caleblareau
commented
7 years ago Hi @jamesdalg -- two things
1) when calling loop anchors, see that you only have 926, which leads to a very small number of loops. This is a problem that I've experienced for some HiChIP datasets newer than those described by Mumbach et al. but I haven't found an immediate solution.
2) The incomplete output that you seem to be referring to is a function of the sankey diagrams and DT tables not rendering properly. It's hard to know what's causing this with your current output. Can you verify that all the R package dependencies are up to date? What versions of the packages and R are you using?
bash-4.1$ hichipper --out output_real yaml/one.yaml Thu Oct 26 16:53:47 EDT 2017: Starting hichipper pipeline v0.7.0 Thu Oct 26 16:53:47 EDT 2017: Parsing user parameters Anchors removed due to excessive size (likely at ends of chromosomes): 0 Thu Oct 26 16:53:50 EDT 2017: Processing d1 Thu Oct 26 16:53:50 EDT 2017: Total_PETs=164332898 Thu Oct 26 16:53:51 EDT 2017: Mapped_unique_quality_pairs=1888170 Thu Oct 26 16:53:51 EDT 2017: Mapped_unique_quality_valid_pairs=627403 Thu Oct 26 16:53:51 EDT 2017: Intersecting PETs with anchors Thu Oct 26 16:53:51 EDT 2017: Finished the anchor merging. Thu Oct 26 16:54:23 EDT 2017: Intrachromosomal_valid_small=163462 Thu Oct 26 16:54:24 EDT 2017: Intrachromosomal_valid_med=394048 Thu Oct 26 16:54:25 EDT 2017: Intrachromosomal_valid_large=69902 Thu Oct 26 16:54:25 EDT 2017: Total number of anchors used: 926 Thu Oct 26 16:54:25 EDT 2017: Total number of reads in anchors: 410414 Thu Oct 26 16:54:31 EDT 2017: Mapped_unique_intra_quality_anchor=20288 Thu Oct 26 16:54:31 EDT 2017: Mapped_unique_intra_quality_anchor_small=13632 Thu Oct 26 16:54:31 EDT 2017: Mapped_unique_intra_quality_anchor_med=6090 Thu Oct 26 16:54:31 EDT 2017: Mapped_unique_intra_quality_anchor_large=566 Thu Oct 26 16:54:31 EDT 2017: Loop_PETs=6090 Thu Oct 26 16:54:31 EDT 2017: ['Rscript', u'output_real/qcReport.R', '/usr/local/Anaconda/envs_app/hichipper/0.7.0/lib/python2.7/site-packages/hichipper', 'output_real', '/spin1/users/dalgleishjl/hichipper/tests', '0.7.0', 'd1'] /spin1/users/dalgleishjl/hichipper/tests
processing file: qcReport_make.Rmd |... | 5% inline R code fragments
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|........................... | 42% label: unnamed-chunk-4 (with options) List of 4 $ echo : logi FALSE $ message : logi FALSE $ warning : logi FALSE $ out.width: chr "\textwidth"
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Using count as value column: use value.var to override. |................................................... | 79% ordinary text without R code
|....................................................... | 84% label: unnamed-chunk-8 (with options) List of 4 $ echo : logi FALSE $ message : logi FALSE $ warning : logi FALSE $ out.width: chr "\textwidth"
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output file: qcReport_make.knit.md
/usr/local/apps/pandoc/1.15.0.6/bin/pandoc +RTS -K512m -RTS qcReport_make.utf8.md --to html --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash --output output_real.hichipper.qcreport.html --smart --email-obfuscation none --self-contained --standalone --section-divs --template /usr/local/apps/R/gcc_4.9.1/library/rmarkdown/rmd/h/default.html --highlight-style pygments --css /usr/local/apps/R/gcc_4.9.1/library/rmarkdown/rmarkdown/templates/html_vignette/resources/vignette.css --include-in-header /spin1/scratch/dalgleishjl/RtmpR3VvG1/rmarkdown-str62f25b19add6.html --mathjax --variable 'mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' output1 is a zipped copy of the results for test data and seems to have an html file that doesn't have complete output.
Output created: output_real.hichipper.qcreport.html Warning messages: 1: Transformation introduced infinite values in continuous x-axis 2: Removed 13419 rows containing non-finite values (stat_bin). Processing: d1 output1.zip