Error : Multiple query file is only supported with the SAM output format

[jnarayan81]

How to fix following error ?

python merge_wrapper.py Hdata/extended_10K.fa Hdata/final.genome.scf.fasta 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, out.delta error no: 400 Traceback (most recent call last): File "merge_wrapper.py", line 174, in subprocess.call(mergercall) File "/home/urbe/anaconda3/lib/python3.6/subprocess.py", line 267, in call with Popen(*popenargs, **kwargs) as p: File "/home/urbe/anaconda3/lib/python3.6/subprocess.py", line 709, in init restore_signals, start_new_session) File "/home/urbe/anaconda3/lib/python3.6/subprocess.py", line 1344, in _execute_child raise child_exception_type(errno_num, err_msg, err_filename) FileNotFoundError: [Errno 2] No such file or directory: 'quickmerge': 'quickmerge'

---

After fixing quickmerge executable

Following error occurs: python merge_wrapper.py Hdata/extended_10K.fa Hdata/final.genome.scf.fasta 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, out.delta error no: 400

[mahulchak]

I think there are two issues here:

1. The Python wrapper was written for MUMmer 3.x command line. The command for nucmer in MUMmer 4 (which you seem to be using) is slightly different. We will fix the wrapper to resolve this. In the mean time you can run quickmerge without the wrapper because the delta file format seems to be same between MUMmer.

2. The second issue is that quickmerge is not in your path. We will check why this is happening. But you can simply add the quickmerge folder manually to your path.

Let us know if you face any other problem.

On Mon, Aug 13, 2018 at 5:59 PM Jitendra Narayan notifications@github.com wrote:

How to fix following error ?

python merge_wrapper.py Hdata/extended_10K.fa Hdata/final.genome.scf.fasta 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, out.delta error no: 400 Traceback (most recent call last): File "merge_wrapper.py", line 174, in subprocess.call(mergercall) File "/home/urbe/anaconda3/lib/python3.6/subprocess.py", line 267, in call with Popen(*popenargs, *kwargs) as p: File "/home/urbe/anaconda3/lib/python3.6/subprocess.py", line 709, in init* restore_signals, start_new_session) File "/home/urbe/anaconda3/lib/python3.6/subprocess.py", line 1344, in _execute_child raise child_exception_type(errno_num, err_msg, err_filename) FileNotFoundError: [Errno 2] No such file or directory: 'quickmerge': 'quickmerge'

— 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/32, or mute the thread https://github.com/notifications/unsubscribe-auth/AHMD6KqsWSR5NmhHgWzr54GEA5ffDMF3ks5uQb1ggaJpZM4V6833 .

[ShuChen1986]

I think there are two issues here: 1. The Python wrapper was written for MUMmer 3.x command line. The command for nucmer in MUMmer 4 (which you seem to be using) is slightly different. We will fix the wrapper to resolve this. In the mean time you can run quickmerge without the wrapper because the delta file format seems to be same between MUMmer. 2. The second issue is that quickmerge is not in your path. We will check why this is happening. But you can simply add the quickmerge folder manually to your path. Let us know if you face any other problem. … On Mon, Aug 13, 2018 at 5:59 PM Jitendra Narayan @.> wrote: How to fix following error ? python merge_wrapper.py Hdata/extended_10K.fa Hdata/final.genome.scf.fasta 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, out.delta error no: 400 Traceback (most recent call last): File "merge_wrapper.py", line 174, in subprocess.call(mergercall) File "/home/urbe/anaconda3/lib/python3.6/subprocess.py", line 267, in call with Popen(popenargs, kwargs) as p: File "/home/urbe/anaconda3/lib/python3.6/subprocess.py", line 709, in init restore_signals, start_new_session) File "/home/urbe/anaconda3/lib/python3.6/subprocess.py", line 1344, in _execute_child raise child_exception_type(errno_num, err_msg, err_filename) FileNotFoundError: [Errno 2] No such file or directory: 'quickmerge': 'quickmerge' — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#32>, or mute the thread https://github.com/notifications/unsubscribe-auth/AHMD6KqsWSR5NmhHgWzr54GEA5ffDMF3ks5uQb1ggaJpZM4V6833 .

Hi, I was running mummer4 manually, but still got the same error info: Error: Multiple query file is only supported with the SAM output format