Start 11:50 AM 2/24/12

#fail with 14 threads

retry running 8. (recall that might be the suggested limit)

#fail

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tried different

appears to be problem with reference.

trying locally

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robertsmac:bsmap-2.42 sr320$ ./bsmap -a /Volumes/Bay3/Software/bismark_v0.6.4/filtered_Unlabeled_NoIndex_L003_R1_trimmed.fastq -d /Volumes/Bay3/Software/bismark_v0.6.4/temp/Combined_fosmids_cd_hit_mod.fa -o /Volumes/Bay3\ scratch/BSMAP_output_trimmed_CombFosmids_cdhit_mod.sam -p 1

!!!! Seems to be working 

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next day complete

139600000 reads finished. 31791 secs passed

139650000 reads finished. 31801 secs passed

139660651 reads finished. 31803 secs passed

Total number of aligned reads: 76152522 (55%)

Done.

Finished at Fri Feb 24 22:01:12 2012

Total time consumed:  31803 secs

robertsmac:bsmap-2.42 sr320$ 

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vsualize in CLC 5.0

Placing both the SAM out put and reference on Galaxy…

SAM FILE: http://main.g2.bx.psu.edu/datasets/42a1545a56ba1545/display?username=sr320&to_ext=sam&slug=repository    (~12 GB)

REFERENCE: http://main.g2.bx.psu.edu/datasets/d4a56e6992f8319e/display?username=sr320&to_ext=fasta&slug=repository

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Tablea should open 

updtate: crashed