Failure on Illumina-ONT hybrid assembly

[nickloman]

Hi there

Hybrid assembly gives following error:

Using CABOG from is MaSuRCA-3.2.6/bin/../CA8/Linux-amd64/bin Running mega-reads correction/assembly Using mer size 15 for mapping, B=15, d=0.02 Estimated Genome Size 368796815 Estimated Ploidy 1 Using 12 threads Output prefix mr.41.15.15.0.02 Using 30x of the longest ONT reads Reducing super-read k-mer size Mega-reads pass 1 Running locally in 1 batch compute_psa 4935290 1781966868

Processed 500000 super reads, irreducible 381804, processing 2222 super reads per second Processed 1000000 super reads, irreducible 706011, processing 1818 super reads per second Processed 1500000 super reads, irreducible 1042813, processing 1930 super reads per second Processed 2000000 super reads, irreducible 1421777, processing 1779 super reads per second Processed 2500000 super reads, irreducible 1876509, processing 1779 super reads per second Mega-reads pass 2 Running locally in 1 batch compute_psa 2280190 2472577921 Refining alignments ERROR: failed to merge alignments at position 487 Please file a bug report xargs: refine.sh: exited with status 255; aborting Joining awk: cmd. line:1: fatal: cannot open file `mr.41.15.15.0.02.all.txt' for reading (No such file or directory) MaSuRCA-3.2.6/bin/mega_reads_assemble_cluster.sh: line 504: mr.41.15.15.0.02.all.txt: No such file or directory mega-reads joining failed [Tue Jul 24 22:56:40 UTC 2018] Assembly stopped or failed, see CA.mr.41.15.15.0.02.log

Can you give any advice?

Nick

[nm100]

You might be running out of RAM Look at this issue: https://github.com/alekseyzimin/masurca/issues/37

[nickloman]

Hopefully not - I have 3Tb - and nothing in the syslog - but I can re-run and monitor?