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ablab / spades

SPAdes Genome Assembler
http://ablab.github.io/spades/
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err code: -24 SPAdes/3.12.0 #200

Closed jzehnpfennig closed 5 years ago

jzehnpfennig commented 6 years ago

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

asl commented 6 years ago

Hello

Thank you for your interest in SPAdes.

What is the filesystem on /mnt/home/zehnp1jrCMICH/ ?

jzehnpfennig commented 6 years ago

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

asl commented 6 years ago

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?

jzehnpfennig commented 6 years ago

Can someone who doesn't have administrative rights to the computer system do that?

asl commented 6 years ago

Sure. Just specify some other directory (located elsewhere) via SPAdes --tmp-dir option.

jzehnpfennig commented 6 years ago

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

asl commented 6 years ago

Well, it should be not located on /mnt/home. Somewhere else more suitable as a scratch dir.

jzehnpfennig commented 6 years ago

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

asl commented 6 years ago

Yes. This is known issue that was fixed in SPAdes 3.13.0. Consider upgrading.