Mosaik reference sequence format

[JamesBearman]

I am trying to to run mobster however it has this error,
ERROR: It seems that the input file (../resources/mobiome/54_mobiles_inclHERVK.dat) is not in the MOSAIK reference sequence archive format.
Exit value: 1
530138 [main] FATAL Mobster - Mobiome mapping finished with non-normal exit value: 1
530139 [main] FATAL Mobster - Therefore Mobster execution is terminated
I am running this on linux any advice would be appreciated.
Thanks
James

[jyhehir]

Hi James, Can you confirm the size of the 54_mobiles.dat.Have you used git lfs to get them? Regards,Jayne On Thursday, 7 December 2017, 16:58, JamesBearman <notifications@github.com> wrote: I am trying to to run mobster however it has this error, ERROR: It seems that the input file (../resources/mobiome/54_mobiles_inclHERVK.dat) is not in the MOSAIK reference sequence archive format. Exit value: 1 530138 [main] FATAL Mobster - Mobiome mapping finished with non-normal exit value: 1 530139 [main] FATAL Mobster - Therefore Mobster execution is terminated I am running this on linux any advice would be appreciated. Thanks James— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.

[JamesBearman]

Hi Jayne
I have reinstalled mobster using lfs to get them now obtaining this error

• loading jump positions database into memory... finished.
  /bin/sh: line 1: 30758 Segmentation fault (core dumped) /data/Install/MOSAIK/bin/MosaikAligner -in ./NA12878TestDefaultMobster_potential.dat -out ./NA12878TestDefaultMobster_mappedpotentials -ia ../resources/mobiome/54_mobiles_inclHERVK.dat -hs 9 -mmp 0.1 -act 20 -j ../resources/mobiome/54_mobiles_inclHERVK_hs9 -p 2 -annpe ../resources/MOSAIK/2.1.26.pe.100.0065.ann -annse ../resources/MOSAIK/2.1.26.se.100.005.ann -quiet
  Exit value: 139
  579977 [main] FATAL Mobster - Mobiome mapping finished with non-normal exit value: 139
  579977 [main] FATAL Mobster - Therefore Mobster execution is terminated

file size is 88Kb for the .dat file
Thanks you
James

[jyhehir]

Hi James, Looks that you have solved the resources problem, this is an error in Mosaik a 3rd party module of Mobster.Have you tried the demo provided by Mosaik?Which platform are you on? Regards,Jayne On Monday, 11 December 2017, 19:37, JamesBearman <notifications@github.com> wrote: Hi Jayne I have reinstalled mobster using lfs to get them now obtaining this error - loading jump positions database into memory... finished. /bin/sh: line 1: 30758 Segmentation fault (core dumped) /data/Install/MOSAIK/bin/MosaikAligner -in ./NA12878TestDefaultMobster_potential.dat -out ./NA12878TestDefaultMobster_mappedpotentials -ia ../resources/mobiome/54_mobiles_inclHERVK.dat -hs 9 -mmp 0.1 -act 20 -j ../resources/mobiome/54_mobiles_inclHERVK_hs9 -p 2 -annpe ../resources/MOSAIK/2.1.26.pe.100.0065.ann -annse ../resources/MOSAIK/2.1.26.se.100.005.ann -quiet Exit value: 139 579977 [main] FATAL Mobster - Mobiome mapping finished with non-normal exit value: 139 579977 [main] FATAL Mobster - Therefore Mobster execution is terminated file size is 88Kb for the .dat file Thanks you James— You are receiving this because you commented. Reply to this email directly, view it on GitHub, or mute the thread.