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Find all significant local alignments between reads
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LAsort and LAmerge error: cannot open #86

Closed daniellezhang closed 4 years ago

daniellezhang commented 5 years ago

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'

gt1 commented 5 years ago

The issue seems to be a broken dust track. Could you check the output of DBdust?

thegenemyers commented 5 years ago

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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daniellezhang commented 5 years ago

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

thegenemyers commented 5 years ago

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|

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/thegenemyers/DALIGNER/issues/86#issuecomment-424218285, or mute the thread https://github.com/notifications/unsubscribe-auth/AGkkNllRyHg4jtjQ0_mHUzj-uelxt-1Gks5uecgmgaJpZM4W18hN.