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Rscript execution error
I installed Merqury (v1.3) through conda. After running merqury under conda environment:
merqury.sh $WD/Carex_hic.meryl $REF Carex_pctg
I got the most expected outputs such as qv, completeness, and hist files, but no plots were generated. After checking the log file, I found the error:
For 86366741 distinct 20-mers (with 24 bits used for indexing and 16 bits for tags):
0.125 GB memory for kmer indices - 16777216 elements 64 bits wide)
0.161 GB memory for kmer tags - 86366741 elements 16 bits wide)
0.050 GB memory for kmer values - 86366741 elements 5 bits wide)
0.336 GB memory
Will load 86366741 kmers. Skipping 0 (too low) and 0 (too high) kmers.
Allocating space for 86382869 suffixes of 16 bits each -> 1382125904 bits (0.161 GB) in blocks of 32.000 MB
86382869 values of 5 bits each -> 431914345 bits (0.050 GB) in blocks of 32.000 MB
Loaded 86366741 kmers. Skipped 0 (too low) and 0 (too high) kmers.
-- Opening input sequences 'carex_ctg.hic.p_ctg.fasta'.
-- Opening output file '-'.
Bye!
Found 1 command tree.
PROCESSING TREE #1 using 48 threads.
opIntersect
Carex_hic.meryl
carex_ctg.hic.p_ctg.meryl
output to read.k20.carex_ctg.hic.p_ctg.meryl
Cleaning up.
Bye.
Found 1 command tree.
Found 1 command tree.
Found 1 command tree.
Rscript execution error: No such file or directory
So for some reason, merqury could not find Rscript, but if I run which Rscript
, I got:
/PATH/bin/conda-envs/envs/merqury/bin/Rscript
And I also ran Rscript ./plot_spectra_cn.R
I got the same error as following:
Rscript execution error: No such file or directory