maximum reference limited

[huangziyan11111]

I run this command:/psd/biosoft/quickmerge/merge_wrapper.py -pre test_canu -hco 5.0 -c 1.5 -l 310000 -lm 7000 DBG2OLC.fasta canu.sub.fasta while I got an error about the maximum reference: ############################################### 1: PREPARING DATA 2,3: RUNNING mummer AND CREATING CLUSTERS

reading input file "test_canu.ntref" of length 1107738543

construct suffix tree for sequence of length 1107738543

(maximum reference length is 536870908)

(maximum query length is 4294967295)

process 11077385 characters per dot

/psd/biosoft/MUMmer3.23/mummer: suffix tree construction failed: textlen=1107738543 larger than maximal textlen=536870908 ERROR: mummer and/or mgaps returned non-zero ERROR: Could not parse delta file, test_canu.delta error no: 400 Traceback (most recent call last): File "/psd/biosoft/quickmerge/merge_wrapper.py", line 174, in subprocess.call(mergercall) File "/usr/local/Python-2.7.9/lib/python2.7/subprocess.py", line 522, in call return Popen(*popenargs, **kwargs).wait() File "/usr/local/Python-2.7.9/lib/python2.7/subprocess.py", line 710, in init errread, errwrite) File "/usr/local/Python-2.7.9/lib/python2.7/subprocess.py", line 1335, in _execute_child raise child_exception OSError: [Errno 2] No such file or directory ###############################################

How can I solve this error? Increasing the maximum reference length? And how to do? Thank you for your attention.

[esolares]

Hi

Thank you for your email. Have you tried to run it without the wrapper?

On Thu, Aug 2, 2018, 12:30 PM huangziyan11111 [email protected] wrote:

I run this command:/psd/biosoft/quickmerge/merge_wrapper.py -pre test_canu -hco 5.0 -c 1.5 -l 310000 -lm 7000 DBG2OLC.fasta canu.sub.fasta while I got an error about the maximum reference: ############################################### 1: PREPARING DATA 2,3: RUNNING mummer AND CREATING CLUSTERS reading input file "test_canu.ntref" of length 1107738543 construct suffix tree for sequence of length 1107738543 (maximum reference length is 536870908) (maximum query length is 4294967295) process 11077385 characters per dot

/psd/biosoft/MUMmer3.23/mummer: suffix tree construction failed: textlen=1107738543 larger than maximal textlen=536870908 ERROR: mummer and/or mgaps returned non-zero ERROR: Could not parse delta file, test_canu.delta error no: 400 Traceback (most recent call last): File "/psd/biosoft/quickmerge/merge_wrapper.py", line 174, in subprocess.call(mergercall) File "/usr/local/Python-2.7.9/lib/python2.7/subprocess.py", line 522, in call return Popen(*popenargs, **kwargs).wait() File "/usr/local/Python-2.7.9/lib/python2.7/subprocess.py", line 710, in init errread, errwrite) File "/usr/local/Python-2.7.9/lib/python2.7/subprocess.py", line 1335, in _execute_child raise child_exception OSError: [Errno 2] No such file or directory ###############################################

How can I solve this error? Increasing the maximum reference length? And how to do? Thank you for your attention.

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[mahulchak]

I think the error is because of MUMmer. Your assembly is too large for it. I think you will either have to compile a 64 bit MUMmer v3 or use MUMmer v4.

On Thu, Aug 2, 2018 at 3:35 AM esolares [email protected] wrote:

Hi

Thank you for your email. Have you tried to run it without the wrapper?

On Thu, Aug 2, 2018, 12:30 PM huangziyan11111 [email protected] wrote:

I run this command:/psd/biosoft/quickmerge/merge_wrapper.py -pre test_canu -hco 5.0 -c 1.5 -l 310000 -lm 7000 DBG2OLC.fasta canu.sub.fasta while I got an error about the maximum reference: ############################################### 1: PREPARING DATA 2,3: RUNNING mummer AND CREATING CLUSTERS reading input file "test_canu.ntref" of length 1107738543 construct suffix tree for sequence of length 1107738543 (maximum reference length is 536870908) (maximum query length is 4294967295) process 11077385 characters per dot

/psd/biosoft/MUMmer3.23/mummer: suffix tree construction failed: textlen=1107738543 larger than maximal textlen=536870908 ERROR: mummer and/or mgaps returned non-zero ERROR: Could not parse delta file, test_canu.delta error no: 400 Traceback (most recent call last): File "/psd/biosoft/quickmerge/merge_wrapper.py", line 174, in subprocess.call(mergercall) File "/usr/local/Python-2.7.9/lib/python2.7/subprocess.py", line 522, in call return Popen(*popenargs, **kwargs).wait() File "/usr/local/Python-2.7.9/lib/python2.7/subprocess.py", line 710, in init errread, errwrite) File "/usr/local/Python-2.7.9/lib/python2.7/subprocess.py", line 1335, in _execute_child raise child_exception OSError: [Errno 2] No such file or directory ###############################################

How can I solve this error? Increasing the maximum reference length? And how to do? Thank you for your attention.

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.

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