You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
Mobster keeps failing on mobiome mapping with both bwa and mosaik. I have checked my input/output, mobiome command and formatting of the properties file and there are no mistakes; it is how the example properties file is formatted. It is also strange as it seems to run the commands but fails when it sees the value in the MOBIOME_MAPPING_TOOL field.
Here is the error output for Mosaik (BWA gives the same too):
4720367 [main] INFO org.umcn.me.pairedend.PotentialMEIReadFinder - Processed 10500000 mobile read pairs that have split read or certain size
4824111 [main] INFO org.umcn.me.pairedend.PotentialMEIReadFinder - Found nr of potential mobile pairs supporting MEI events: 22915732
4824112 [main] INFO org.umcn.me.pairedend.PotentialMEIReadFinder - Of which 10511452 are of split-read nature.
4824125 [main] INFO org.umcn.me.pairedend.PotentialMEIReadFinder - [PMRF] PotentialMEIReadFinder ran in : 80 min, 24 sec
^[[1;33m^[[0m- loading jump key database into memory... finished.
loading jump positions database into memory... finished.
^[[0m
Exit value: 0
14448617 [main] INFO org.umcn.me.pairedend.RefAndMEPairFinder - Using potential .bam file: /apache-maven-3.6.3/mobster/target/MEI_2$
14448617 [main] INFO org.umcn.me.pairedend.RefAndMEPairFinder - Using output prefix: apache-maven-3.6.3/mobster/target/MEI_2
14448617 [main] INFO org.umcn.me.pairedend.RefAndMEPairFinder - Mapping tool used for mobile mapping: mosaik
14448617 [main] INFO org.umcn.me.pairedend.RefAndMEPairFinder - Paired-end reads: true
14448617 [main] INFO org.umcn.me.pairedend.RefAndMEPairFinder - Setting sample name to: MEI_2
14448617 [main] INFO org.umcn.me.pairedend.RefAndMEPairFinder - Using temp: /tmp/mob_16586391568628742
15023253 [main] INFO org.umcn.me.pairedend.RefAndMEPairFinder - Found: 2550 unique-unique pairs with both ends mapping to mobile ref, excluding filtere$
15023254 [main] INFO org.umcn.me.pairedend.RefAndMEPairFinder - These reads are filtered
15023258 [main] INFO org.umcn.me.pairedend.RefAndMEPairFinder - Using max mobiome mappings of (-1 is disabled) : -1
15023263 [main] ERROR org.umcn.me.pairedend.RefAndMEPairFinder - No support for the following mapping tool: mosaik
15023274 [main] ERROR org.umcn.me.pairedend.RefAndMEPairFinder - No support for the following mapping tool: mosaik
15023274 [main] ERROR org.umcn.me.pairedend.RefAndMEPairFinder - No support for the following mapping tool: mosaik
The text was updated successfully, but these errors were encountered:
Hi there,
Mobster keeps failing on mobiome mapping with both bwa and mosaik. I have checked my input/output, mobiome command and formatting of the properties file and there are no mistakes; it is how the example properties file is formatted. It is also strange as it seems to run the commands but fails when it sees the value in the MOBIOME_MAPPING_TOOL field.
Here is the error output for Mosaik (BWA gives the same too):
4720367 [main] INFO org.umcn.me.pairedend.PotentialMEIReadFinder - Processed 10500000 mobile read pairs that have split read or certain size
4824111 [main] INFO org.umcn.me.pairedend.PotentialMEIReadFinder - Found nr of potential mobile pairs supporting MEI events: 22915732
4824112 [main] INFO org.umcn.me.pairedend.PotentialMEIReadFinder - Of which 10511452 are of split-read nature.
4824125 [main] INFO org.umcn.me.pairedend.PotentialMEIReadFinder - [PMRF] PotentialMEIReadFinder ran in : 80 min, 24 sec
^[[1;33m^[[0m- loading jump key database into memory... finished.
^[[0m
Exit value: 0
14448617 [main] INFO org.umcn.me.pairedend.RefAndMEPairFinder - Using potential .bam file: /apache-maven-3.6.3/mobster/target/MEI_2$
14448617 [main] INFO org.umcn.me.pairedend.RefAndMEPairFinder - Using output prefix: apache-maven-3.6.3/mobster/target/MEI_2
14448617 [main] INFO org.umcn.me.pairedend.RefAndMEPairFinder - Mapping tool used for mobile mapping: mosaik
14448617 [main] INFO org.umcn.me.pairedend.RefAndMEPairFinder - Paired-end reads: true
14448617 [main] INFO org.umcn.me.pairedend.RefAndMEPairFinder - Setting sample name to: MEI_2
14448617 [main] INFO org.umcn.me.pairedend.RefAndMEPairFinder - Using temp: /tmp/mob_16586391568628742
15023253 [main] INFO org.umcn.me.pairedend.RefAndMEPairFinder - Found: 2550 unique-unique pairs with both ends mapping to mobile ref, excluding filtere$
15023254 [main] INFO org.umcn.me.pairedend.RefAndMEPairFinder - These reads are filtered
15023258 [main] INFO org.umcn.me.pairedend.RefAndMEPairFinder - Using max mobiome mappings of (-1 is disabled) : -1
15023263 [main] ERROR org.umcn.me.pairedend.RefAndMEPairFinder - No support for the following mapping tool: mosaik
15023274 [main] ERROR org.umcn.me.pairedend.RefAndMEPairFinder - No support for the following mapping tool: mosaik
15023274 [main] ERROR org.umcn.me.pairedend.RefAndMEPairFinder - No support for the following mapping tool: mosaik
The text was updated successfully, but these errors were encountered: