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r3fang / SnapATAC

Analysis Pipeline for Single Cell ATAC-seq
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"error: the following snap files do not contain PM session" #101

Closed hjack123 closed 4 years ago

hjack123 commented 4 years ago

what could be the reason that I have finished snaptools snap-add-pmat but x.sp = addPmatToSnap(x.sp); still says snap file dosent contain PM session?

r3fang commented 4 years ago

What is the error message?

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On Sep 22, 2019, at 5:34 AM, hjack123 notifications@github.com wrote:

what could be the reason that I have finished snaptools snap-add-pmat but x.sp = addPmatToSnap(x.sp); still says snap file dosent contain PM session?

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hjack123 commented 4 years ago

snaptools snap-add-pmat --snap-file A549.snap --peak-file ../snapATAC/snap.atac.peaks.combined.bed

Traceback (most recent call last): File "/home/data/apps/anaconda3/envs/py27/bin/snaptools", line 38, in parse_args()
File "/home/data/apps/anaconda3/envs/py27/lib/python2.7/site-packages/snaptools/parser.py", line 176, in parse_args verbose=args.verbose) File "/home/data/apps/anaconda3/envs/py27/lib/python2.7/site-packages/snaptools/add_pmat.py", line 170, in snap_pmat f = h5py.File(snap_file, "a", libver='earliest'); File "/home/data/apps/anaconda3/envs/py27/lib/python2.7/site-packages/h5py/_hl/files.py", line 394, in init swmr=swmr) File "/home/data/apps/anaconda3/envs/py27/lib/python2.7/site-packages/h5py/_hl/files.py", line 184, in make_fid fid = h5f.create(name, h5f.ACC_EXCL, fapl=fapl, fcpl=fcpl) File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper File "h5py/h5f.pyx", line 105, in h5py.h5f.create IOError: Unable to create file (unable to open file: name = 'A549.snap', errno = 17, error message = 'File exists', flags = 15, o_flags = c2)

r3fang commented 4 years ago

Can you use snap-del to remove pmat? And addd it again?

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On Sep 22, 2019, at 9:43 AM, hjack123 notifications@github.com wrote:

snaptools snap-add-pmat --snap-file A549.snap --peak-file ../snapATAC/snap.atac.peaks.combined.bed

Traceback (most recent call last): File "/home/data/apps/anaconda3/envs/py27/bin/snaptools", line 38, in parse_args() File "/home/data/apps/anaconda3/envs/py27/lib/python2.7/site-packages/snaptools/parser.py", line 176, in parse_args verbose=args.verbose) File "/home/data/apps/anaconda3/envs/py27/lib/python2.7/site-packages/snaptools/add_pmat.py", line 170, in snap_pmat f = h5py.File(snap_file, "a", libver='earliest'); File "/home/data/apps/anaconda3/envs/py27/lib/python2.7/site-packages/h5py/_hl/files.py", line 394, in init swmr=swmr) File "/home/data/apps/anaconda3/envs/py27/lib/python2.7/site-packages/h5py/_hl/files.py", line 184, in make_fid fid = h5f.create(name, h5f.ACC_EXCL, fapl=fapl, fcpl=fcpl) File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper File "h5py/h5f.pyx", line 105, in h5py.h5f.create IOError: Unable to create file (unable to open file: name = 'A549.snap', errno = 17, error message = 'File exists', flags = 15, o_flags = c2)

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hjack123 commented 4 years ago

Hi when I did that it says

snaptools snap-del --snap-file A549.snap --session-name PM

error: --session-name PM does not exist in A549.snap

On Sun, Sep 22, 2019 at 9:57 AM Rongxin Fang notifications@github.com wrote:

Can you use snap-del to remove pmat? And addd it again?

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On Sep 22, 2019, at 9:43 AM, hjack123 notifications@github.com wrote:

snaptools snap-add-pmat --snap-file A549.snap --peak-file ../snapATAC/snap.atac.peaks.combined.bed

Traceback (most recent call last): File "/home/data/apps/anaconda3/envs/py27/bin/snaptools", line 38, in parse_args() File "/home/data/apps/anaconda3/envs/py27/lib/python2.7/site-packages/snaptools/parser.py", line 176, in parse_args verbose=args.verbose) File "/home/data/apps/anaconda3/envs/py27/lib/python2.7/site-packages/snaptools/add_pmat.py", line 170, in snap_pmat f = h5py.File(snap_file, "a", libver='earliest'); File "/home/data/apps/anaconda3/envs/py27/lib/python2.7/site-packages/h5py/_hl/files.py", line 394, in init swmr=swmr) File "/home/data/apps/anaconda3/envs/py27/lib/python2.7/site-packages/h5py/_hl/files.py", line 184, in make_fid fid = h5f.create(name, h5f.ACC_EXCL, fapl=fapl, fcpl=fcpl) File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper File "h5py/h5f.pyx", line 105, in h5py.h5f.create IOError: Unable to create file (unable to open file: name = 'A549.snap', errno = 17, error message = 'File exists', flags = 15, o_flags = c2)

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