Testing out Pilon

Objective: Test out using Pilon on the MiSeq and PGM data Approach: Running Pilon using bash commands, evaluate revise reference relative to HGAP and GenBank LT2

Testing single paried end dataset



In [10]:

    
%%bash
java -Xmx4G -jar ../utilities/pilon-1.10.jar \
                --genome ../data/RM8375/ref/CFSAN008157.HGAP.fasta \
                --frags ../analysis/bioinf/sequence_purity/mapping/SRR1555296.bam \
                --changes --vcf --tracks \
                --fix "all" --debug #note --fix "all" default









    



Pilon version 1.10 Tue Nov 18 20:14:04 2014 -0500
Genome: ../data/RM8375/ref/CFSAN008157.HGAP.fasta
OpenJDK 64-Bit Server VM warning: INFO: os::commit_memory(0x00000007b2500000, 20447232, 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 20447232 bytes for committing reserved memory.
# An error report file with more information is saved as:
# /notebooks/dev/hs_err_pid246.log

Error with head, needed to rerun bwa with revised params file

Error with memory allocation, not sure if too many applicaitons running on laptop, or docker memory restrictions

re-running after closing windows and restarting finder (hung up on moving files to trash)
Need to look into changing amount of memory allocated to ipython notebook



In [12]:

    
%%bash 
python ../analysis/bioinf/sequence_purity/run_bwa_mem_pe.py \
        ../analysis/bioinf/sequence_purity/bwa_mem_pipeline_params.txt

Merging bams



In [5]:

    
At



In [6]:

    
%%bash
ls ../data/RM8375/PGM/bam/*bam >HGAP.PGM.bams
samtools merge -b HGAP.PGM.bams HGAP_PGM.bam
samtools index HGAP_PGM.bam