Open ganiatgithub opened 5 years ago
If it helps, my command is:
metaWRAP assembly \
-1 /Path_to_reads/reads_1.fastq \
-2 /Path_to_reads/reads_2.fastq \
-o /Path_to_output/ \
-m 500 \
-t 24 \
--metaspades
Last few lines of the log:
== Running assembler: K55
0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /30days/uqgni1/jiaoyang/metaWRAP/assembly_out/metaspades/K55/configs/config.info
0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /30days/uqgni1/jiaoyang/metaWRAP/assembly_out/metaspades/K55/configs/mda_mode.info
0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /30days/uqg
.........
3:25:45.269 1G / 13G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 1746267506 bytes occupied (3.70972 bits per kmer).
3:25:47.379 5G / 13G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers
3:28:23.328 5G / 13G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished.
3:28:23.329 5G / 13G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph
3:28:23.332 5G / 13G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths
For metaSPAdes there are already checkpoints implemented if you are using metawrap v>1.1.5. If the job times out just re-run it on the same output folder and it should continue where it left off.
It worked, thank you!
Hello there,
Thank you for the cool program. I ran the assembly function on a server but killed due to not enough walltime after 72 hours. Is it possible to pick up a job from some check points? i.e. == Running assembler: K55
That would be fantastic.
Cheers