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| Code Block |
|---|
| language | bash |
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| title | Generic command |
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|
breseq -j 96 -r NC_012967.1.gbk -o run_output/<XX>K <ID>_1.fastq <ID>_2.fastq &> logs/<XX>K.log.txt
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And its parts can be explained as follows:
| part | purpose |
|---|
| -j 96 | use 9 6 processors/threads speeding things up by less than a factor of 9 as 6 as discussed in earlier tutorials |
| -o run_output/<xx>k | directs all output to the run_output directory, AND creates a new directory with 2 digits (<XX>) followed by a K for individual samples data. If we don't include the second part referencing the individual sample, breseq would write the output from all of the runs on top of one other. The program will undoubtedly get confused, possibly crash, but definitely not be analyzable |
| <ID> | this is just used to denote read1 and or read2 ... note that in our acutal commands they reference the fastq files, and are supplied without an option |
| &> logs/<XX>00K.log.txt | Redirect both the standard output and the standard error streams to a file called <XX>00k.log.txt. and put that file in a directory named logs. The &> are telling the command line to send the streams to that file. |
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| Info |
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- Each stampede2 compute node has 68 48 processors available.
- We have 7 samples to run, so by requesting 9 6 processors, we allow all 7 samples to start at the same time leaving 5 6 unused processors.
- If we had requested 10 7 processors for each sample, only 6 samples would start initially and the 7th would start after the first finishes.
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| Code Block |
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| language | bash |
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| title | This is the expected nano command, not the text that goes in the file. |
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| collapse | true |
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|
nano breseq_commands |
| No Format |
|---|
breseq -j 96 -r NC_012967.1.gbk -o run_output/00K SRR030252_1.fastq SRR030252_2.fastq &> logs/00K.log.txt
breseq -j 96 -r NC_012967.1.gbk -o run_output/02K SRR030253_1.fastq SRR030253_2.fastq &> logs/02K.log.txt
breseq -j 96 -r NC_012967.1.gbk -o run_output/05K SRR030254_1.fastq SRR030254_2.fastq &> logs/05K.log.txt
breseq -j 96 -r NC_012967.1.gbk -o run_output/10K SRR030255_1.fastq SRR030255_2.fastq &> logs/10K.log.txt
breseq -j 96 -r NC_012967.1.gbk -o run_output/15K SRR030256_1.fastq SRR030256_2.fastq &> logs/15K.log.txt
breseq -j 96 -r NC_012967.1.gbk -o run_output/20K SRR030257_1.fastq SRR030257_2.fastq &> logs/20K.log.txt
breseq -j 96 -r NC_012967.1.gbk -o run_output/40K SRR030258_1.fastq SRR030258_2.fastq &> logs/40K.log.txt |
...