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k-mer based assembly evaluation
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running merqury.sh, error is "merqury-1.3/eval/spectra-cn.sh: line 24: meryl: command not found" #100

Closed zhaoyuhe-zyh closed 9 months ago

zhaoyuhe-zyh commented 1 year ago

when i running merqury.sh script, the xxx.spectra.cn.log was like: 03.Software/merqury/merqury-1.3/eval/spectra-cn.sh: line 24: meryl: command not found ModuleCmd_Load.c(204):ERROR:105: Unable to locate a modulefile for 'R' 03.Software/merqury/merqury-1.3/build/filt.sh: line 16: meryl: command not found Processing file Lycoris-all.hist Running time : 0 h 0 m 0 sec

03.Software/merqury/merqury-1.3/build/filt.sh: line 33: meryl: command not found 03.Software/merqury/merqury-1.3/eval/spectra-cn.sh: line 64: meryl: command not found 03.Software/merqury/merqury-1.3/eval/spectra-cn.sh: line 81: meryl: command not found 03.Software/merqury/merqury-1.3/eval/spectra-cn.sh: line 82: meryl: command not found 03.Software/merqury/merqury-1.3/eval/spectra-cn.sh: line 88: meryl: command not found 03.Software/merqury/merqury-1.3/eval/spectra-cn.sh: line 89: meryl: co Copy = 2 ..

Copy = 3 ..

Copy = 4 ..

Copy >4 ..

Copy numbers in k-mers found only in asm

No asm2_fa given. Done.

Lyco-genome only

Write output

Get asm only for spectra-asm

Plot out1.spectra-asm.hist

Rscript 03.Software/merqury/merqury-1.3/plot/plot_spectra_cn.R -f out1.spectra-asm.hist -o out1.spectra-asm -z out1.dist_only.hist

Clean up

Done! tory 03.Software/merqury/merqury-1.3/eval/spectra-cn.sh: line 88: meryl: command not found 03.Software/merqury/merqury-1.3/eval/spectra-cn.sh: line 89: meryl: command not found rm: cannot remove ‘read.k.Lyco-genome.3.meryl’: No such file or directory 03.Software/merqury/merqury-1.3/eval/spectra-cn.sh: line 88: meryl: command not found 03.Software/merqury/merqury-1.3/eval/spectra-cn.sh: line 89: meryl: command not found rm: cannot remove ‘read.k.Lyco-genome.4.meryl’: No such file or directory 03.Software/merqury/merqury-1.3/eval/spectra-cn.sh: line 95: meryl: command not found 03.Software/merqury/merqury-1.3/eval/spectra-cn.sh: line 96: meryl: command not found

Does anyone know how to solve this?

arangrhie commented 1 year ago

Seems like meryl is not installed? How did you installed Merqury?

arangrhie commented 9 months ago

Please use meryl v1.4.1!