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r3fang / SnapATAC

Analysis Pipeline for Single Cell ATAC-seq
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error in bedGraphToBigWig #37

Open Shiywa opened 5 years ago

Shiywa commented 5 years ago

hi, rongxing when i have installed the package bedGraphToBigWig, i found that i can't use it because shared library.

$bedGraphToBigWig
bedGraphToBigWig: error while loading shared libraries: libssl.so.1.0.0: cannot open shared object file: No such file or directory

could you please give me some suggestions ?

regards !

r3fang commented 5 years ago

Try to install it use conda, maybe it can solve this problem. I never saw this error

Sent from my iPhone

On May 19, 2019, at 3:24 AM, ChickenWangSY notifications@github.com wrote:

hi, rongxing when i have installed the package bedGraphToBigWig, i found that i can't use it because shared library.

$bedGraphToBigWig bedGraphToBigWig: error while loading shared libraries: libssl.so.1.0.0: cannot open shared object file: No such file or directory could you please give me some suggestions ?

regards !

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Shiywa commented 5 years ago

Hi. rongxing i have installed the bedGrapgToBigwig and when i run it as 

$/hwfssz1/ST_MCHRI/CLINIC/SOFTWARES/kent/bin/linux64/bedGraphToBigWig mouse_olfactory_bulb_mm10_2012.10_treat_pileup.bdg /zfssz2/ST_MCHRI/COHORT/wangshiyou/software/mm10/mm10_2012/mm10.chrom.sizes2 mouse_olfactory_bulb_mm10_2012.10_treat_pileup.bw
b'chrUn_GL456385' is not found in chromosome sizes file

is the b'chrUn_GL456385 a binary format ? I checked my chrom.size and chrUn_GL456385 existed. should i transform my chrom.size to a binary file ?

r3fang commented 5 years ago

can you show me a few lines in bdg and chrom.size file

Shiywa commented 5 years ago

my .bdg looks like :

$less mouse_olfactory_bulb_mm10_2012.9_treat_pileup.bdg | head
b'chrUn_GL456385'       0       8364    0.00000
b'chrUn_GL456385'       8364    8437    0.14107
b'chrUn_GL456385'       8437    8634    0.00000
b'chrUn_GL456385'       8634    8707    0.14107
b'chrUn_GL456385'       8707    33936   0.00000
b'chrUn_GL456385'       33936   34009   0.14107
b'chr2' 0       3057872 0.00000
b'chr2' 3057872 3057945 0.14107
b'chr2' 3057945 3058972 0.00000
b'chr2' 3058972 3059045 0.14107

and my chrom.size looks like : 

$less /zfssz2/ST_MCHRI/COHORT/wangshiyou/software/mm10/mm10_2012/mm10.chrom.sizes2| head
chr10   130694993
chr11   122082543
chr12   120129022
chr13   120421639
chr14   124902244
chr15   104043685
chr16   98207768
chr17   94987271
chr18   90702639
chr19   61431566
r3fang commented 5 years ago

what is your python version?

Shiywa commented 5 years ago 
$python
Python 3.7.1 (default, Dec 14 2018, 19:28:38)
[GCC 7.3.0] :: Anaconda, Inc. on linux
Type "help", "copyright", "credits" or "license" for more information.
>>>
r3fang commented 5 years ago

the problem is snaptools not bedGraphToBigWig. Can you do the following things and let me know the result?

$ snaptools

can you show me the version of your snaptools?

Shiywa commented 5 years ago 
$snaptools
usage: snaptools [-h]  ...

Program: snaptools (A module for working with snap files in Python)
Version: 1.4.7
Contact: Rongxin Fang
E-mail:  r4fang@gmail.com

optional arguments:
  -h, --help        show this help message and exit

functions:

    dex-fastq       De-multicomplex fastq file.
    index-genome    Index reference genome.
    align-paired-end
                    Align paired-end reads.
    align-single-end
                    Align single-end reads.
    snap-pre        Create a snap file from bam or bed file.
    snap-add-bmat   Add cell x bin count matrix to snap file.
    snap-add-pmat   Add cell x peak count matrix to snap file.
    snap-add-gmat   Add cell x gene count matrix to snap file.
    snap-del        Delete a session.
(
r3fang commented 5 years ago

Let's assume that your snap file is demo.snap

library(SnapATAC);
x.sp = createSnap("demo.snap", "demo");
reads.gr = extractReads(x.sp@barcode[1], files=x.sp@file[1])
reads.gr

what is reads.gr?

Shiywa commented 5 years ago 
GRanges object with 49785 ranges and 2 metadata columns:
          seqnames              ranges strand |          barcode
             <Rle>           <IRanges>  <Rle> |      <character>
      [1]    chr10   44644403-44644535      * | AAACAACGAAGTCGGA
      [2]    chr13   46193742-46194068      * | AAACAACGAAGTCGGA
      [3]    chr13     9093389-9093614      * | AAACAACGAAGTCGGA
      [4]    chr10   24278542-24278631      * | AAACAACGAAGTCGGA
      [5]    chr17   34828613-34828664      * | AAACAACGAAGTCGGA
      ...      ...                 ...    ... .              ...
  [49781]    chr14   73374108-73374548      * | AAACAACGAAGTCGGA
  [49782]     chr3   88467636-88467710      * | AAACAACGAAGTCGGA
  [49783]     chr8   54966051-54966395      * | AAACAACGAAGTCGGA
  [49784]     chr2 151574793-151574921      * | AAACAACGAAGTCGGA
  [49785]     chr7 141195801-141195868      * | AAACAACGAAGTCGGA
                                                                                                                                       file
                                                                                                                                <character>
      [1] /zfssz2/ST_MCHRI/COHORT/wangshiyou/scATAC/data_transfer/mouse_olfactory_bulb/result_mm10_2012/mouse_olfactory_bulb_mm10_2012.snap
      [2] /zfssz2/ST_MCHRI/COHORT/wangshiyou/scATAC/data_transfer/mouse_olfactory_bulb/result_mm10_2012/mouse_olfactory_bulb_mm10_2012.snap
      [3] /zfssz2/ST_MCHRI/COHORT/wangshiyou/scATAC/data_transfer/mouse_olfactory_bulb/result_mm10_2012/mouse_olfactory_bulb_mm10_2012.snap
      [4] /zfssz2/ST_MCHRI/COHORT/wangshiyou/scATAC/data_transfer/mouse_olfactory_bulb/result_mm10_2012/mouse_olfactory_bulb_mm10_2012.snap
      [5] /zfssz2/ST_MCHRI/COHORT/wangshiyou/scATAC/data_transfer/mouse_olfactory_bulb/result_mm10_2012/mouse_olfactory_bulb_mm10_2012.snap
      ...                                                                                                                               ...
  [49781] /zfssz2/ST_MCHRI/COHORT/wangshiyou/scATAC/data_transfer/mouse_olfactory_bulb/result_mm10_2012/mouse_olfactory_bulb_mm10_2012.snap
  [49782] /zfssz2/ST_MCHRI/COHORT/wangshiyou/scATAC/data_transfer/mouse_olfactory_bulb/result_mm10_2012/mouse_olfactory_bulb_mm10_2012.snap
  [49783] /zfssz2/ST_MCHRI/COHORT/wangshiyou/scATAC/data_transfer/mouse_olfactory_bulb/result_mm10_2012/mouse_olfactory_bulb_mm10_2012.snap
  [49784] /zfssz2/ST_MCHRI/COHORT/wangshiyou/scATAC/data_transfer/mouse_olfactory_bulb/result_mm10_2012/mouse_olfactory_bulb_mm10_2012.snap
  [49785] /zfssz2/ST_MCHRI/COHORT/wangshiyou/scATAC/data_transfer/mouse_olfactory_bulb/result_mm10_2012/mouse_olfactory_bulb_mm10_2012.snap
  -------
  seqinfo: 28 sequences from an unspecified genome; no seqlengths
>
r3fang commented 5 years ago

Umm this is wired. last thing:

> echo "AAACAACGAAGTCGGA" > barcode.txt
> snaptools dump-fragment --snap-file mouse_olfactory_bulb_mm10_2012.snap --barcode-file barcode.txt --output-file mouse_olfactory_bulb_mm10_2012.bed.gz
> zcat mouse_olfactory_bulb_mm10_2012.bed.gz | head

what is the output?

Shiywa commented 5 years ago 
$zcat mouse_olfactory_bulb_mm10_2012.bed.gz | head
b'chr10'        44644403        44644536        AAACAACGAAGTCGGA
b'chr13'        46193742        46194069        AAACAACGAAGTCGGA
b'chr13'        9093389 9093615 AAACAACGAAGTCGGA
b'chr10'        24278542        24278632        AAACAACGAAGTCGGA
b'chr17'        34828613        34828665        AAACAACGAAGTCGGA
b'chr19'        4489037 4489150 AAACAACGAAGTCGGA
b'chr14'        76507154        76507293        AAACAACGAAGTCGGA
b'chr10'        101817127       101817197       AAACAACGAAGTCGGA
b'chr1' 64337615        64337758        AAACAACGAAGTCGGA
b'chr12'        5182127 5182318 AAACAACGAAGTCGGA
r3fang commented 5 years ago

i see. its a compatible issue with Python 3.7.0 for SnapTools. I will update snaptools ASAP and let you know

Shiywa commented 5 years ago

much thanks for your jobs. : )

r3fang commented 5 years ago

no problem, happy to help

yasserIRCM commented 5 years ago

Hi there.

we have the same problem, b's are being added to the narrowpeak files as well as the bedgraphs. do you have any updates on these issues

yasserIRCM commented 5 years ago

I removed manually all [b'] at the beginin of each line and it worked flawlessly