Tilt refinement FileNotFoundError - fsc_masked_03.txt not found

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Eli Andino-Frydman

unread,
Jul 26, 2024, 3:36:08 PM7/26/24
to EMAN2
Hello,

I'm trying to troubleshoot this error when I try to run e2spt_refine_new.py. The particle refinement iterations work fine but when it gets to tilt refinement (iter 3), it produces a number of errors (IndexError: list index out of range, Exception: 'spt_17/threed_03_even.hdf' is not an existing regular file!, FileNotFoundError: spt_17/fsc_masked_03.txt not found). I'd really appreciate if someone could help me figure what the issue is.

$ e2version.py
EMAN 2.99.47 ( GITHUB: 2023-03-04 13:31 - commit: 3f313008c3185410fe859663e763dffb9c0b6fcc )
Your EMAN2 is running on: Linux-5.15.0-113-generic-x86_64-with-glibc2.31 5.15.0-113-generic
Your Python version is: 3.9.16


$ e2spt_refine_new.py --ptcls=sets/vault_48p.lst --ref=sptsgd_02/output_cls0.hdf --startres=50.0 --goldstandard --sym=d39 --iters=p,p,t --tophat=local --parallel=thread:24 --threads=12


----ERROR----

######## iter 3 ##########
### Subtilt translational refinement....
e2spt_subtlt_local.py --ref spt_17/threed_02.hdf --path spt_17 --iter 3 --maxres 60.50 --parallel thread:24 --aliptcls3d spt_17/aliptcls3d_02.lst --smooth 100 --smoothN 15 --refine_trans --goldcontinue
/mnt/storage/eman2.99.47/lib/python3.9/site-packages/numpy/core/getlimits.py:500: UserWarning: The value of the smallest subnormal for <class 'numpy.float64'> type is zero.
setattr(self, word, getattr(machar, word).flat[0])
/mnt/storage/eman2.99.47/lib/python3.9/site-packages/numpy/core/getlimits.py:89: UserWarning: The value of the smallest subnormal for <class 'numpy.float64'> type is zero.
return self._float_to_str(self.smallest_subnormal)
/mnt/storage/eman2.99.47/lib/python3.9/site-packages/numpy/core/getlimits.py:500: UserWarning: The value of the smallest subnormal for <class 'numpy.float32'> type is zero.
setattr(self, word, getattr(machar, word).flat[0])
/mnt/storage/eman2.99.47/lib/python3.9/site-packages/numpy/core/getlimits.py:89: UserWarning: The value of the smallest subnormal for <class 'numpy.float32'> type is zero.
return self._float_to_str(self.smallest_subnormal)
2597 jobs on 24 CPUs
Error executing: <e2spt_subtlt_local.SptAlignTask object at 0x7f06d29d04c0>
Traceback (most recent call last):
File "/mnt/storage/eman2.99.47/bin/e2parallel.py", line 96, in main
ret=task.execute(empty_func)
File "/mnt/storage/eman2.99.47/bin/e2spt_subtlt_local.py", line 247, in execute
ip=[i for i,d in enumerate(d2d) if d["idx3d"]==dc["idx3d"]][0]
IndexError: list index out of range


Error executing: <e2spt_subtlt_local.SptAlignTask object at 0x7ff35434c4c0>
Traceback (most recent call last):
File "/mnt/storage/eman2.99.47/bin/e2parallel.py", line 96, in main
ret=task.execute(empty_func)
File "/mnt/storage/eman2.99.47/bin/e2spt_subtlt_local.py", line 247, in execute
ip=[i for i,d in enumerate(d2d) if d["idx3d"]==dc["idx3d"]][0]
IndexError: list index out of range


Error executing: <e2spt_subtlt_local.SptAlignTask object at 0x7f30d1b924c0>
Traceback (most recent call last):
File "/mnt/storage/eman2.99.47/bin/e2parallel.py", line 96, in main
ret=task.execute(empty_func)
File "/mnt/storage/eman2.99.47/bin/e2spt_subtlt_local.py", line 247, in execute
ip=[i for i,d in enumerate(d2d) if d["idx3d"]==dc["idx3d"]][0]
IndexError: list index out of range


Error executing: <e2spt_subtlt_local.SptAlignTask object at 0x7f5fc8a4a4c0>
Traceback (most recent call last):
File "/mnt/storage/eman2.99.47/bin/e2parallel.py", line 96, in main
ret=task.execute(empty_func)
File "/mnt/storage/eman2.99.47/bin/e2spt_subtlt_local.py", line 247, in execute
ip=[i for i,d in enumerate(d2d) if d["idx3d"]==dc["idx3d"]][0]
IndexError: list index out of range


Error executing: <e2spt_subtlt_local.SptAlignTask object at 0x7f1db068d4c0>
Traceback (most recent call last):
File "/mnt/storage/eman2.99.47/bin/e2parallel.py", line 96, in main
ret=task.execute(empty_func)
File "/mnt/storage/eman2.99.47/bin/e2spt_subtlt_local.py", line 247, in execute
ip=[i for i,d in enumerate(d2d) if d["idx3d"]==dc["idx3d"]][0]
IndexError: list index out of range


Error executing: <e2spt_subtlt_local.SptAlignTask object at 0x7f6e3856b4c0>
Traceback (most recent call last):
File "/mnt/storage/eman2.99.47/bin/e2parallel.py", line 96, in main
ret=task.execute(empty_func)
File "/mnt/storage/eman2.99.47/bin/e2spt_subtlt_local.py", line 247, in execute
ip=[i for i,d in enumerate(d2d) if d["idx3d"]==dc["idx3d"]][0]
IndexError: list index out of range


Error executing: <e2spt_subtlt_local.SptAlignTask object at 0x7f537c0ac4c0>
Traceback (most recent call last):
File "/mnt/storage/eman2.99.47/bin/e2parallel.py", line 96, in main
ret=task.execute(empty_func)
File "/mnt/storage/eman2.99.47/bin/e2spt_subtlt_local.py", line 247, in execute
ip=[i for i,d in enumerate(d2d) if d["idx3d"]==dc["idx3d"]][0]
IndexError: list index out of range


Error executing: <e2spt_subtlt_local.SptAlignTask object at 0x7fa1d95e44c0>
Error executing: <e2spt_subtlt_local.SptAlignTask object at 0x7fbccdc0c4c0>
Traceback (most recent call last):
File "/mnt/storage/eman2.99.47/bin/e2parallel.py", line 96, in main
ret=task.execute(empty_func)
File "/mnt/storage/eman2.99.47/bin/e2spt_subtlt_local.py", line 247, in execute
ip=[i for i,d in enumerate(d2d) if d["idx3d"]==dc["idx3d"]][0]
IndexError: list index out of range


Traceback (most recent call last):
File "/mnt/storage/eman2.99.47/bin/e2parallel.py", line 96, in main
ret=task.execute(empty_func)
File "/mnt/storage/eman2.99.47/bin/e2spt_subtlt_local.py", line 247, in execute
ip=[i for i,d in enumerate(d2d) if d["idx3d"]==dc["idx3d"]][0]
IndexError: list index out of range


Error executing: <e2spt_subtlt_local.SptAlignTask object at 0x7f006a3974c0>
Traceback (most recent call last):
File "/mnt/storage/eman2.99.47/bin/e2parallel.py", line 96, in main
ret=task.execute(empty_func)
File "/mnt/storage/eman2.99.47/bin/e2spt_subtlt_local.py", line 247, in execute
ip=[i for i,d in enumerate(d2d) if d["idx3d"]==dc["idx3d"]][0]
IndexError: list index out of range


Error executing: <e2spt_subtlt_local.SptAlignTask object at 0x7f21294eb4c0>
Traceback (most recent call last):
File "/mnt/storage/eman2.99.47/bin/e2parallel.py", line 96, in main
ret=task.execute(empty_func)
File "/mnt/storage/eman2.99.47/bin/e2spt_subtlt_local.py", line 247, in execute
ip=[i for i,d in enumerate(d2d) if d["idx3d"]==dc["idx3d"]][0]
IndexError: list index out of range


Error executing: <e2spt_subtlt_local.SptAlignTask object at 0x7f75f20224c0>
Traceback (most recent call last):
File "/mnt/storage/eman2.99.47/bin/e2parallel.py", line 96, in main
ret=task.execute(empty_func)
File "/mnt/storage/eman2.99.47/bin/e2spt_subtlt_local.py", line 247, in execute
ip=[i for i,d in enumerate(d2d) if d["idx3d"]==dc["idx3d"]][0]
IndexError: list index out of range


Error executing: <e2spt_subtlt_local.SptAlignTask object at 0x7f4ff25514c0>
Traceback (most recent call last):
File "/mnt/storage/eman2.99.47/bin/e2parallel.py", line 96, in main
ret=task.execute(empty_func)
File "/mnt/storage/eman2.99.47/bin/e2spt_subtlt_local.py", line 247, in execute
ip=[i for i,d in enumerate(d2d) if d["idx3d"]==dc["idx3d"]][0]
IndexError: list index out of range


Error executing: <e2spt_subtlt_local.SptAlignTask object at 0x7f6f061134c0>
Traceback (most recent call last):
File "/mnt/storage/eman2.99.47/bin/e2parallel.py", line 96, in main
ret=task.execute(empty_func)
File "/mnt/storage/eman2.99.47/bin/e2spt_subtlt_local.py", line 247, in execute
ip=[i for i,d in enumerate(d2d) if d["idx3d"]==dc["idx3d"]][0]
IndexError: list index out of range


Error executing: <e2spt_subtlt_local.SptAlignTask object at 0x7f4af93e64c0>
Traceback (most recent call last):
File "/mnt/storage/eman2.99.47/bin/e2parallel.py", line 96, in main
ret=task.execute(empty_func)
File "/mnt/storage/eman2.99.47/bin/e2spt_subtlt_local.py", line 247, in execute
ip=[i for i,d in enumerate(d2d) if d["idx3d"]==dc["idx3d"]][0]
IndexError: list index out of range


Error executing: <e2spt_subtlt_local.SptAlignTask object at 0x7ff2381544c0>
Traceback (most recent call last):
File "/mnt/storage/eman2.99.47/bin/e2parallel.py", line 96, in main
ret=task.execute(empty_func)
File "/mnt/storage/eman2.99.47/bin/e2spt_subtlt_local.py", line 247, in execute
ip=[i for i,d in enumerate(d2d) if d["idx3d"]==dc["idx3d"]][0]
IndexError: list index out of range


Error executing: <e2spt_subtlt_local.SptAlignTask object at 0x7f65098814c0>
Traceback (most recent call last):
File "/mnt/storage/eman2.99.47/bin/e2parallel.py", line 96, in main
ret=task.execute(empty_func)
File "/mnt/storage/eman2.99.47/bin/e2spt_subtlt_local.py", line 247, in execute
ip=[i for i,d in enumerate(d2d) if d["idx3d"]==dc["idx3d"]][0]
IndexError: list index out of range


Error executing: <e2spt_subtlt_local.SptAlignTask object at 0x7f2d602444c0>
Traceback (most recent call last):
File "/mnt/storage/eman2.99.47/bin/e2parallel.py", line 96, in main
ret=task.execute(empty_func)
File "/mnt/storage/eman2.99.47/bin/e2spt_subtlt_local.py", line 247, in execute
ip=[i for i,d in enumerate(d2d) if d["idx3d"]==dc["idx3d"]][0]
IndexError: list index out of range


Error executing: <e2spt_subtlt_local.SptAlignTask object at 0x7f868eb114c0>
Traceback (most recent call last):
File "/mnt/storage/eman2.99.47/bin/e2parallel.py", line 96, in main
ret=task.execute(empty_func)
File "/mnt/storage/eman2.99.47/bin/e2spt_subtlt_local.py", line 247, in execute
ip=[i for i,d in enumerate(d2d) if d["idx3d"]==dc["idx3d"]][0]
IndexError: list index out of range


Error executing: <e2spt_subtlt_local.SptAlignTask object at 0x7f9e1d7984c0>
Traceback (most recent call last):
File "/mnt/storage/eman2.99.47/bin/e2parallel.py", line 96, in main
ret=task.execute(empty_func)
File "/mnt/storage/eman2.99.47/bin/e2spt_subtlt_local.py", line 247, in execute
ip=[i for i,d in enumerate(d2d) if d["idx3d"]==dc["idx3d"]][0]
IndexError: list index out of range


Error executing: <e2spt_subtlt_local.SptAlignTask object at 0x7f6d167184c0>
Traceback (most recent call last):
File "/mnt/storage/eman2.99.47/bin/e2parallel.py", line 96, in main
ret=task.execute(empty_func)
File "/mnt/storage/eman2.99.47/bin/e2spt_subtlt_local.py", line 247, in execute
ip=[i for i,d in enumerate(d2d) if d["idx3d"]==dc["idx3d"]][0]
IndexError: list index out of range


Error executing: <e2spt_subtlt_local.SptAlignTask object at 0x7f1b6882e4c0>
Traceback (most recent call last):
File "/mnt/storage/eman2.99.47/bin/e2parallel.py", line 96, in main
ret=task.execute(empty_func)
File "/mnt/storage/eman2.99.47/bin/e2spt_subtlt_local.py", line 247, in execute
ip=[i for i,d in enumerate(d2d) if d["idx3d"]==dc["idx3d"]][0]
IndexError: list index out of range


Error running task : 0
e2spa_make3d.py --input spt_17/aliptcls2d_03.lst --output spt_17/threed_03_even.hdf --keep 0.95 --clsid even --outsize 256 --sym d39 --parallel thread:24
Error executing: <e2spt_subtlt_local.SptAlignTask object at 0x7f5438cb64c0>
Traceback (most recent call last):
File "/mnt/storage/eman2.99.47/bin/e2parallel.py", line 96, in main
ret=task.execute(empty_func)
File "/mnt/storage/eman2.99.47/bin/e2spt_subtlt_local.py", line 247, in execute
ip=[i for i,d in enumerate(d2d) if d["idx3d"]==dc["idx3d"]][0]
IndexError: list index out of range


Error executing: <e2spt_subtlt_local.SptAlignTask object at 0x7fc7e6a2e4c0>
Traceback (most recent call last):
File "/mnt/storage/eman2.99.47/bin/e2parallel.py", line 96, in main
ret=task.execute(empty_func)
File "/mnt/storage/eman2.99.47/bin/e2spt_subtlt_local.py", line 247, in execute
ip=[i for i,d in enumerate(d2d) if d["idx3d"]==dc["idx3d"]][0]
IndexError: list index out of range


/mnt/storage/eman2.99.47/lib/python3.9/site-packages/numpy/core/getlimits.py:500: UserWarning: The value of the smallest subnormal for <class 'numpy.float64'> type is zero.
setattr(self, word, getattr(machar, word).flat[0])
/mnt/storage/eman2.99.47/lib/python3.9/site-packages/numpy/core/getlimits.py:89: UserWarning: The value of the smallest subnormal for <class 'numpy.float64'> type is zero.
return self._float_to_str(self.smallest_subnormal)
/mnt/storage/eman2.99.47/lib/python3.9/site-packages/numpy/core/getlimits.py:500: UserWarning: The value of the smallest subnormal for <class 'numpy.float32'> type is zero.
setattr(self, word, getattr(machar, word).flat[0])
/mnt/storage/eman2.99.47/lib/python3.9/site-packages/numpy/core/getlimits.py:89: UserWarning: The value of the smallest subnormal for <class 'numpy.float32'> type is zero.
return self._float_to_str(self.smallest_subnormal)
Traceback (most recent call last):
File "/mnt/storage/eman2.99.47/bin/e2spa_make3d.py", line 445, in <module>
main()
File "/mnt/storage/eman2.99.47/bin/e2spa_make3d.py", line 63, in main
tmp=EMData(options.input,0,True)
File "/mnt/storage/eman2.99.47/lib/python3.9/site-packages/EMAN2.py", line 2880, in db_emd_init
self.read_image(*parms)
File "/mnt/storage/eman2.99.47/lib/python3.9/site-packages/EMAN2.py", line 2927, in db_read_image
return LSXFile(fsp).read_into_image(self,*parms)
File "/mnt/storage/eman2.99.47/lib/python3.9/site-packages/EMAN2.py", line 2638, in read_into_image
n,fsp,jsondict=self.read(N)
File "/mnt/storage/eman2.99.47/lib/python3.9/site-packages/EMAN2.py", line 2590, in read
if n>=self.n : raise IndexError("Attempt to read record {} from #LSX {} with {} records".format(n,self.path,self.n))
IndexError: Attempt to read record 0 from #LSX spt_17/aliptcls2d_03.lst with 0 records
e2proc3d.py spt_17/threed_03_even.hdf spt_17/threed_raw_even.hdf --compressbits 12
Traceback (most recent call last):
File "/mnt/storage/eman2.99.47/bin/e2proc3d.py", line 856, in <module>
main()
File "/mnt/storage/eman2.99.47/bin/e2proc3d.py", line 174, in main
infile, _ = parse_infile_arg(infile)
File "/mnt/storage/eman2.99.47/lib/python3.9/site-packages/EMAN2.py", line 1087, in parse_infile_arg
raise Exception(f"'{fname}' is not an existing regular file!")
Exception: 'spt_17/threed_03_even.hdf' is not an existing regular file!
e2spa_make3d.py --input spt_17/aliptcls2d_03.lst --output spt_17/threed_03_odd.hdf --keep 0.95 --clsid odd --outsize 256 --sym d39 --parallel thread:24
/mnt/storage/eman2.99.47/lib/python3.9/site-packages/numpy/core/getlimits.py:500: UserWarning: The value of the smallest subnormal for <class 'numpy.float64'> type is zero.
setattr(self, word, getattr(machar, word).flat[0])
/mnt/storage/eman2.99.47/lib/python3.9/site-packages/numpy/core/getlimits.py:89: UserWarning: The value of the smallest subnormal for <class 'numpy.float64'> type is zero.
return self._float_to_str(self.smallest_subnormal)
/mnt/storage/eman2.99.47/lib/python3.9/site-packages/numpy/core/getlimits.py:500: UserWarning: The value of the smallest subnormal for <class 'numpy.float32'> type is zero.
setattr(self, word, getattr(machar, word).flat[0])
/mnt/storage/eman2.99.47/lib/python3.9/site-packages/numpy/core/getlimits.py:89: UserWarning: The value of the smallest subnormal for <class 'numpy.float32'> type is zero.
return self._float_to_str(self.smallest_subnormal)
Traceback (most recent call last):
File "/mnt/storage/eman2.99.47/bin/e2spa_make3d.py", line 445, in <module>
main()
File "/mnt/storage/eman2.99.47/bin/e2spa_make3d.py", line 63, in main
tmp=EMData(options.input,0,True)
File "/mnt/storage/eman2.99.47/lib/python3.9/site-packages/EMAN2.py", line 2880, in db_emd_init
self.read_image(*parms)
File "/mnt/storage/eman2.99.47/lib/python3.9/site-packages/EMAN2.py", line 2927, in db_read_image
return LSXFile(fsp).read_into_image(self,*parms)
File "/mnt/storage/eman2.99.47/lib/python3.9/site-packages/EMAN2.py", line 2638, in read_into_image
n,fsp,jsondict=self.read(N)
File "/mnt/storage/eman2.99.47/lib/python3.9/site-packages/EMAN2.py", line 2590, in read
if n>=self.n : raise IndexError("Attempt to read record {} from #LSX {} with {} records".format(n,self.path,self.n))
IndexError: Attempt to read record 0 from #LSX spt_17/aliptcls2d_03.lst with 0 records
e2proc3d.py spt_17/threed_03_odd.hdf spt_17/threed_raw_odd.hdf --compressbits 12
Traceback (most recent call last):
File "/mnt/storage/eman2.99.47/bin/e2proc3d.py", line 856, in <module>
main()
File "/mnt/storage/eman2.99.47/bin/e2proc3d.py", line 174, in main
infile, _ = parse_infile_arg(infile)
File "/mnt/storage/eman2.99.47/lib/python3.9/site-packages/EMAN2.py", line 1087, in parse_infile_arg
raise Exception(f"'{fname}' is not an existing regular file!")
Exception: 'spt_17/threed_03_odd.hdf' is not an existing regular file!
e2refine_postprocess.py --even spt_17/threed_03_even.hdf --tophat local --threads 12 --restarget 60.50 --sym d39
Use iteration number 3.
Traceback (most recent call last):
File "/mnt/storage/eman2.99.47/bin/e2refine_postprocess.py", line 563, in <module>
main()
File "/mnt/storage/eman2.99.47/bin/e2refine_postprocess.py", line 116, in main
hdr=EMData(evenfile,0,1)
File "/mnt/storage/eman2.99.47/lib/python3.9/site-packages/EMAN2.py", line 2880, in db_emd_init
self.read_image(*parms)
File "/mnt/storage/eman2.99.47/lib/python3.9/site-packages/EMAN2.py", line 2932, in db_read_image
fsp, idxs = parse_infile_arg(fsp)
File "/mnt/storage/eman2.99.47/lib/python3.9/site-packages/EMAN2.py", line 1087, in parse_infile_arg
raise Exception(f"'{fname}' is not an existing regular file!")
Exception: 'spt_17/threed_03_even.hdf' is not an existing regular file!
Traceback (most recent call last):
File "/mnt/storage/eman2.99.47/bin/e2spt_refine_new.py", line 416, in <module>
main()
File "/mnt/storage/eman2.99.47/bin/e2spt_refine_new.py", line 319, in main
r=calc_resolution(f"{path}/fsc_masked_{itr:02d}.txt")
File "/mnt/storage/eman2.99.47/bin/e2spt_refine_new.py", line 399, in calc_resolution
fsc=np.loadtxt(fscfile)
File "/mnt/storage/eman2.99.47/lib/python3.9/site-packages/numpy/lib/npyio.py", line 1318, in loadtxt
arr = _read(fname, dtype=dtype, comment=comment, delimiter=delimiter,
File "/mnt/storage/eman2.99.47/lib/python3.9/site-packages/numpy/lib/npyio.py", line 955, in _read
fh = np.lib._datasource.open(fname, 'rt', encoding=encoding)
File "/mnt/storage/eman2.99.47/lib/python3.9/site-packages/numpy/lib/_datasource.py", line 193, in open
return ds.open(path, mode, encoding=encoding, newline=newline)
File "/mnt/storage/eman2.99.47/lib/python3.9/site-packages/numpy/lib/_datasource.py", line 533, in open
raise FileNotFoundError(f"{path} not found.")
FileNotFoundError: spt_17/fsc_masked_03.txt not found.

------------

Best,
Eli

Muyuan Chen

unread,
Jul 26, 2024, 3:46:45 PM7/26/24
to em...@googlegroups.com
That is a strange error... Did you extract particles the standard way using e2spt_extract? Did anything strange happen during the 'p' iterations? 

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Andrea Dallapé

unread,
May 1, 2025, 7:08:55 PMMay 1
to EMAN2
Hi,

did you find a solution? I'm having the same error.
I extracted the particles the standard way (it's a filament):

e2spt_extract.py --boxsz_unbin=250 --newlabel=MT_bin2.lst --threads=8 --alltomograms --shrink=2.0 --tltkeep=1.0 --compressbits=8 --parallel=thread:4 --curves=0 --curves_overlap=.5

I then run a refinement

e2spt_refine_new.py --ptcls sets/MT_bin2.lst --ref sptsgd_00/output_cls0.hdf --sym c1 --curve --parallel thread:32 --startres 30 --iters=p4,t2 --keep=0.95 --threads=32

But at iter 5 (subtilt translational refinement) I get this error:
OSError: spt_01/fsc_masked_05.txt not found.

The complete error is in the file attached.

How did you solve?
Thank you so much for any help,
Andrea

error_eman2_fsc_mask_not_found.rtf

Muyuan Chen

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May 1, 2025, 7:20:48 PMMay 1
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Still, this is strange. It essentially says it cannot find the 2D particle it is reading for some reason. It should not normally happen because the program has already read that particle just a few lines ago. One thing is to run the e2spt_subtlt_local command with an additional --debug options and see if there is any useful output. If it runs through it without errors, it means there are some particles (but not the first few particles) that has something wrong that triggers the issue. If so, maybe send me the spt_01/particles_info_Xd.json and I will try to figure it out...
Muyuan

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<error_eman2_fsc_mask_not_found.rtf>

Andrea Dallapé

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May 1, 2025, 7:57:48 PMMay 1
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Hi Muyuan,

here:

e2spt_subtlt_local.py --ref spt_01/threed_04.hdf --path spt_01 --iter 5 --maxres 21.76 --parallel thread:32 --aliptcls3d spt_01/aliptcls3d_04.lst --smooth 100 --smoothN 15 --refine_trans --goldcontinue --debug
128 jobs on 32 CPUs
0
loading metadata from spt_01/particle_info_2d.lst, spt_01/particle_info_3d.lst...
max res: 21.76, max box size 60

Traceback (most recent call last):
  File "/home/janlevinson/micromamba/envs/eman2/bin/e2spt_subtlt_local.py", line 486, in <module>
    main()
  File "/home/janlevinson/micromamba/envs/eman2/bin/e2spt_subtlt_local.py", line 67, in main
    ret=task.execute(print)
  File "/home/janlevinson/micromamba/envs/eman2/bin/e2spt_subtlt_local.py", line 262, in execute

    ip=[i for i,d in enumerate(d2d) if d["idx3d"]==dc["idx3d"]][0]
IndexError: list index out of range

Any idea?

Andrea

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Muyuan Chen

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May 1, 2025, 7:59:15 PMMay 1
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Hmm.... I probably still need spt_01/particle_info_2d.lst, spt_01/particle_info_3d.lst...

Andrea Dallapé

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May 1, 2025, 8:09:31 PMMay 1
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Hi Muyuan,

here the files (all the .lst files).

Thank you,
Andrea

To view this discussion visit https://groups.google.com/d/msgid/eman2/8E1DDE5F-63B9-4AC9-9222-8F692844E0C1%40gmail.com.
spt_01.zip

Muyuan Chen

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May 1, 2025, 9:11:02 PMMay 1
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I see. So the issue is with the particle_info_3d.lst file. Inside it refers to sets/10ts002_MT_2_bin2.lst and a few other lst files. Having lst file linking to other lst file is theoretically possible but cause problems in various programs. 

That would imply the input, sets/MT_bin2.lst is a lst with lst too, but I don't think they can be created automatically as a part of the pipeline. I guess you just combined a few lst files in text editor? 

It should be fixed by creating a list that refers to the actual hdf files in sets/10ts002_MT_2_bin2.lst. I think if you run something like "e2proclst.py sets/10ts002_MT_2_bin2.lst sets/10ts002_MT_3_bin2.lst xxxx.lst xxxx --create sets/mt_all.lst", it should produce a lst file containing hdf only. Unless of course sets/10ts002_MT_3_bin2.lst is also a lst within lst...

Muyuan

Andrea Dallapé

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May 1, 2025, 9:16:49 PMMay 1
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Aahhhh!

Yes, I did a mistake with the ID classes of the curves, so I extracted singularly from each tomo and the combined the lst files with e2buildstack:

e2buildstack.pay sets/*.lst —output sets/MT_bin2.lst

I was hoping it was working. I didn’t think this could have been the reason.
I will check this and let you know.

Thank you!
Andrea

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