MACS peaks calling from bedgraph data, ChIP-Seq

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#1

Hello,
Please I want to call the peaks from bigwig file, so I converted it to bedgraph formate, and run MACS, it worked really fine and I got the output, however suddenly it turned red and gave me this message:
The job creating this dataset has been resubmitted

 NFO  @ Sun, 02 Jun 2019 12:45:55: 
# Command line: callpeak -t /data/dnb02/galaxy_db/files/009/613/dataset_9613622.dat --name bigWigToBedGraph_on_data_13 --format BAM --gsize 2700000000 --keep-dup 1 --qvalue 0.05 --mfold 5 50 --bw 300
# ARGUMENTS LIST:

I have no idea what happened! and how to fix it!
Could you please help me!
Thank you in advance!
Sham

1 Like
#2

Hi @shamjdeed

What public server are you working at?

Appears to be Galaxy EU https://usegalaxy.eu. But please confirm.

If working somewhere else, please note the URL (if public) or describe more about your local/cloud Galaxy (what Galaxy version, where/how you sourced and installed it, last time it was updated).

There are some known issues with metadata assignments with a fix in progress but not finalized yet/deployed to all public servers yet.

Meanwhile, allow the job to rerun. If it fails, try running it again. As far as I know, only some clusters are presenting with this problem as a server-side issue (or at least at Galaxy Main https://usegalaxy.org – which doesn’t automatically rerun failed jobs, so you are not working there).

The problem could also be due to inputs, parameters, or other issues. Once we know where you are working, we can follow-up based on that information.

Thanks!

cc @bjoern.gruening @hxr @nate

#3

Hello @ jennaj,
Thank you for your reply
Yes I am using Galaxy EU, and I am in Hungary! (Galaxy Version 2.1.1.20160309.6), I did not install it I use it on line after signing in in my account!
I run it again and it did not work!
Thank you!

#4

Hello @ jennaj,
Thank you for your reply
Yes I am using Galaxy EU, and I am in Hungary! (Galaxy Version 2.1.1.20160309.6), I did not install it I use it on line after signing in in my account!
I run it again and it did not work!
Thank you

#5

Hi @shamjdeed

Whenever you have errors like these, we recommend submitting a bug report. That’s often a fast way to get help.

Looking at the (i) information icon, and checking the stderr and stdout, I see the following.

INFO  @ Sun, 02 Jun 2019 12:45:55: 
# Command line: callpeak -t /data/dnb02/galaxy_db/files/009/613/dataset_9613622.dat --name bigWigToBedGraph_on_data_13 --format BAM --gsize 2700000000 --keep-dup 1 --qvalue 0.05 --mfold 5 50 --bw 300
# ARGUMENTS LIST:
# name = bigWigToBedGraph_on_data_13
# format = BAM
# ChIP-seq file = ['/data/dnb02/galaxy_db/files/009/613/dataset_9613622.dat']
# 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 off
 
INFO  @ Sun, 02 Jun 2019 12:45:55: #1 read tag files... 
INFO  @ Sun, 02 Jun 2019 12:45:55: #1 read treatment tags... 
Exception struct.error: 'unpack requires a string argument of length 4' in 'MACS2.IO.Parser.BAMParser.tsize' ignored
Traceback (most recent call last):
  File "/usr/local/tools/_conda/envs/mulled-v1-9745eaf08708c75d5cb939b005b2fbbcc13ccefcb86602af9e1bf012d47be274/bin/macs2", line 4, in <module>
    __import__('pkg_resources').run_script('MACS2==2.1.1.20160309', 'macs2')
  File "/usr/local/tools/_conda/envs/mulled-v1-9745eaf08708c75d5cb939b005b2fbbcc13ccefcb86602af9e1bf012d47be274/lib/python2.7/site-packages/pkg_resources/__init__.py", line 750, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/usr/local/tools/_conda/envs/mulled-v1-9745eaf08708c75d5cb939b005b2fbbcc13ccefcb86602af9e1bf012d47be274/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1534, in run_script
    exec(script_code, namespace, namespace)
  File "/usr/local/tools/_conda/envs/mulled-v1-9745eaf08708c75d5cb939b005b2fbbcc13ccefcb86602af9e1bf012d47be274/lib/python2.7/site-packages/MACS2-2.1.1.20160309-py2.7-linux-x86_64.egg/EGG-INFO/scripts/macs2", line 617, in <module>
    
  File "/usr/local/tools/_conda/envs/mulled-v1-9745eaf08708c75d5cb939b005b2fbbcc13ccefcb86602af9e1bf012d47be274/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 "/usr/local/tools/_conda/envs/mulled-v1-9745eaf08708c75d5cb939b005b2fbbcc13ccefcb86602af9e1bf012d47be274/lib/python2.7/site-packages/MACS2-2.1.1.20160309-py2.7-linux-x86_64.egg/MACS2/callpeak_cmd.py", line 73, in run
  File "/usr/local/tools/_conda/envs/mulled-v1-9745eaf08708c75d5cb939b005b2fbbcc13ccefcb86602af9e1bf012d47be274/lib/python2.7/site-packages/MACS2-2.1.1.20160309-py2.7-linux-x86_64.egg/MACS2/callpeak_cmd.py", line 399, in load_tag_files_options
  File "MACS2/IO/Parser.pyx", line 880, in MACS2.IO.Parser.BAMParser.build_fwtrack (MACS2/IO/Parser.c:13703)
  File "MACS2/IO/Parser.pyx", line 893, in MACS2.IO.Parser.BAMParser.build_fwtrack (MACS2/IO/Parser.c:13111)
  File "MACS2/IO/Parser.pyx", line 877, in MACS2.IO.Parser.BAMParser.get_references (MACS2/IO/Parser.c:12886)
struct.error: unpack requires a string argument of length 4

maybe this is helpful to you?

1 Like
#6

Thank you for your help!