nchernia
commented
7 years ago It looks like you have a space between "-" and "D". This would cause problems. You also do not need quotes around early or HindIII, though I'm not sure it will harm anything.
For your "module load" commands, you need to directly modify the juicer.sh script. These won't get carried over into the jobs that are launched by Juicer.
Since you've already split the files, you certainly don't need to send Juicer as a job, just run it from the command line and it will launch. We usually launch in a screen anyway (and not as a job) but you don't even need to do that if the splits directory has already been created.
Fix the error with the -D, remove the aligned directory (it should be empty), and add these lines to the top of the juicer.sh script (under the version):
load_bwa="module load BWA" load_java="module load Java"
Then try again.
On Thu, Sep 14, 2017 at 10:48 AM, Sameet notifications@github.com wrote:
Hi,
I have the following directory structure:
references: total 8374528 -rwxr-xr-x+ 1 sm2556 mane 3157608038 <(315)%20760-8038> Sep 13 12:32 Homo_sapiens_assembly19.fasta -rw-r--r--+ 1 sm2556 mane 6663 Sep 13 13:31 Homo_sapiens_assembly19.fasta.amb -rw-r--r--+ 1 sm2556 mane 939 Sep 13 13:31 Homo_sapiens_assembly19.fasta.ann -rw-r--r--+ 1 sm2556 mane 3095694072 Sep 13 13:30 Homo_sapiens_assembly19.fasta.bwt -rw-r--r--+ 1 sm2556 mane 773923497 Sep 13 13:31 Homo_sapiens_assembly19.fasta.pac -rw-r--r--+ 1 sm2556 mane 1547847040 Sep 13 13:44 Homo_sapiens_assembly19.fasta.sa -rw-r--r--+ 1 sm2556 mane 377 Sep 13 15:19 Homo_sapiens_assembly19.sizes
restriction_sites: total 15360 -rw-r--r--+ 1 sm2556 mane 7762896 Sep 13 11:45 hg19_HindIII_new.txt -rw-r--r--+ 1 sm2556 mane 7762896 Sep 13 11:45 hg19_HindIII.txt
scripts: total 92800 -rwxr-xr-x+ 1 sm2556 mane 3519 Sep 13 11:26 check.sh -rwxr-xr-x+ 1 sm2556 mane 15349 Sep 13 11:26 chimeric_blacklist.awk -rwxr-xr-x+ 1 sm2556 mane 1971 Sep 13 11:26 cleanup.sh -rwxr-xr-x+ 1 sm2556 mane 3584 Sep 13 11:26 collisions.awk -rwxr-xr-x+ 1 sm2556 mane 1616 Sep 13 11:26 countligations.sh -rwxr-xr-x+ 1 sm2556 mane 13448 Sep 13 11:26 diploid.pl -rw-r--r--+ 1 sm2556 mane 2449 Sep 13 11:26 diploid_split.awk -rwxr-xr-x+ 1 sm2556 mane 5325 Sep 13 11:26 dups.awk -rw-r--r--+ 1 sm2556 mane 3726 Sep 13 11:26 fragment_4dnpairs.pl -rwxr-xr-x+ 1 sm2556 mane 3711 Sep 13 11:26 fragment.pl -rw-r--r--+ 1 sm2556 mane 30745856 Sep 13 12:31 juicebox -rw-r--r--+ 1 sm2556 mane 30745856 Sep 13 12:30 Juicebox.jar -rw-r--r--+ 1 sm2556 mane 30751431 Sep 13 12:30 juicebox_tools.7.0.jar -rwxr-xr-x+ 1 sm2556 mane 2388 Sep 13 11:26 juicer_arrowhead.sh -rwxr-xr-x+ 1 sm2556 mane 3269 Sep 13 11:26 juicer_hiccups.sh -rwxr-xr-x+ 1 sm2556 mane 3651 Sep 13 11:26 juicer_postprocessing.sh -rwxr-xr-x+ 1 sm2556 mane 41529 Sep 13 11:26 juicer.sh -rwxr-xr-x+ 1 sm2556 mane 4659 Sep 13 11:26 LibraryComplexity.class -rwxr-xr-x+ 1 sm2556 mane 7204 Sep 13 11:26 LibraryComplexity.java -rwxr-xr-x+ 1 sm2556 mane 2354 Sep 13 11:26 makemega_addstats.awk -rwxr-xr-x+ 1 sm2556 mane 12782 Sep 13 11:26 mega.sh -rwxr-xr-x+ 1 sm2556 mane 2455 Sep 13 11:26 relaunch_prep.sh -rwxr-xr-x+ 1 sm2556 mane 5200 Sep 13 11:26 split_rmdups.awk -rwxr-xr-x+ 1 sm2556 mane 14572 Sep 13 11:26 statistics.pl -rwxr-xr-x+ 1 sm2556 mane 1751 Sep 13 11:26 stats_sub.awk
fastq: total 0 lrwxrwxrwx 1 sm2556 mane 67 Sep 13 15:33 S1_003_HiC_R1.fastq.gz -> ../../analysis jul052016/S1_003_HiC/Unaligned/S1_003_HiC_1.fastq.gz lrwxrwxrwx 1 sm2556 mane 67 Sep 13 15:34 S1_003_HiC_R2.fastq.gz -> ../../analysis-jul052016/S1_003_HiC/Unaligned/S1_003_HiC_2.fastq.gz
My run.sh script for the SLURM batch submission looks as follows:
!/bin/bash
SBATCH --partition=general
SBATCH --job-name=Juicer
SBATCH --ntasks=1 --nodes=1
SBATCH --mem-per-cpu=6000
module load BWA; module load Java; bash /home/sm2556/project/hic-golden-uconn-feb0222016/hic-analysis-sept142017/scripts/juicer.sh -g hg19 -d /home/sm2556/project/hic-golden-uconn-feb0222016/hic-analysis-sept142017 -q general -l general -a 'Reference' -S 'early' -p /home/sm2556/project/hic-golden-uconn-feb022216/hic-analysis-sept142017/references/Homo_sapiens_assembly19.sizes -s 'HindIII' -y /home/sm2556/project/hic-golden-uconn-feb0222016/hic-analysis-sept142017/restriction_sites/hg19_HindIII.txt - D /home/sm2556/project/hic-golden-uconn-feb0222016/hic-analysis-sept142017 -x
I get tons of error messages about dependencies not being satisfied, but I still get the part of script that "split" the fastq.gz file correctly, but still ends with error. The actual bwa mem call never happens on the cluster. When I tried to run the script in the CPU mode it started the alignment. But my files are too big, and CPU mode will take a long time. Am I doing something wrong?
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sameet
Aannaw
sa501428
Hi,
I have the following directory structure:
My run.sh script for the SLURM batch submission looks as follows:
The scripts folder was copied from the cloned GitHub repository of the
juicer/SLURM/scripts.I get tons of error messages about dependencies not being satisfied, but I still get the part of script that "split" the fastq.gz file correctly, but still ends with error. The actual
bwa memcall never happens on the cluster. When I tried to run the script in the CPU mode it started the alignment. But my files are too big, and CPU mode will take a long time. Am I doing something wrong?