Case Study: Yeast U4/U6.U5 tri-snRNP

Troubleshooting
1

Hello,
I am practicing with the 10073 dataset. I was able to import the particles and was able to start the ab-initio reconstruction process. It runs but fails after a while with “Input/Output error!” Anyone run into similar problem?

[CPU: 841.0 MB] ----------- Iteration 2 (epoch 0.002). radwn 15.20 resolution 35.00A minisize 90 beta 0.10

[CPU: 834.5 MB] – Class 0 – lr: 0.40 eps: 5.21 step ratio : 0.1550 ESS R: 89.186 S: 4.031 Class Size: 12.6% (Average: 42.4%)

[CPU: 850.5 MB] – Class 1 – lr: 0.40 eps: 5.21 step ratio : 0.3470 ESS R: 246.470 S: 4.647 Class Size: 87.4% (Average: 57.6%)

[CPU: 850.7 MB] Done iteration 00002 of 01690 in 5.204s. Total time 27.7s.

[CPU: 906.8 MB] ----------- Iteration 3 (epoch 0.003). radwn 15.20 resolution 35.00A minisize 90 beta 0.10

[CPU: 907.5 MB] – Class 0 – lr: 0.40 eps: 5.52 step ratio : 0.0554 ESS R: 123.513 S: 3.874 Class Size: 8.3% (Average: 40.2%)

[CPU: 907.5 MB] – Class 1 – lr: 0.40 eps: 5.52 step ratio : 0.4529 ESS R: 400.362 S: 4.410 Class Size: 91.7% (Average: 59.8%)

[CPU: 907.5 MB] Done iteration 00003 of 01690 in 5.176s. Total time 32.9s.

[CPU: 907.5 MB] ----------- Iteration 4 (epoch 0.003). radwn 15.20 resolution 35.00A minisize 90 beta 0.10

[CPU: 844.3 MB] – Class 0 – lr: 0.40 eps: 5.09 step ratio : 0.1182 ESS R: 100.811 S: 4.233 Class Size: 8.2% (Average: 38.2%)

[CPU: 844.3 MB] – Class 1 – lr: 0.40 eps: 5.09 step ratio : 0.4160 ESS R: 186.314 S: 3.820 Class Size: 91.8% (Average: 61.8%)

[CPU: 844.3 MB] Done iteration 00004 of 01690 in 4.912s. Total time 37.8s.

[CPU: 860.2 MB] ----------- Iteration 5 (epoch 0.004). radwn 15.20 resolution 35.00A minisize 90 beta 0.10

[CPU: 812.9 MB] – Class 0 – lr: 0.40 eps: 5.48 step ratio : 0.0815 ESS R: 137.370 S: 3.888 Class Size: 8.9% (Average: 36.5%)

[CPU: 828.7 MB] – Class 1 – lr: 0.40 eps: 5.48 step ratio : 0.4314 ESS R: 251.847 S: 3.931 Class Size: 91.1% (Average: 63.5%)

[CPU: 828.8 MB] Done iteration 00005 of 01690 in 4.941s. Total time 42.8s.

[CPU: 860.7 MB] ----------- Iteration 6 (epoch 0.005). radwn 15.20 resolution 35.00A minisize 90 beta 0.10
[CPU: 668.7 MB] Traceback (most recent call last):
File “cryosparc_worker/cryosparc_compute/run.py”, line 84, in cryosparc_compute.run.main
File “cryosparc_worker/cryosparc_compute/jobs/abinit/run.py”, line 304, in cryosparc_compute.jobs.abinit.run.run_homo_abinit
File “cryosparc_worker/cryosparc_compute/engine/engine.py”, line 1149, in cryosparc_compute.engine.engine.process
File “cryosparc_worker/cryosparc_compute/engine/engine.py”, line 1150, in cryosparc_compute.engine.engine.process
File “cryosparc_worker/cryosparc_compute/engine/engine.py”, line 1027, in cryosparc_compute.engine.engine.process.work
File “cryosparc_worker/cryosparc_compute/engine/engine.py”, line 87, in cryosparc_compute.engine.engine.EngineThread.load_image_data_gpu
File “/raid-18/LS/smarius/tmalla/cryosparc/cryosparc_worker/cryosparc_compute/particles.py”, line 113, in get_original_real_data
return self.blob.view().copy()
File “/raid-18/LS/smarius/tmalla/cryosparc/cryosparc_worker/cryosparc_compute/blobio/mrc.py”, line 126, in view
return self.get()
File “/raid-18/LS/smarius/tmalla/cryosparc/cryosparc_worker/cryosparc_compute/blobio/mrc.py”, line 121, in get
_, data, total_time = prefetch.synchronous_native_read(self.fname, idx_start = self.page, idx_limit = self.page+1)
File “cryosparc_worker/cryosparc_compute/blobio/prefetch.py”, line 64, in cryosparc_compute.blobio.prefetch.synchronous_native_read
RuntimeError: fread 486: Input/output error
2

Hi @73km,

Could you run the “Check Particles” job on this dataset and see if any of the files are corrupt? This error means that cryoSPARC couldn’t read the whole file because it’s smaller than it should be - as if it has been truncated or something like that.

If the particles all check fine, my next question would be whether the files are being read from a local hard drive (i.e. physically attached to the computer that’s doing the processing) or if it’s being read from a network? If the latter, does this error always happen, or is it intermittent?

Thanks,
Harris

3

Okay, I found the “Check particles” job by updating to new patch. The job found two corrupted data files. Using the output from this job [Which has the same number of particles even though there were corruptions], resulted in same error. Although the error now points the same data file that was shown corrupted by the “check particles” job. Am I supposed to manually delete these files and run?

4

Even manually deleting the corrupted files didn’t work.

Output from Check Particles*******************
[CPU: 99.3 MB] Found 2 corrupted data files:

[CPU: 99.3 MB] [’/home/tmalla/Data/tmalla/EM/practice/10073/P5/J8/imported/11Jul15_6234_cor_bin2_extractedparticles_11Jul15unchecked_shiny200-22Jun11Jul-7frames.mrcs’, ‘/home/tmalla/Data/tmalla/EM/practice/10073/P5/J8/imported/11Jul15_6353_cor_bin2_extractedparticles_11Jul15unchecked_shiny200-22Jun11Jul-7frames.mrcs’]

[CPU: 80.1 MB] --------------------------------------------------------------

[CPU: 80.1 MB] Compiling job outputs…

[CPU: 80.1 MB] Passing through outputs for output group particles from input group particles

[CPU: 121.3 MB] This job outputted results [‘blob’]

[CPU: 121.3 MB] Loaded output dset with 138899 items

[CPU: 121.3 MB] Passthrough results [‘ctf’, ‘alignments3D’]

[CPU: 177.2 MB] Loaded passthrough dset with 138899 items

[CPU: 177.4 MB] Intersection of output and passthrough has 138899 items

[CPU: 74.1 MB] Checking outputs for output group particles

[CPU: 74.9 MB] Updating job size…

[CPU: 74.9 MB] Exporting job and creating csg files…

[CPU: 74.9 MB] ***************************************************************
[CPU: 74.9 MB] Job complete. Total time 64.02s

Output from Ab-initio reconstruction*******************
[CPU: 955.4 MB] – Class 0 – lr: 0.40 eps: 2.88 step ratio : 0.2390 ESS R: 327.072 S: 3.814 Class Size: 100.0% (Average: 100.0%)

[CPU: 955.5 MB] Done iteration 00029 of 01228 in 4.106s. Total time 129.5s.

[CPU: 955.5 MB] ----------- Iteration 30 (epoch 0.020). radwn 15.20 resolution 35.00A minisize 90 beta 0.10

[CPU: 819.8 MB] Traceback (most recent call last): File “cryosparc_worker/cryosparc_compute/run.py”, line 84, in cryosparc_compute.run.main File “cryosparc_worker/cryosparc_compute/jobs/abinit/run.py”, line 304, in cryosparc_compute.jobs.abinit.run.run_homo_abinit File “cryosparc_worker/cryosparc_compute/engine/engine.py”, line 1149, in cryosparc_compute.engine.engine.process File “cryosparc_worker/cryosparc_compute/engine/engine.py”, line 1150, in cryosparc_compute.engine.engine.process File “cryosparc_worker/cryosparc_compute/engine/engine.py”, line 1027, in cryosparc_compute.engine.engine.process.work File “cryosparc_worker/cryosparc_compute/engine/engine.py”, line 87, in cryosparc_compute.engine.engine.EngineThread.load_image_data_gpu File “/raid-18/LS/smarius/tmalla/cryosparc/cryosparc_worker/cryosparc_compute/particles.py”, line 15, in get_original_real_data return self.blob.view().copy() File “/raid-18/LS/smarius/tmalla/cryosparc/cryosparc_worker/cryosparc_compute/blobio/mrc.py”, line 115, in view return self.get() File “/raid-18/LS/smarius/tmalla/cryosparc/cryosparc_worker/cryosparc_compute/blobio/mrc.py”, line 110, in get _, data, total_time = prefetch.synchronous_native_read(self.fname, idx_start = self.page, idx_limit = self.page+1) File “cryosparc_worker/cryosparc_compute/blobio/prefetch.py”, line 64, in cryosparc_compute.blobio.prefetch.synchronous_native_read RuntimeError: fread 486: Input/output error [arguments] /home/tmalla/Data/tmalla/EM/practice/10073/P5/J8/imported/11Jul15_6234_cor_bin2_extractedparticles_11Jul15unchecked_shiny200-22Jun11Jul-7frames.mrcs, 0, 0, 92, 93, 2, 40

Outputs

particles_all_classes

particleCount: 90

particles_class_0

particleCount: 90

volume_class_0

volume_class_0

volumeCount: 1

sentinel

5

Hi @73km,

After deleting the corrupt files you’ll have to re-run the import particles job (and all subsequent jobs). Were you going straight into ab-initio from import particles?

–Harris

1 Like
6

Yes, I was going straight to ab-initio from importing. I saw that on forum. After deleting the original files from data, I also had to edit the star file. Otherwise the job spits out this error
“AssertionError: Files referenced by the input star file are missing.” The tutorial page has a link for updated star file but because the name is identical to original star file, I must not have used the correct star file.
But the job ran. Thanks!

1 Like