search

tangerzhang / ALLHiC

ALLHiC: phasing and scaffolding polyploid genomes based on Hi-C data
170 stars 39 forks source link

ALLHiC_plot : AttributeError #170

Open Willtao2023 opened 1 year ago

Willtao2023 commented 1 year ago

This my command: ALLHiC_plot -b sorted.bam -a groups.agp -l chrn.list -s 50k -o ./heatmap-pdf

error happened in step2 :Get signal matrix [17:27:39] Step1: Get chromosome length [17:27:39] Step2: Get signal matrix Traceback (most recent call last): File "/newlustre/home/jfgui/Wangtao/software/ALLHiC/bin/ALLHiC_plot", line 250, in ALLHiC_plot(bam, agp, chrlist, npzfile, minsize, binsize, outdir) File "/newlustre/home/jfgui/Wangtao/software/ALLHiC/bin/ALLHiC_plot", line 226, in ALLHiC_plot bin_offset_min_size, read_count_whole_genome_min_size = calc_read_count_per_min_size(chr_len_db, chr_order, bam, agp, min_size) File "/newlustre/home/jfgui/Wangtao/software/ALLHiC/bin/ALLHiC_plot", line 80, in calc_read_count_per_min_size ctg1 = line.reference_name AttributeError: 'pysam.calignmentfile.AlignedSegment' object has no attribute 'reference_name'

Thank you for your suggestions

Willtao2023 commented 1 year ago

Problem had been solved when I installed the "pysam" software.