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
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.