Running Pilon on MiSeq data mapped to Genbank LT2, HGAP_MiSeq Pilon, and HGAP_PGM Pilon references

Merging bams



In [10]:

    
%%bash
ls ../sequence_purity/mapping_2015_01_09/HGAP_MiSeq*bam >HGAP_MiSeq.miseq.bams
samtools merge -b HGAP_MiSeq.miseq.bams HGAP_MiSeq_merged.bam
samtools index HGAP_MiSeq_merged.bam



In [14]:

    
%%bash
ls ../sequence_purity/mapping_2015_01_09/HGAP_PGM*bam >HGAP_PGM.miseq.bams
samtools merge -b HGAP_PGM.miseq.bams HGAP_PGM_miseq_merged.bam
samtools index HGAP_PGM_miseq_merged.bam



In [15]:

    
%%bash
ls ../sequence_purity/mapping_2015_01_09/NC_003197.1*bam >NC_003197.1.miseq.bams
samtools merge -b NC_003197.1.miseq.bams NC_003197.1_miseq_merged.bam
samtools index NC_003197.1_miseq_merged.bam

Running Pilon on Merged bams



In [11]:

    
%%bash
java -Xmx8G -jar ../../../utilities/pilon-1.10.jar \
                --genome ../../../data/RM8375/ref/HGAP_MiSeq.fasta \
                --frags HGAP_MiSeq_merged.bam \
                --changes --vcf --tracks \
                --fix "all" --output HGAP_MiSeq.miseq









    



Pilon version 1.10 Tue Nov 18 20:14:04 2014 -0500
Genome: ../../../data/RM8375/ref/HGAP_MiSeq.fasta
Fixing bases, gaps, local
Input genome size: 4951418
Scanning BAMs
HGAP_MiSeq_merged.bam: 34493957 reads, 0 filtered, 34468442 mapped, 34419526 proper, 33184 stray, insert size 227+/-113
Processing unitig_0|quiver|quiver|quiver|pilon:1-4857490
frags HGAP_MiSeq_merged.bam: OpenJDK 64-Bit Server VM warning: INFO: os::commit_memory(0x00000007a3780000, 77070336, 0) failed; error='Cannot allocate memory' (errno=12)
#
# There is insufficient memory for the Java Runtime Environment to continue.
# Native memory allocation (malloc) failed to allocate 77070336 bytes for committing reserved memory.
# An error report file with more information is saved as:
# /notebooks/analysis/bioinf/genome_structure/hs_err_pid60.log



In [ ]:

    
started at 5:50 PM



In [8]:

    
%%bash
java -Xmx8G -jar ../../../utilities/pilon-1.10.jar \
                --genome ../../../data/RM8375/ref/HGAP_PGM.fasta \
                --unpaired HGAP_PGM_miseq_merged.bam \
                --changes --vcf --tracks \
               --fix "all" --debug --output HGAP_PGM.miseq



In [ ]:

    
%%bash
java -Xmx8G -jar ../../../utilities/pilon-1.10.jar \
                --genome ../../../data/RM8375/ref/NC_003197.1.fasta \
                --unpaired NC_003197.1_miseq_merged.bam \
                --changes --vcf --tracks \
               --fix "all" --debug --output NC_003197.1.miseq