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Old 01-18-2013, 01:01 AM   #21
ppoudel
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Thanks Tom.
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Old 01-24-2013, 01:42 AM   #22
amolkolte
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I have been running GSNAP as a part of trinity pipeline.

To begin with, I have paired ends reads of 7GB of size for each read file.
The pipeline has executed the following code,

Code:
gsnap -d target.gmap -D . -A sam -N 1 -w 10000 -n 20 -t 45 /home/amol/trimmed_datasets/AP_treated/R33_APT_s_3_1_trimmed.fastq /home/amol/trimmed_datasets/AP_treated/R33_APT_s_3_2_trimmed.fastq
More that 30 hours have been passed and the script is showing a message "Starting alignment". I can see (using top) that, gsnap is taking resources but at the same time its showing the process status as 'sleeping'

Can anyone please explain.

Thanks
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Old 01-29-2013, 02:07 AM   #23
amolkolte
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After running for 6 days, gsnap finally generated an 34 GB sam file.

Alternatively, I noticed at later point that you can monitor the output file size under your 'gsnap_out' directory and estimate where the alignment have reached.

Code:
du -h gsnap_out/gsnap.sam
File size would increase as the alignment proceeds and you can make sure that the program is running.
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