Open TRGOLLA opened 5 years ago
Hi Thiru,
It looks like there are two different errors here.
First, the quickmerge
executable needs to be in your PATH for the wrapper to find it. I think that's what's causing the "FileNotFoundError: [Errno 2] No such file or directory: 'quickmerge': 'quickmerge'" error.
Second, there's something weird happening with your input files. It looks like you've got nucmer
in your path, which is good, but then you get this error: "Error: Multiple query file is only supported with the SAM output format". I believe this is caused by the use of MUMmer 4 rather than MUMmer 3, which has a slightly different argument format. We're working on adding support for MUMmer 4, but in the meantime, try running this again with MUMmer 3 in your PATH to see if that fixes it. See also the related issue:
Hi James,
I use only MUmmer 3 and have added them in my path but still didn't fine nucmer. export PATH=$PATH:/home/tg484/quickmerge:/home/tg484/quickmerge/MUMmer3.23
Usage: nucmer [options] ref:path qry:path+
Use --help for more information
ERROR: Could not parse delta file, Dbia_merge_wrapper.delta
error no: 400
0 quickmerge
On Tue, Apr 16, 2019 at 10:56 AM James Baldwin-Brown < notifications@github.com> wrote:
Hi Thiru,
It looks like there are two different errors here.
First, the quickmerge executable needs to be in your PATH for the wrapper to find it. I think that's what's causing the "FileNotFoundError: [Errno 2] No such file or directory: 'quickmerge': 'quickmerge'" error.
Second, there's something weird happening with your input files. It looks like you've got nucmer in your path, which is good, but then you get this error: "Error: Multiple query file is only supported with the SAM output format". I believe this is caused by the use of MUMmer 4 rather than MUMmer 3, which has a slightly different argument format. We're working on adding support for MUMmer 4, but in the meantime, try running this again with MUMmer 3 in your PATH to see if that fixes it. See also the related issue:
32 https://github.com/mahulchak/quickmerge/issues/32
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-- Best regards
G.Tirupathi Rao, Senior Research Fellow, Centre For Cellular and Molecular Biology(CCMB), Hyderabad,India.
Hi Thiru,
I'm having trouble explaining your error. Based on the fact that you get a usage message, it looks like nucmer
is in your path, and quickmerge should be as well if you're using the export
line above. I think we need to look a little more at your data. Can you post either your complete .fasta files, or the first few records from each one? Also, do you get a correctly-formatted .delta file from nucmer? Please attach that as well if you can.
Hi,
Also I would try prependig your path by doing the following:
PATH:/location/to/your/binaries:$PATH
There should also be a .qmbashrc in the install directory of quickmerge.
Thank you,
Edwin
On Wed, Apr 17, 2019, 9:14 AM James Baldwin-Brown notifications@github.com wrote:
Hi Thiru,
I'm having trouble explaining your error. Based on the fact that you get a usage message, it looks like nucmer is in your path, and quickmerge should be as well if you're using the export line above. I think we need to look a little more at your data. Can you post either your complete .fasta files, or the first few records from each one? Also, do you get a correctly-formatted .delta file from nucmer? Please attach that as well if you can.
— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/mahulchak/quickmerge/issues/39#issuecomment-484155399, or mute the thread https://github.com/notifications/unsubscribe-auth/AEI6viaPUz5kLyuJNQ-0QMlFJqXdk18vks5vh0a9gaJpZM4cyaYN .
Hi all,
I have got an error when I run merge_warpper.py. Can anyone suggest how to fix the following error? I used the following script.
/home/tg484/quickmerge/merge_wrapper.py -p Dbia_merge_wrapper Dbia_min1000_Illumina.fasta Dbia_min1000_nanopore.fasta -hco 5.0 -c 1.5 -l 2791184 -ml 15000 Error: Multiple query file is only supported with the SAM output format Usage: nucmer [options] ref:path qry:path+ Use --help for more information ERROR: Could not parse delta file, Dbia_merge_wrapper.delta error no: 400 Traceback (most recent call last): File "/home/tg484/quickmerge/merge_wrapper.py", line 176, in
subprocess.call(mergercall)
File "/home/tg484/anaconda3/lib/python3.6/subprocess.py", line 287, in call
with Popen(*popenargs, **kwargs) as p:
File "/home/tg484/anaconda3/lib/python3.6/subprocess.py", line 729, in init
restore_signals, start_new_session)
File "/home/tg484/anaconda3/lib/python3.6/subprocess.py", line 1364, in _execute_child
raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'quickmerge': 'quickmerge'
Thank you, Thiru