_add_line... 
INFO  @ Tue, 22 Jan 2019 16:17:17: start X-correlation... 
Traceback (most recent call last):
  File ".snakemake/conda/afea0091/bin/macs2", line 622, in <module>
    main()
  File ".snakemake/conda/afea0091/bin/macs2", line 57, in main
    run( args )
  File ".snakemake/conda/afea0091/lib/python2.7/site-packages/MACS2/callpeak_cmd.py", line 178, in run
    opt = options
  File "MACS2/PeakModel.pyx", line 108, in MACS2.PeakModel.PeakModel.__init__ (MACS2/PeakModel.c:2435)
  File "MACS2/PeakModel.pyx", line 150, in MACS2.PeakModel.PeakModel.build (MACS2/PeakModel.c:3007)
  File "MACS2/PeakModel.pyx", line 230, in MACS2.PeakModel.PeakModel.__paired_peak_model (MACS2/PeakModel.c:4263)
ValueError: max() arg is an empty sequence
visze commented 5 years ago

any update here?