Pre Script

module load python/3.7.7-fasrc01
conda activate sortmerna

Script

#!/bin/bash
DB1="DBsortmerna"

DBRoot="/n/holystore01/LABS/huttenhower_lab/Users/george.weingart/KneadData_eval/sortmerna/Databases"/${DB1}
Reads="/n/holystore01/LABS/huttenhower_lab/Users/george.weingart/KneadData_eval/sortmerna/Hu90Mi10/human_microbial_mixed.fastq"
mkdir Workdir${DB1}
Workdir="/n/holystore01/LABS/huttenhower_lab/Users/george.weingart/KneadData_eval/sortmerna/run_sortmerna/Workdir"${DB1}
nohup sortmerna --ref ${DBRoot}/${DB1}.fasta  --reads ${Reads}  -workdir ${Workdir} -fastx -sam> sortmerna_DBsortmerna.log &



LOG:

(base) [george.weingart@hutlab12 run_sortmerna]$ module load python/3.7.7-fasrc01

The following have been reloaded with a version change:
  1) python/2.7.14-fasrc01 => python/3.7.7-fasrc01

(base) [george.weingart@hutlab12 run_sortmerna]$ conda activate sortmerna
(sortmerna) [george.weingart@hutlab12 run_sortmerna]$ DB1="DBsortmerna"
(sortmerna) [george.weingart@hutlab12 run_sortmerna]$ DBRoot="/n/holystore01/LABS/huttenhower_lab/Users/george.weingart/KneadData_eval/sortmerna/Databases"/${DB1}
(sortmerna) [george.weingart@hutlab12 run_sortmerna]$ Reads="/n/holystore01/LABS/huttenhower_lab/Users/george.weingart/KneadData_eval/sortmerna/Hu90Mi10/human_microbial_mixed.fastq"
(sortmerna) [george.weingart@hutlab12 run_sortmerna]$ mkdir Workdir${DB1}
(sortmerna) [george.weingart@hutlab12 run_sortmerna]$ Workdir="/n/holystore01/LABS/huttenhower_lab/Users/george.weingart/KneadData_eval/sortmerna/run_sortmerna/Workdir"${DB1}
(sortmerna) [george.weingart@hutlab12 run_sortmerna]$ nohup sortmerna --ref ${DBRoot}/${DB1}.fasta  --reads ${Reads}  -workdir ${Workdir} -fastx -sam> sortmerna_DBsortmerna.log &
[1] 14620
(sortmerna) [george.weingart@hutlab12 run_sortmerna]$ nohup: ignoring input and redirecting stderr to stdout

(sortmerna) [george.weingart@hutlab12 run_sortmerna]$ 



[1]+  Segmentation fault      nohup sortmerna --ref ${DBRoot}/${DB1}.fasta --reads ${Reads} -workdir ${Workdir} -fastx -sam > sortmerna_DBsortmerna.log