merge_wrapper.py run errors

[TRGOLLA]

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

[jgbaldwinbrown]

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:

#https://github.com/mahulchak/quickmerge/issues/32

[TRGOLLA]

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 < [email protected]> 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

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/mahulchak/quickmerge/issues/39#issuecomment-483697197, or mute the thread https://github.com/notifications/unsubscribe-auth/AuDZ4q0xHRmlHS8rsevBmatUTBIumfpUks5vheSVgaJpZM4cyaYN .

-- Best regards

G.Tirupathi Rao, Senior Research Fellow, Centre For Cellular and Molecular Biology(CCMB), Hyderabad,India.

[jgbaldwinbrown]

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.

[esolares]

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 [email protected] 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 .