Trying to get the NovaSeq data assembled using SOAPdenovo2 on the Mox HPC node we have and it will not work.
Tried a couple of times and it hasn’t run successfully. Here are links to the files used on Mox (including the batch script and slurm output files). I made slight changes to the formatting of the batch script because I thought there was something wrong. Specifically, the slurm output file in the 20180215 runs does not accurately reflect the command I issued (i.e.
1> ass.log is command, but slurm shows
- 20180215_soapdenovo2_novaseq_geoduck: This failed for no obvious reason. The slurm output file simply indicates the job was killed and the SOAPdenov2 error log doesn’t contain any info regarding why the job failed.
20180218_soapdenovo2_novaseq_geoduck/: This failed because there wasn’t enough memory(!!??) – see below for more info.
NOTE: In the 20180218 run, I have excluded transferring the core dump file due to its crazy size:
Here’s the error log generated by SOAPdenovo2 in the 20180218 run (the last line is all you really need to see, though):
Version 2.04: released on July 13th, 2012 Compile May 10 2017 12:50:52 ******************** Pregraph ******************** Parameters: pregraph -s /gscratch/scrubbed/samwhite/20180218_soapdenovo2_novaseq_geoduck/soap_config -K 117 -p 24 -o /gscratch/scrubbed/samwhite/20180218_soapdenovo2_novaseq_geoduck/ In /gscratch/scrubbed/samwhite/20180218_soapdenovo2_novaseq_geoduck/soap_config, 1 lib(s), maximum read length 150, maximum name length 256. 24 thread(s) initialized. Import reads from file: /gscratch/scrubbed/samwhite/20180129_trimmed_again/AD002_S9_L001_R1_001_val_1_val_1.fq.gz Import reads from file: /gscratch/scrubbed/samwhite/20180129_trimmed_again/AD002_S9_L001_R2_001_val_2_val_2.fq.gz --- 100000000th reads. --- 200000000th reads. --- 300000000th reads. Import reads from file: /gscratch/scrubbed/samwhite/20180129_trimmed_again/AD002_S9_L002_R1_001_val_1_val_1.fq.gz Import reads from file: /gscratch/scrubbed/samwhite/20180129_trimmed_again/AD002_S9_L002_R2_001_val_2_val_2.fq.gz --- 400000000th reads. --- 500000000th reads. --- 600000000th reads. --- 700000000th reads. Import reads from file: /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR005_S4_L001_R1_001_val_1_val_1.fq.gz Import reads from file: /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR005_S4_L001_R2_001_val_2_val_2.fq.gz Import reads from file: /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR005_S4_L002_R1_001_val_1_val_1.fq.gz Import reads from file: /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR005_S4_L002_R2_001_val_2_val_2.fq.gz Import reads from file: /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR006_S3_L001_R1_001_val_1_val_1.fq.gz Import reads from file: /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR006_S3_L001_R2_001_val_2_val_2.fq.gz Import reads from file: /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR006_S3_L002_R1_001_val_1_val_1.fq.gz Import reads from file: /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR006_S3_L002_R2_001_val_2_val_2.fq.gz Import reads from file: /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR012_S1_L001_R1_001_val_1_val_1.fq.gz Import reads from file: /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR012_S1_L001_R2_001_val_2_val_2.fq.gz Import reads from file: /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR012_S1_L002_R1_001_val_1_val_1.fq.gz Import reads from file: /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR012_S1_L002_R2_001_val_2_val_2.fq.gz Import reads from file: /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR013_AD013_S2_L001_R1_001_val_1_val_1.fq.gz Import reads from file: /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR013_AD013_S2_L001_R2_001_val_2_val_2.fq.gz --- 800000000th reads. --- 900000000th reads. -- Out of memory --
I guess I’ll explore some other options for assembling these? I’m having a difficult time accepting that 500GB of RAM is insufficient, but that seems to be the case. Ouch.