I am currently running the pipeline with a subset of my samples, since coassembling 40 metagenomic samples with SPAdes requires too much memory even when I requested 1,000 GB of it. In any case, I could do the assembly of this subset in a bit more than 3 days and then it got stucked at the graphextraction step. Since I work in a batch-based server in which we need to submit jobs with a time limit up to 5 days, the pipeline could not finish on time. I have been trying to restart the pipeline from the assembly, which was the last complete step, but when I do ./bin/STRONG /path/to/results/ --config /path/to/config.yaml graphextraction --threads 24 --verbose it gives two errors: The first one says the directory is locked, which I tried to solve setting the flag --unlock; the second error is that it doesn't recognize graphextraction. Finally, I did not specify any step, hoping STRONG would see that the assembly was done and would continue from there, but this time, "AssertionError" occured. I tried then to move away the "uncomplete" folders of annotation, binning, subgraphs, and profile, in case that was the origin of the issue, but it didn't help.
Dear authors,
I am currently running the pipeline with a subset of my samples, since coassembling 40 metagenomic samples with SPAdes requires too much memory even when I requested 1,000 GB of it. In any case, I could do the assembly of this subset in a bit more than 3 days and then it got stucked at the
graphextractionstep. Since I work in a batch-based server in which we need to submit jobs with a time limit up to 5 days, the pipeline could not finish on time. I have been trying to restart the pipeline from theassembly, which was the last complete step, but when I do./bin/STRONG /path/to/results/ --config /path/to/config.yaml graphextraction --threads 24 --verboseit gives two errors: The first one says the directory is locked, which I tried to solve setting the flag--unlock; the second error is that it doesn't recognizegraphextraction. Finally, I did not specify any step, hoping STRONG would see that the assembly was done and would continue from there, but this time, "AssertionError" occured. I tried then to move away the "uncomplete" folders of annotation, binning, subgraphs, and profile, in case that was the origin of the issue, but it didn't help.This was the last error message:
STRONG_NC_PC_restart-6309608.txt
Thank you in advance for the help and sorry for the bothering.
Regards, Cristian