Open huangziyan11111 opened 6 years ago
Hi
Thank you for your email. Have you tried to run it without the wrapper?
On Thu, Aug 2, 2018, 12:30 PM huangziyan11111 notifications@github.com 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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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 notifications@github.com 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 notifications@github.com 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.
— 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/30, or mute the thread < https://github.com/notifications/unsubscribe-auth/AEI6vtTpDqQ3338uViQG39Qthsxs9wa2ks5uMnGygaJpZM4Vrkm7
.
— 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/30#issuecomment-409794989, or mute the thread https://github.com/notifications/unsubscribe-auth/AHMD6FIcFAytdj1vF0YDUGqNQKkaxbMJks5uMnM3gaJpZM4Vrkm7 .
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.