Closed daniellezhang closed 4 years ago
The issue seems to be a broken dust track. Could you check the output of DBdust?
This looks like a very out of date version of the code base. If this is not the most reason version at github, please download again and retry. There is no problem with LAsort and LAmerge, daligner did not run because there is no dust track, did you produce one with DBdust? -- Gene
On 9/24/18, 2:18 AM, daniellezhang wrote:
I have followed the example in DAZZ_DB to create stimulated data to test out daligner. But I receive the following error message. Similar error occur when I tried to use daligner with lambda phage data.
unix306 554 % HPCdaligner -mdust -t5 G | csh -v
daligner -t5 -mdust G.1 G.1 daligner: Track 'dust' annotation file is junk daligner -t5 -mdust G.2 G.1 G.2 daligner: Track 'dust' annotation file is junk
LAsort G.1.G.1.C0 G.1.G.1.N0 G.1.G.1.C1 G.1.G.1.N1 G.1.G.1.C2 G.1.G.1.N2 G.1.G.1.C3 G.1.G.1.N3 && LAmerge L1.1.1 G.1.G.1.C0.S G.1.G.1.N0.S G.1.G.1.C1.S G.1.G.1.N1.S G.1.G.1.C2.S G.1.G.1.N2.S G.1.G.1.C3.S G.1.G.1.N3.S && rm G.1.G.1.C0.S.las G.1.G.1.N0.S.las G.1.G.1.C1.S.las G.1.G.1.N1.S.las G.1.G.1.C2.S.las G.1.G.1.N2.S.las G.1.G.1.C3.S.las G.1.G.1.N3.S.las LAsort: Cannot open ./G.1.G.1.C0.las for 'r' LAsort G.1.G.2.C0 G.1.G.2.N0 G.1.G.2.C1 G.1.G.2.N1 G.1.G.2.C2 G.1.G.2.N2 G.1.G.2.C3 G.1.G.2.N3 && LAmerge L1.1.2 G.1.G.2.C0.S G.1.G.2.N0.S G.1.G.2.C1.S G.1.G.2.N1.S G.1.G.2.C2.S G.1.G.2.N2.S G.1.G.2.C3.S G.1.G.2.N3.S && rm G.1.G.2.C0.S.las G.1.G.2.N0.S.las G.1.G.2.C1.S.las G.1.G.2.N1.S.las G.1.G.2.C2.S.las G.1.G.2.N2.S.las G.1.G.2.C3.S.las G.1.G.2.N3.S.las LAsort: Cannot open ./G.1.G.2.C0.las for 'r' LAsort G.2.G.1.C0 G.2.G.1.N0 G.2.G.1.C1 G.2.G.1.N1 G.2.G.1.C2 G.2.G.1.N2 G.2.G.1.C3 G.2.G.1.N3 && LAmerge L1.2.1 G.2.G.1.C0.S G.2.G.1.N0.S G.2.G.1.C1.S G.2.G.1.N1.S G.2.G.1.C2.S G.2.G.1.N2.S G.2.G.1.C3.S G.2.G.1.N3.S && rm G.2.G.1.C0.S.las G.2.G.1.N0.S.las G.2.G.1.C1.S.las G.2.G.1.N1.S.las G.2.G.1.C2.S.las G.2.G.1.N2.S.las G.2.G.1.C3.S.las G.2.G.1.N3.S.las LAsort: Cannot open ./G.2.G.1.C0.las for 'r' LAsort G.2.G.2.C0 G.2.G.2.N0 G.2.G.2.C1 G.2.G.2.N1 G.2.G.2.C2 G.2.G.2.N2 G.2.G.2.C3 G.2.G.2.N3 && LAmerge L1.2.2 G.2.G.2.C0.S G.2.G.2.N0.S G.2.G.2.C1.S G.2.G.2.N1.S G.2.G.2.C2.S G.2.G.2.N2.S G.2.G.2.C3.S G.2.G.2.N3.S && rm G.2.G.2.C0.S.las G.2.G.2.N0.S.las G.2.G.2.C1.S.las G.2.G.2.N1.S.las G.2.G.2.C2.S.las G.2.G.2.N2.S.las G.2.G.2.C3.S.las G.2.G.2.N3.S.las LAsort: Cannot open ./G.2.G.2.C0.las for 'r'
LAmerge G.1 L1.1.1 L1.1.2 && rm L1.1.1.las L1.1.2.las LAmerge: Cannot open ./L1.1.1.las for 'r' LAmerge G.2 L1.2.1 L1.2.2 && rm L1.2.1.las L1.2.2.las LAmerge: Cannot open ./L1.2.1.las for 'r'
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This looks like a very out of date version of the code base. If this is not the most reason version at github, please download again and retry. There is no problem with LAsort and LAmerge, daligner did not run because there is no dust track, did you produce one with DBdust? -- Gene … On 9/24/18, 2:18 AM, daniellezhang wrote: I have followed the example in DAZZ_DB to create stimulated data to test out daligner. But I receive the following error message. Similar error occur when I tried to use daligner with lambda phage data. ------------------------------------------------------------------------ unix306 554 % HPCdaligner -mdust -t5 G | csh -v daligner -t5 -mdust G.1 G.1 daligner: Track 'dust' annotation file is junk daligner -t5 -mdust G.2 G.1 G.2 daligner: Track 'dust' annotation file is junk LAsort G.1.G.1.C0 G.1.G.1.N0 G.1.G.1.C1 G.1.G.1.N1 G.1.G.1.C2 G.1.G.1.N2 G.1.G.1.C3 G.1.G.1.N3 && LAmerge L1.1.1 G.1.G.1.C0.S G.1.G.1.N0.S G.1.G.1.C1.S G.1.G.1.N1.S G.1.G.1.C2.S G.1.G.1.N2.S G.1.G.1.C3.S G.1.G.1.N3.S && rm G.1.G.1.C0.S.las G.1.G.1.N0.S.las G.1.G.1.C1.S.las G.1.G.1.N1.S.las G.1.G.1.C2.S.las G.1.G.1.N2.S.las G.1.G.1.C3.S.las G.1.G.1.N3.S.las LAsort: Cannot open ./G.1.G.1.C0.las for 'r' LAsort G.1.G.2.C0 G.1.G.2.N0 G.1.G.2.C1 G.1.G.2.N1 G.1.G.2.C2 G.1.G.2.N2 G.1.G.2.C3 G.1.G.2.N3 && LAmerge L1.1.2 G.1.G.2.C0.S G.1.G.2.N0.S G.1.G.2.C1.S G.1.G.2.N1.S G.1.G.2.C2.S G.1.G.2.N2.S G.1.G.2.C3.S G.1.G.2.N3.S && rm G.1.G.2.C0.S.las G.1.G.2.N0.S.las G.1.G.2.C1.S.las G.1.G.2.N1.S.las G.1.G.2.C2.S.las G.1.G.2.N2.S.las G.1.G.2.C3.S.las G.1.G.2.N3.S.las LAsort: Cannot open ./G.1.G.2.C0.las for 'r' LAsort G.2.G.1.C0 G.2.G.1.N0 G.2.G.1.C1 G.2.G.1.N1 G.2.G.1.C2 G.2.G.1.N2 G.2.G.1.C3 G.2.G.1.N3 && LAmerge L1.2.1 G.2.G.1.C0.S G.2.G.1.N0.S G.2.G.1.C1.S G.2.G.1.N1.S G.2.G.1.C2.S G.2.G.1.N2.S G.2.G.1.C3.S G.2.G.1.N3.S && rm G.2.G.1.C0.S.las G.2.G.1.N0.S.las G.2.G.1.C1.S.las G.2.G.1.N1.S.las G.2.G.1.C2.S.las G.2.G.1.N2.S.las G.2.G.1.C3.S.las G.2.G.1.N3.S.las LAsort: Cannot open ./G.2.G.1.C0.las for 'r' LAsort G.2.G.2.C0 G.2.G.2.N0 G.2.G.2.C1 G.2.G.2.N1 G.2.G.2.C2 G.2.G.2.N2 G.2.G.2.C3 G.2.G.2.N3 && LAmerge L1.2.2 G.2.G.2.C0.S G.2.G.2.N0.S G.2.G.2.C1.S G.2.G.2.N1.S G.2.G.2.C2.S G.2.G.2.N2.S G.2.G.2.C3.S G.2.G.2.N3.S && rm G.2.G.2.C0.S.las G.2.G.2.N0.S.las G.2.G.2.C1.S.las G.2.G.2.N1.S.las G.2.G.2.C2.S.las G.2.G.2.N2.S.las G.2.G.2.C3.S.las G.2.G.2.N3.S.las LAsort: Cannot open ./G.2.G.2.C0.las for 'r' LAmerge G.1 L1.1.1 L1.1.2 && rm L1.1.1.las L1.1.2.las LAmerge: Cannot open ./L1.1.1.las for 'r' LAmerge G.2 L1.2.1 L1.2.2 && rm L1.2.1.las L1.2.2.las LAmerge: Cannot open ./L1.2.1.las for 'r' — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#86>, or mute the thread https://github.com/notifications/unsubscribe-auth/AGkkNsmamO0uZjpOBZOaNC3qMcXuZgsOks5ueCS4gaJpZM4W18hN.
Thanks for pointing that out Gene. I tried again with the latest version on github rather than bioconda and the message about dust has disappeared. However, when I tried to use LAshow, I received the following message: unix306 725 % LAshow -c -a:G -w50 G.1 | more LAshow: -: is an illegal option
I admit the error message is weird but the option -a:G is not legal. The call should be something like LAshow -c -a -w50 G.db G.1.las -- Gene
On 9/25/18, 8:07 AM, daniellezhang wrote:
This looks like a very out of date version of the code base. If this is not the most reason version at github, please download again and retry. There is no problem with LAsort and LAmerge, daligner did not run because there is no dust track, did you produce one with DBdust? -- Gene … <#> On 9/24/18, 2:18 AM, daniellezhang wrote: I have followed the example in DAZZ_DB to create stimulated data to test out daligner. But I receive the following error message. Similar error occur when I tried to use daligner with lambda phage data. ------------------------------------------------------------------------ unix306 554 % HPCdaligner -mdust -t5 G | csh -v daligner -t5 -mdust G.1 G.1 daligner: Track 'dust' annotation file is junk daligner -t5 -mdust G.2 G.1 G.2 daligner: Track 'dust' annotation file is junk LAsort G.1.G.1.C0 G.1.G.1.N0 G.1.G.1.C1 G.1.G.1.N1 G.1.G.1.C2 G.1.G.1.N2 G.1.G.1.C3 G.1.G.1.N3 && LAmerge L1.1.1 G.1.G.1.C0.S G.1.G.1.N0.S G.1.G.1.C1.S G.1.G.1.N1.S G.1.G.1.C2.S G.1.G.1.N2.S G.1.G.1.C3.S G.1.G.1.N3.S && rm G.1.G.1.C0.S.las G.1.G.1.N0.S.las G.1.G.1.C1.S.las G.1.G.1.N1.S.las G.1.G.1.C2.S.las G.1.G.1.N2.S.las G.1.G.1.C3.S.las G.1.G.1.N3.S.las LAsort: Cannot open ./G.1.G.1.C0.las for 'r' LAsort G.1.G.2.C0 G.1.G.2.N0 G.1.G.2.C1 G.1.G.2.N1 G.1.G.2.C2 G.1.G.2.N2 G.1.G.2.C3 G.1.G.2.N3 && LAmerge L1.1.2 G.1.G.2.C0.S G.1.G.2.N0.S G.1.G.2.C1.S G.1.G.2.N1.S G.1.G.2.C2.S G.1.G.2.N2.S G.1.G.2.C3.S G.1.G.2.N3.S && rm G.1.G.2.C0.S.las G.1.G.2.N0.S.las G.1.G.2.C1.S.las G.1.G.2.N1.S.las G.1.G.2.C2.S.las G.1.G.2.N2.S.las G.1.G.2.C3.S.las G.1.G.2.N3.S.las LAsort: Cannot open ./G.1.G.2.C0.las for 'r' LAsort G.2.G.1.C0 G.2.G.1.N0 G.2.G.1.C1 G.2.G.1.N1 G.2.G.1.C2 G.2.G.1.N2 G.2.G.1.C3 G.2.G.1.N3 && LAmerge L1.2.1 G.2.G.1.C0.S G.2.G.1.N0.S G.2.G.1.C1.S G.2.G.1.N1.S G.2.G.1.C2.S G.2.G.1.N2.S G.2.G.1.C3.S G.2.G.1.N3.S && rm G.2.G.1.C0.S.las G.2.G.1.N0.S.las G.2.G.1.C1.S.las G.2.G.1.N1.S.las G.2.G.1.C2.S.las G.2.G.1.N2.S.las G.2.G.1.C3.S.las G.2.G.1.N3.S.las LAsort: Cannot open ./G.2.G.1.C0.las for 'r' LAsort G.2.G.2.C0 G.2.G.2.N0 G.2.G.2.C1 G.2.G.2.N1 G.2.G.2.C2 G.2.G.2.N2 G.2.G.2.C3 G.2.G.2.N3 && LAmerge L1.2.2 G.2.G.2.C0.S G.2.G.2.N0.S G.2.G.2.C1.S G.2.G.2.N1.S G.2.G.2.C2.S G.2.G.2.N2.S G.2.G.2.C3.S G.2.G.2.N3.S && rm G.2.G.2.C0.S.las G.2.G.2.N0.S.las G.2.G.2.C1.S.las G.2.G.2.N1.S.las G.2.G.2.C2.S.las G.2.G.2.N2.S.las G.2.G.2.C3.S.las G.2.G.2.N3.S.las LAsort: Cannot open ./G.2.G.2.C0.las for 'r' LAmerge G.1 L1.1.1 L1.1.2 && rm L1.1.1.las L1.1.2.las LAmerge: Cannot open ./L1.1.1.las for 'r' LAmerge G.2 L1.2.1 L1.2.2 && rm L1.2.1.las L1.2.2.las LAmerge: Cannot open ./L1.2.1.las for 'r' — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#86 <https://github.com/thegenemyers/DALIGNER/issues/86>>, or mute the thread https://github.com/notifications/unsubscribe-auth/AGkkNsmamO0uZjpOBZOaNC3qMcXuZgsOks5ueCS4gaJpZM4W18hN.
Thanks for pointing that out Gene. I tried again with the latest version on github rather than bioconda and the message about dust has disappeared. However, when I tried to use LAshow, I received the following message: |unix306 725 % LAshow -c -a:G -w50 G.1 | more LAshow: -: is an illegal option|
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I have followed the example in DAZZ_DB to create stimulated data to test out daligner. But I receive the following error message. Similar error occur when I tried to use daligner with lambda phage data.
unix306 554 % HPCdaligner -mdust -t5 G | csh -v
daligner -t5 -mdust G.1 G.1 daligner: Track 'dust' annotation file is junk daligner -t5 -mdust G.2 G.1 G.2 daligner: Track 'dust' annotation file is junk
LAsort G.1.G.1.C0 G.1.G.1.N0 G.1.G.1.C1 G.1.G.1.N1 G.1.G.1.C2 G.1.G.1.N2 G.1.G.1.C3 G.1.G.1.N3 && LAmerge L1.1.1 G.1.G.1.C0.S G.1.G.1.N0.S G.1.G.1.C1.S G.1.G.1.N1.S G.1.G.1.C2.S G.1.G.1.N2.S G.1.G.1.C3.S G.1.G.1.N3.S && rm G.1.G.1.C0.S.las G.1.G.1.N0.S.las G.1.G.1.C1.S.las G.1.G.1.N1.S.las G.1.G.1.C2.S.las G.1.G.1.N2.S.las G.1.G.1.C3.S.las G.1.G.1.N3.S.las LAsort: Cannot open ./G.1.G.1.C0.las for 'r' LAsort G.1.G.2.C0 G.1.G.2.N0 G.1.G.2.C1 G.1.G.2.N1 G.1.G.2.C2 G.1.G.2.N2 G.1.G.2.C3 G.1.G.2.N3 && LAmerge L1.1.2 G.1.G.2.C0.S G.1.G.2.N0.S G.1.G.2.C1.S G.1.G.2.N1.S G.1.G.2.C2.S G.1.G.2.N2.S G.1.G.2.C3.S G.1.G.2.N3.S && rm G.1.G.2.C0.S.las G.1.G.2.N0.S.las G.1.G.2.C1.S.las G.1.G.2.N1.S.las G.1.G.2.C2.S.las G.1.G.2.N2.S.las G.1.G.2.C3.S.las G.1.G.2.N3.S.las LAsort: Cannot open ./G.1.G.2.C0.las for 'r' LAsort G.2.G.1.C0 G.2.G.1.N0 G.2.G.1.C1 G.2.G.1.N1 G.2.G.1.C2 G.2.G.1.N2 G.2.G.1.C3 G.2.G.1.N3 && LAmerge L1.2.1 G.2.G.1.C0.S G.2.G.1.N0.S G.2.G.1.C1.S G.2.G.1.N1.S G.2.G.1.C2.S G.2.G.1.N2.S G.2.G.1.C3.S G.2.G.1.N3.S && rm G.2.G.1.C0.S.las G.2.G.1.N0.S.las G.2.G.1.C1.S.las G.2.G.1.N1.S.las G.2.G.1.C2.S.las G.2.G.1.N2.S.las G.2.G.1.C3.S.las G.2.G.1.N3.S.las LAsort: Cannot open ./G.2.G.1.C0.las for 'r' LAsort G.2.G.2.C0 G.2.G.2.N0 G.2.G.2.C1 G.2.G.2.N1 G.2.G.2.C2 G.2.G.2.N2 G.2.G.2.C3 G.2.G.2.N3 && LAmerge L1.2.2 G.2.G.2.C0.S G.2.G.2.N0.S G.2.G.2.C1.S G.2.G.2.N1.S G.2.G.2.C2.S G.2.G.2.N2.S G.2.G.2.C3.S G.2.G.2.N3.S && rm G.2.G.2.C0.S.las G.2.G.2.N0.S.las G.2.G.2.C1.S.las G.2.G.2.N1.S.las G.2.G.2.C2.S.las G.2.G.2.N2.S.las G.2.G.2.C3.S.las G.2.G.2.N3.S.las LAsort: Cannot open ./G.2.G.2.C0.las for 'r'
LAmerge G.1 L1.1.1 L1.1.2 && rm L1.1.1.las L1.1.2.las LAmerge: Cannot open ./L1.1.1.las for 'r' LAmerge G.2 L1.2.1 L1.2.2 && rm L1.2.1.las L1.2.2.las LAmerge: Cannot open ./L1.2.1.las for 'r'