Closed DoaneAS closed 5 years ago
Thanks for the tip @DoaneAS; could you do a ls -lrtRh
in your HiC-Pro output directory just so I can see how exactly it produces files?
Sure thing. Here's the hic_results
folder. Let me know if you need the alignments, though they look to be the same as previous versions.
The symlink to validPairs file as a workaround was my addition after the HiC-Pro run.
./hic_results:
total 0
drwxr-xr-x 6 asd2007 oelab 4.0K Sep 26 01:02 data
drwxr-xr-x 6 asd2007 oelab 4.0K Sep 26 05:32 stats
drwxr-xr-x 6 asd2007 oelab 4.0K Sep 26 06:20 matrix
drwxr-xr-x 6 asd2007 oelab 4.0K Sep 26 08:08 pic
./hic_results/data:
total 512K
drwxr-xr-x 2 asd2007 oelab 128K Sep 27 01:03 H3K27ac_CTRL
./hic_results/data/H3K27ac_CTRL:
total 55G
-rw-r--r-- 1 asd2007 oelab 0 Sep 25 22:09 AD_HiChIP_8_S8_L001_001_genome.bwt2pairs.SinglePairs
-rw-r--r-- 1 asd2007 oelab 0 Sep 25 22:09 AD_HiChIP_8_S8_L001_001_genome.bwt2pairs.FiltPairs
-rw-r--r-- 1 asd2007 oelab 120M Sep 25 22:20 AD_HiChIP_8_S8_L001_001_genome.bwt2pairs.DEPairs
-rw-r--r-- 1 asd2007 oelab 75M Sep 25 22:20 AD_HiChIP_8_S8_L001_001_genome.bwt2pairs.REPairs
-rw-r--r-- 1 asd2007 oelab 6.7M Sep 25 22:20 AD_HiChIP_8_S8_L001_001_genome.bwt2pairs.SCPairs
-rw-r--r-- 1 asd2007 oelab 38K Sep 25 22:20 AD_HiChIP_8_S8_L001_001_genome.bwt2pairs.DumpPairs
-rw-r--r-- 1 asd2007 oelab 318 Sep 25 22:20 AD_HiChIP_8_S8_L001_001_genome.bwt2pairs.RSstat
-rw-r--r-- 1 asd2007 oelab 1.8G Sep 25 23:16 lowpassAD_HiChIP_10_S10_L004_001_genome.bwt2pairs.validPairs
-rw-r--r-- 1 asd2007 oelab 24G Sep 26 06:53 H3K27ac_CTRL.allValidPairs
lrwxrwxrwx 1 asd2007 oelab 135 Sep 27 01:03 H3K27ac_CTRL.allValidPairs_allValidPairs -> H3K27ac_CTRL/H3K27ac_CTRL.allValidPairs
./hic_results/stats/H3K27ac_CTRL:
total 0
-rw-r--r-- 1 asd2007 oelab 163 Sep 26 06:58 H3K27ac_CTRL_allValidPairs.mergestat
-rw-r--r-- 1 asd2007 oelab 353 Sep 26 07:30 H3K27ac_CTRL_R1.mmapstat
-rw-r--r-- 1 asd2007 oelab 353 Sep 26 07:30 H3K27ac_CTRL_R2.mmapstat
-rw-r--r-- 1 asd2007 oelab 625 Sep 26 07:30 H3K27ac_CTRL.mpairstat
-rw-r--r-- 1 asd2007 oelab 593 Sep 26 07:30 H3K27ac_CTRL.mRSstat
./hic_results/matrix:
total 0
drwxr-xr-x 4 asd2007 oelab 4.0K Sep 26 08:09 H3K27ac_CTRL
./hic_results/matrix/H3K27ac_CTRL:
total 0
drwxr-xr-x 7 asd2007 oelab 4.0K Sep 26 06:01 raw
drwxr-xr-x 7 asd2007 oelab 4.0K Sep 26 08:27 iced
./hic_results/matrix/H3K27ac_CTRL/raw:
total 0
drwxr-xr-x 2 asd2007 oelab 4.0K Sep 26 05:50 20000
drwxr-xr-x 2 asd2007 oelab 4.0K Sep 26 05:53 40000
drwxr-xr-x 2 asd2007 oelab 4.0K Sep 26 05:56 150000
drwxr-xr-x 2 asd2007 oelab 4.0K Sep 26 05:59 500000
drwxr-xr-x 2 asd2007 oelab 4.0K Sep 26 06:01 1000000
./hic_results/matrix/H3K27ac_CTRL/raw/20000:
total 1.6G
-rw-r--r-- 1 asd2007 oelab 4.5M Sep 26 07:33 H3K27ac_CTRL_20000_abs.bed
-rw-r--r-- 1 asd2007 oelab 1.6G Sep 26 07:33 H3K27ac_CTRL_20000.matrix
...
./hic_results/matrix/H3K27ac_CTRL/iced:
total 0
drwxr-xr-x 2 asd2007 oelab 4.0K Sep 26 08:17 20000
drwxr-xr-x 2 asd2007 oelab 4.0K Sep 26 08:23 40000
drwxr-xr-x 2 asd2007 oelab 4.0K Sep 26 08:27 150000
drwxr-xr-x 2 asd2007 oelab 4.0K Sep 26 08:27 500000
drwxr-xr-x 2 asd2007 oelab 4.0K Sep 26 08:27 1000000
thanks!
I download the new version and this problem is not fixed. But i found a solution, you just modify the two file (interactionsCall.sh, hichipperHelp.py), and you will avoid this error.
I've created pull request #63 to fix this while still retaining support for runs by older HiC-Pro versions.
HiC-Pro does not (or no longer) outputs files that will match
*_allValidPairs
glob, rather the files are named<Sample>.allValidPairs
. It's easy enough to make symlinks that match your glob pattern, but probably an easy fix on your end in the hichipper code to fix this.thanks for the great package!