# Assembly – Geoduck Illumina NovaSeq SOAPdenovo2 on Mox (FAIL)

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 > ass.log).

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.

/gscratch/scrubbed/samwhite/20180129_trimmed_again/NR005_S4_L001_R1_001_val_1_val_1.fq.gz
/gscratch/scrubbed/samwhite/20180129_trimmed_again/NR005_S4_L001_R2_001_val_2_val_2.fq.gz
/gscratch/scrubbed/samwhite/20180129_trimmed_again/NR005_S4_L002_R1_001_val_1_val_1.fq.gz
/gscratch/scrubbed/samwhite/20180129_trimmed_again/NR005_S4_L002_R2_001_val_2_val_2.fq.gz
/gscratch/scrubbed/samwhite/20180129_trimmed_again/NR006_S3_L001_R1_001_val_1_val_1.fq.gz
/gscratch/scrubbed/samwhite/20180129_trimmed_again/NR006_S3_L001_R2_001_val_2_val_2.fq.gz
/gscratch/scrubbed/samwhite/20180129_trimmed_again/NR006_S3_L002_R1_001_val_1_val_1.fq.gz
/gscratch/scrubbed/samwhite/20180129_trimmed_again/NR006_S3_L002_R2_001_val_2_val_2.fq.gz
/gscratch/scrubbed/samwhite/20180129_trimmed_again/NR012_S1_L001_R1_001_val_1_val_1.fq.gz
/gscratch/scrubbed/samwhite/20180129_trimmed_again/NR012_S1_L001_R2_001_val_2_val_2.fq.gz
/gscratch/scrubbed/samwhite/20180129_trimmed_again/NR012_S1_L002_R1_001_val_1_val_1.fq.gz
/gscratch/scrubbed/samwhite/20180129_trimmed_again/NR012_S1_L002_R2_001_val_2_val_2.fq.gz