search

hildebra / lotus2

Amplicon sequencing pipelines suitable for SSU (16S, 18S), LSU (23S, 28S) and ITS.
http://lotus2.earlham.ac.uk/
GNU General Public License v3.0
52 stars 17 forks source link

Problem with example trial #25

Closed assemahajemlrefaei closed 1 year ago

assemahajemlrefaei commented 1 year ago

I have tried to run the example and got errors everytime. I managed to troubleshoot all of those related to DADA2 ASV clustering but now I get an error with building LAMDA index:

'Building LAMBDA index anew (may take up to an hour first time).. CMD failed: /home/assem/Downloads/lotus2/lotus2//bin//lambda/lambda_indexer -p blastn -t 1 -d /home/assem/Downloads/lotus2/lotus2//DB//SLV_138.1_SSU.fasta
see myTestRun2/LotuSLogS/LotuS_progout.log for error log'

Attached is the progout.log and that's its last part:

'Writing OTU matrix to myTestRun2/OTU.txt Recruited 214 reads in OTU matrix Done Time taken: : 3ms [M::mm_idx_gen::0.0021.02] collected minimizers [M::mm_idx_gen::0.0031.02] sorted minimizers [M::main::0.0031.02] loaded/built the index for 1 target sequence(s) [M::mm_mapopt_update::0.0031.02] mid_occ = 1000 [M::mm_idx_stat] kmer size: 21; skip: 11; is_hpc: 0; #seq: 1 [M::mm_idx_stat::0.0031.02] distinct minimizers: 900 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.984 [M::worker_pipeline::0.0031.02] mapped 15 sequences [M::main] Version: 2.17-r941 [M::main] CMD: /home/assem/Downloads/lotus2/lotus2//bin//minimap2-2.17_x64-linux/minimap2 -x sr --sr -u both --secondary=no -N 30 -c -t 1 -o myTestRun2/tmpFiles//otu_seeds.fna.phiX.0.cont_hit.paf /home/assem/Downloads/lotus2/lotus2//DB//phiX.fasta myTestRun2/tmpFiles//otu_seeds.fna [M::main] Real time: 0.004 sec; CPU: 0.004 sec; Peak RSS: 0.003 GB Loading Subject Sequences and Ids... done. Dumping Subj Ids... done. No Seg-File specified, no masking will take place. Dumping binary seqan mask file... done.

Dumping unreduced Subj Sequences... done. Generating 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% (1) SuffixArray |Killed'

LotuS_progout.log

hildebra commented 1 year ago

Hey, I think this is an out-of-mem error (or out of diskspace) from LAMBDA, please try to rerun on a computer with more memory/allocate more mem. Alternatively, you could also use the vsearch/blast aligner options, or just use RDP classifier. best, Falk

assemahajemlrefaei commented 1 year ago

Hi, Thanks for the timely and helpful reply. I will work on that!