Hicexplorer error using hicBuildMatrix: no such file as qc_template.html

Question

[h.long]

Hi,

I am trying to run HiCExplorer but I am encountering the following error when trying to use hicBuildMatrix.

INFO:hicexplorer.hicBuildMatrix:reading ../SRR1956527_1.bam and ../SRR1956527_2.bam to build hic_matrix

INFO:hicexplorer.hicBuildMatrix:processing 5051931 lines took 39.13 secs (129117.7 lines per second)

INFO:hicexplorer.hicBuildMatrix:180288 (3.57%) valid pairs added to matrix

INFO:hicexplorer.hicBuildMatrix:processing 7051931 lines took 65.20 secs (108151.4 lines per second)

INFO:hicexplorer.hicBuildMatrix:1114276 (15.80%) valid pairs added to matrix

INFO:hicexplorer.hicBuildMatrix:processing 23027838 lines took 220.52 secs (104424.5 lines per second)

INFO:hicexplorer.hicBuildMatrix:3537501 (15.36%) valid pairs added to matrix

INFO:hicexplorer.hicBuildMatrix:processing 78042772 lines took 814.61 secs (95803.9 lines per second)

INFO:hicexplorer.hicBuildMatrix:12336153 (15.81%) valid pairs added to matrix

INFO:hicexplorer.hicBuildMatrix:processing 80042772 lines took 847.13 secs (94487.4 lines per second)

INFO:hicexplorer.hicBuildMatrix:13488339 (16.85%) valid pairs added to matrix

Traceback (most recent call last): File "/usr/bin/hicBuildMatrix", line 7, in <module> main() File "/usr/lib/python2.7/site-packages/hicexplorer/hicBuildMatrix.py", line 1465, in main QC.main("-l {} -o {}".format(log_file_name, args.QCfolder).split()) File "/usr/lib/python2.7/site-packages/hicexplorer/hicPrepareQCreport.py", line 284, in main read_orientation_table, table) File "/usr/lib/python2.7/site-packages/hicexplorer/hicPrepareQCreport.py", line 61, in save_html html = open(os.path.join(root, "qc_template.html"), "r") IOError: [Errno 2] No such file or directory: '/usr/lib/python2.7/site-packages/hicexplorer/qc_template.html'

Does anyone know how I can fix this problem?

Thank you!

[yliueagle]

Hi, Have you found a solution? I also met this problem but do not know how to solve it.

Thanks

Answer 1

[wolffj.bioinf]

Hi,

looks like a bug from the pip version. Please use conda package manager.

Best,

Joachim

[yliueagle]

Is it possible that I copy qc_template.html to /usr/lib/python2.7/site-packages/hicexplorer/?

Thanks

[wolffj.bioinf]

Yes should be possible and we updated pip to a fixed version.