Problems about reproduction

[kiworin]

I followed the instructions in readme. I run

elem pipeline -p ./material/positive.fa -m ./material/pattern

But I meet some problems as followed:

num-motifs cannot be larger than number of patterns: 3 set to number of patterns: 1 sh: mkdir -p elem_out info: generate negative sequence by 2mer shuffling sh: dishuffle.py positive.fa >elem_out/negative.fa sh: kmer-psp.py positive.fa elem_out/negative.fa > elem_out/train.fq 2>> elem_out/log sh: mkdir -p elem_out/cv-0 sh: mkdir -p elem_out/cv-1 sh: cp pattern elem_out/pattern_list sh: mkdir -p elem_out/cv-0/train elem_out/cv-0/test sh: kmer-psp.py elem_out/cv-0/train.positive.fa elem_out/cv-0/train.negative.fa > elem_out/cv-0/train/train.fq 2>> elem_out/log sh: kmer-psp.py elem_out/cv-0/test.positive.fa > elem_out/cv-0/test/positive.fq 2>> elem_out/log sh: kmer-psp.py elem_out/cv-0/test.negative.fa > elem_out/cv-0/test/negative.fq 2>> elem_out/log sh: mkdir -p elem_out/cv-1/train elem_out/cv-1/test sh: kmer-psp.py elem_out/cv-1/train.positive.fa elem_out/cv-1/train.negative.fa > elem_out/cv-1/train/train.fq 2>> elem_out/log sh: kmer-psp.py elem_out/cv-1/test.positive.fa > elem_out/cv-1/test/positive.fq 2>> elem_out/log sh: kmer-psp.py elem_out/cv-1/test.negative.fa > elem_out/cv-1/test/negative.fq 2>> elem_out/log sh: find elem_out -name cv-* -type d sh: find elem_out/cv-0/train -name pattern-* -type d k_fold: 0 pattern: 1 sh: motif=sed "1 q;d" 'elem_out/pattern_list' mkdir -p elem_out/cv-0/train/pattern-1 mkdir -p elem_out/cv-0/test/pattern-1 RNAelem --fastq elem_out/cv-0/train/train.fq --max-span 50 --motif-pattern $motif --thread 1 --max-iter 300 --batch-size 64 --out1 elem_out/cv-0/train/pattern-1/train.model --out2 elem_out/cv-0/train/pattern-1/train.raw --out3 elem_out/cv-0/train/pattern-1/train.interim 2>> elem_out/cv-0/train/pattern-1/log RNAelem scan --fastq elem_out/cv-0/test/positive.fq --motif-model elem_out/cv-0/train/pattern-1/train.model --thread 1 --out1 elem_out/cv-0/test/pattern-1/positive.raw 2>> elem_out/cv-0/test/pattern-1/log RNAelem scan --fastq elem_out/cv-0/test/negative.fq --motif-model elem_out/cv-0/train/pattern-1/train.model --thread 1 --out1 elem_out/cv-0/test/pattern-1/negative.raw 2>> elem_out/cv-0/test/pattern-1/log k_fold: 1 pattern: 1 sh: motif=sed "1 q;d" 'elem_out/pattern_list' mkdir -p elem_out/cv-1/train/pattern-1 mkdir -p elem_out/cv-1/test/pattern-1 RNAelem --fastq elem_out/cv-1/train/train.fq --max-span 50 --motif-pattern $motif --thread 1 --max-iter 300 --batch-size 64 --out1 elem_out/cv-1/train/pattern-1/train.model --out2 elem_out/cv-1/train/pattern-1/train.raw --out3 elem_out/cv-1/train/pattern-1/train.interim 2>> elem_out/cv-1/train/pattern-1/log RNAelem scan --fastq elem_out/cv-1/test/positive.fq --motif-model elem_out/cv-1/train/pattern-1/train.model --thread 1 --out1 elem_out/cv-1/test/pattern-1/positive.raw 2>> elem_out/cv-1/test/pattern-1/log RNAelem scan --fastq elem_out/cv-1/test/negative.fq --motif-model elem_out/cv-1/train/pattern-1/train.model --thread 1 --out1 elem_out/cv-1/test/pattern-1/negative.raw 2>> elem_out/cv-1/test/pattern-1/log sh: find elem_out -name cv-* -type d sh: find elem_out/cv-0/train -name pattern-* -type d k_fold,pattern: 0 1 error: not enough values to unpack (expected 2, got 0) k_fold,pattern: 1 1 error: not enough values to unpack (expected 2, got 0) written: elem_out/cv sh: awk '$3<0&&"nan"!=$3' elem_out/cv Traceback (most recent call last): File "/root/local/bin/elem", line 544, in <module> run_rnaelem_select(**options) File "/root/local/bin/elem", line 408, in run_rnaelem_select d_aggr=aggregate(transpose(d_orig),fns=["comma","sum","mean"],key=1,val=[0,2,3]) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/root/local/bin/elem", line 77, in aggregate if len(LL)!=(len(fns)+1):raise RuntimeError("%d!=%d"%(len(LL),len(fns)+1)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ RuntimeError: 1!=4
I didn't change anything, just followed the instruction. Could you please kindly help me fix this problem?