Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

ALLHiC_plot : AttributeError #170

Open
Willtao2023 opened this issue Sep 3, 2023 · 1 comment
Open

ALLHiC_plot : AttributeError #170

Willtao2023 opened this issue Sep 3, 2023 · 1 comment

Comments

@Willtao2023
Copy link

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
Copy link
Author

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

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant