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pre-processing_quality_control [2018/11/08 06:23]
david [Not covered in this lesson]
pre-processing_quality_control [2018/11/08 10:46] (current)
david [Running the programs through an sbatch script]
Line 90: Line 90:
  2 files changed, 13 insertions(+),​ 9 deletions(-)  2 files changed, 13 insertions(+),​ 9 deletions(-)
 </​code>​ </​code>​
 +
 +Check that everything is OK.
 +
 +<​code>​
 +$ make setup
 +</​code>​
 +
 <​code>​ <​code>​
 $ ls $ ls
Line 102: Line 109:
 bin/ bin/
 </​code>​ </​code>​
 +
 +===== A great "​get"​ from git =====
 +
 +One of the greatest benefits of tracking changes is that you can see what you've changed.
 +
 +Let's say that, with an editor, I change line four of 03_scripts/​number_of_reads.sbatch to use a 10 minute time limit instead of 1 minute.
 +<​code>​
 +$ nano 03_scripts/​number_of_reads.sbatch
 +</​code>​
 +
 +Line four now reads:
 +<​code>​
 +#SBATCH --time=0:​10:​00
 +</​code>​
 +
 +I can use git to tell me what's different:
 +
 +<​code>​
 +$ git diff 03_scripts/​number_of_reads.sbatch ​
 +diff --git a/​03_scripts/​number_of_reads.sbatch b/​03_scripts/​number_of_reads.sbatch
 +index 0634563..3106155 100644
 +--- a/​03_scripts/​number_of_reads.sbatch
 ++++ b/​03_scripts/​number_of_reads.sbatch
 +@@ -1,7 +1,7 @@
 + #​!/​usr/​bin/​env bash
 + #​SBATCH --nodes=1 ​ # access with $SLURM_NNODES in the script
 + #​SBATCH --ntasks=1 ​ # access with $SLURM_NTASKS in the script
 +-#SBATCH --time=0:​01:​00
 ++#SBATCH --time=0:​10:​00
 + #​SBATCH --qos=testing # change to "​normal"​ when done testing
 + #​SBATCH --partition=shas-testing # remove "​-testing"​ when done testing
 + #​SBATCH --output=numreads-%j.out
 +</​code>​
 +
 +What if I screwed up?
 +
 +<​code>​
 +$ git checkout 03_scripts/​number_of_reads.sbatch
 +</​code>​
 +
 +Line 4 goes back to the original!
 +<​code>​
 +#SBATCH --time=0:​01:​00
 +</​code>​
 +
  
  
Line 205: Line 257:
 So let's look at one of ours: So let's look at one of ours:
 <​code>​ <​code>​
-$ head -4 01_input/SRR3567552_1.fastq ​+$ head -4 01_input/SRR3567551_1.fastq ​
 @SRR3567552.1 HISEQ:​222:​C3RTWACXX:​1:​1101:​1411:​2064 length=100 @SRR3567552.1 HISEQ:​222:​C3RTWACXX:​1:​1101:​1411:​2064 length=100
 GTGCTTGTGGACTGCTTGGTGGGGCTTGCTCTGCTAGGCGGACTACTTGCGTGCCTTGTTGTAGACGGCCTTGGTAGGTCTCTTGTAGACCGTCGCTTGC GTGCTTGTGGACTGCTTGGTGGGGCTTGCTCTGCTAGGCGGACTACTTGCGTGCCTTGTTGTAGACGGCCTTGGTAGGTCTCTTGTAGACCGTCGCTTGC
Line 217: Line 269:
  
 <​code>​ <​code>​
-$ ls -lh 01_input/SRR3567552_1.fastq ​+$ ls -lh 01_input/SRR3567551_1.fastq ​
 -rw-r--r-- 1 erinnish@colostate.edu erinnishgrp@colostate.edu 6.6G Oct 16 15:14 01_input/​SRR3567552_1.fastq -rw-r--r-- 1 erinnish@colostate.edu erinnishgrp@colostate.edu 6.6G Oct 16 15:14 01_input/​SRR3567552_1.fastq
 </​code>​ </​code>​
Line 235: Line 287:
  
 <​code>​ <​code>​
-$ sbatch 03_scripts/​number_of_reads.sbatch 01_input/SRR3567552_1.fastq+$ sbatch 03_scripts/​number_of_reads.sbatch 01_input/SRR3567551_1.fastq
 </​code>​ </​code>​
  
Line 276: Line 328:
 Summit was still recovering from maintenance yesterday, so my job just sat there, but I expect a file to be created in the directory called ''​numreads-1388630.out''​ containing the line: Summit was still recovering from maintenance yesterday, so my job just sat there, but I expect a file to be created in the directory called ''​numreads-1388630.out''​ containing the line:
 <​code>​ <​code>​
-01_input/SRR3567552_1.fastq has 20654219 reads.+01_input/SRR3567551_1.fastq has 20654219 reads.
 </​code>​ </​code>​
  
pre-processing_quality_control.1541683432.txt.gz ยท Last modified: 2018/11/08 06:23 by david