aryeelab / hichipper

A preprocessing and QC pipeline for HiChIP data
MIT License
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*_allValidPairs: No such file or directory #51

Closed DoaneAS closed 5 years ago

DoaneAS commented 6 years ago

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!

caleblareau commented 6 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?

DoaneAS commented 6 years ago

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!

Czh3 commented 5 years ago

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.

0xaf1f commented 5 years ago

I've created pull request #63 to fix this while still retaining support for runs by older HiC-Pro versions.