Closed jzehnpfennig closed 5 years ago
Hello
Thank you for your interest in SPAdes.
What is the filesystem on /mnt/home/zehnp1jrCMICH/ ?
Hello, I work in a High Performance Computing Cluster (HPCC) through MSU. It is a Network File system. Home space is the storage created for each user account. By default, it is located at /mnt/home/$USER where users log into HPCC. It is set as accessible only by the user. It is often referred as “home directory”. This uses the ZFS file system, which is automatically backed-up hourly for the last 24 hours, daily for the last week and weekly for the last month. Does this help? Thank you, Jessica
Most probably it has broken implementation of memory mapped files (as many network filesystems do). What if you move the SPAdes scratch directory (--tmp-dir) somewhere else?
Can someone who doesn't have administrative rights to the computer system do that?
Sure. Just specify some other directory (located elsewhere) via SPAdes --tmp-dir option.
So something like this:
spades.py --rna --tmp-dir /mnt/home/zehnp1jrCMICH/ENV588/Trimmomatic -t20 --pe1-1 C10S_S15_L008_R1_001.qc.fq.gz --pe1-2 C10S_S15_L008_R2_001.qc.fq.gz --pe1-1 C3S_S7_L008_R1_001.qc.fq.gz --pe1-2 C3S_S7_L008_R2_001.qc.fq.gz --pe1-1 C4S_S4_L008_R1_001.qc.fq.gz --pe1-2 C4S_S4_L008_R2_001.qc.fq.gz --pe1-1 C6S_S1_L008_R1_001.qc.fq.gz --pe1-2 C6S_S1_L008_R2_001.qc.fq.gz --pe1-1 C9S_S10_L008_R1_001.qc.fq.gz --pe1-2 C9S_S10_L008_R2_001.qc.fq.gz -o ENV588_Surface_zone.spades.combined
Well, it should be not located on /mnt/home. Somewhere else more suitable as a scratch dir.
So I ran SPAdes with the tmp-dir option and directed it to my scratch directory. Now I am getting another error. err -6. However SPAdes did run for about 7 hours. Any suggestions on what to do next?
I attached the spades.log and the params.txt file to this one as well. spades.log params.txt
Yes. This is known issue that was fixed in SPAdes 3.13.0. Consider upgrading.
Hello, I am trying to run rnaSPAdes on my RNAseqdata, and I keep running into this error code: == Error == system call for: "['/opt/software/SPAdes/3.12.0-foss-2016b/bin/spades-hammer', '/mnt/home/zehnp1jrCMICH/ENV588/Trimmomatic/ENV588_Surface_zone.s pades.combined/corrected/configs/config.info']" finished abnormally, err code: -24. I attached the params.txt and spades.log file!
params.txt
spades.log