Incomplete prunning

[Alteroldis]

Hi Dr. Zhang,
At first, you create elegant tool. But with my species I be faced with incomplete prunning. My allele.ctg.table include many contigs which incorporated in same group and sequence. The contigs not included at removedb_Allele.txt, prunning.pairs.txt and at the other side, included at removedb_nonBest.txt. I used the command:

ALLHiC_prune -i Allele.ctg.tsv -b $finalbam.bam -r $assembly
ALLHiC_partition -b prunning.bam -r $assembly -e GATC -k 46
ALLHiC_rescue -b $finalbam.bam -r $assembly -c prunning.clusters.txt -i prunning.counts_GATC.txt
allhic extract $finalbam.bam $assembly --RE GATC
allhic optimize group${K}.txt $finalbam.clm
ALLHiC_build $assembly

v.0.9.8 from your repo.
P.S. About half of genes which used for creating allele.table were placed on the same chromosome (group). And half of contig pairs (alleles, haplotigs) from allele.table placed in one group at prunning.clusters.txt file.
P.P.S. "allhic alleles" cmd does not create any tables, only stdout like this:

02:23:31 ParseRecords | NOTICE Parse paffile genome.paf
02:29:15 ReadCSVLines | NOTICE Parse csvfile ../bwa-curr/filt.counts_GATC.txt
02:29:15 Run | NOTICE Success

[13061994]

Could you explain how to construct allele.ctg.table?