Let's use Anna Battenhouse's shell script align_bwa.sh to align the fastq files to the hg19 version of the genome, and the python program launcher_creator.py to create the job submission script. Don't forget that for this to work, you need to have appended $BI/bin to your path. | Expand |
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| Show me how to modify my path... |
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| Show me how to modify my path... |
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| BI="/corral-repl/utexas/BioITeam"
PATH=$PATH:$BI/bin
export PATH |
Move into your scratch directory and then try to figure out how to create and qsub the align_bwa.sh command to align the data file $BI/ngs_course/human_variation/allseqs_R1.fastq against the hg19 reference. Call the output "test". | Expand |
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| title | Make job submission script for mapping & variant calling |
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| echo "align_bwa.sh $BI/ngs_course/human_variation/allseqs_R1.fastq test hg19 1 > aln.test.log 2>&1" > commands
launcher_creator.py -l map_call.sge -n map_call -t 01:00:00 -j commands
module load bwa
module load samtools
qsub map_call.sge
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Caution: If you are using this example outside an SSC course, you must use the -a option to specify a valid allocation (e.g. BME_2012)
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login1$ echo "align_bwa.sh $BI/ngs_course/human_variation/allseqs_R1.fastq test hg19 1" > commands
launcher_creator.py -l map_call.sge -n map_call -t 01:00:00 -j commands
Job file has 1 lines.
Using 12 cores.
Launcher successfully created. Type "qsub map_call.sge" to queue your job.
login1$ qsub map_call.sge
-----------------------------------------------------------------
-- Welcome to the Lonestar4 Westmere/QDR IB Linux Cluster --
-----------------------------------------------------------------
--> Checking that you specified -V...
--> Checking that you specified a time limit...
--> Checking that you specified a queue...
--> Setting project...
--> Checking that you specified a parallel environment...
--> Checking that you specified a valid parallel environment name...
--> Checking that the number of PEs requested is valid...
--> Ensuring absence of dubious h_vmem,h_data,s_vmem,s_data limits...
--> Requesting valid memory configuration (23.4G)...
--> Verifying HOME file-system availability...
--> Verifying WORK file-system availability...
--> Verifying SCRATCH file-system availability...
--> Checking ssh setup...
--> Checking that you didn't request more cores than the maximum...
--> Checking that you don't already have the maximum number of jobs...
--> Checking that you don't already have the maximum number of jobs in queue development...
--> Checking that your time limit isn't over the maximum...
--> Checking available allocation...
--> Submitting job...
Your job 586249 ("map_call") has been submitted
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Note that the input is paired-end data. | Expand |
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| Your directory should have content like this when done (from ls -lt): | Code Block |
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| -rw-r--r-- 1 sphsmith G-801020 5732 May 20 23:01 map_call.o586338
-rw------- 1 sphsmith G-801020 392 May 20 23:01 test.flagstat.txt
-rw------- 1 sphsmith G-801020 2175952 May 20 23:01 test.sorted.bam.bai
-rw------- 1 sphsmith G-801020 334782188 May 20 23:01 test.sorted.bam
-rw-r--r-- 1 sphsmith G-801020 13135 May 20 23:00 map_call.e586338
-rw------- 1 sphsmith G-801020 411244396 May 20 23:00 test.bam
-rw------- 1 sphsmith G-801020 45695040 May 20 22:49 test.read2.sai
-rw------- 1 sphsmith G-801020 45372400 May 20 22:39 test.read1.sai
-rw-r--r-- 1 sphsmith G-801020 0 May 20 22:26 map_call.pe586338
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and samtools flagstat test.sorted.bam should yield: | Code Block |
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| title | samtools flagstat results |
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| Running flagstat...
4546280 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 duplicates
3992274 + 0 mapped (87.81%:nan%)
4546280 + 0 paired in sequencing
2273140 + 0 read1
2273140 + 0 read2
40290 + 0 properly paired (0.89%:nan%)
3636946 + 0 with itself and mate mapped
355328 + 0 singletons (7.82%:nan%)
44128 + 0 with mate mapped to a different chr
15634 + 0 with mate mapped to a different chr (mapQ>=5)
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