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Testing example failed? #57

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malonzm1 opened this issue Feb 10, 2025 · 10 comments
Closed

Testing example failed? #57

malonzm1 opened this issue Feb 10, 2025 · 10 comments
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@frankligy

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@malonzm1
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malonzm1 commented Feb 10, 2025 •
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When I run the test analysis.py, I get the following error:

^M  0%|          | 0/54 [00:00<?, ?it/s]rm: cannot remove './TMHMM_*': No such file or directory
^M  2%|?         | 1/54 [00:00<00:09,  5.51it/s]rm: cannot remove './TMHMM_*': No such file or directory
^M  4%|?         | 2/54 [00:00<00:08,  5.89it/s]rm: cannot remove './TMHMM_*': No such file or directory
^M  6%|?         | 3/54 [00:00<00:08,  6.01it/s]rm: cannot remove './TMHMM_*': No such file or directory
^M  7%|?         | 4/54 [00:00<00:08,  6.04it/s]rm: cannot remove './TMHMM_*': No such file or directory
^M  9%|?         | 5/54 [00:00<00:08,  6.09it/s]rm: cannot remove './TMHMM_*': No such file or directory
^M 11%|?         | 6/54 [00:00<00:07,  6.10it/s]rm: cannot remove './TMHMM_*': No such file or directory
^M 13%|??        | 7/54 [00:01<00:07,  5.91it/s]rm: cannot remove './TMHMM_*': No such file or directory
^M 15%|??        | 8/54 [00:01<00:07,  5.79it/s]rm: cannot remove './TMHMM_*': No such file or directory
^M 17%|??        | 9/54 [00:01<00:07,  5.71it/s]rm: cannot remove './TMHMM_*': No such file or directory
^M 19%|??        | 10/54 [00:01<00:07,  5.85it/s]rm: cannot remove './TMHMM_*': No such file or directory
^M 20%|??        | 11/54 [00:01<00:07,  5.71it/s]rm: cannot remove './TMHMM_*': No such file or directory
^M 22%|???       | 12/54 [00:02<00:07,  5.65it/s]rm: cannot remove './TMHMM_*': No such file or directory
^M 24%|???       | 13/54 [00:02<00:07,  5.80it/s]rm: cannot remove './TMHMM_*': No such file or directory
^M 26%|???       | 14/54 [00:02<00:06,  5.91it/s]rm: cannot remove './TMHMM_*': No such file or directory
^M 28%|???       | 15/54 [00:02<00:06,  5.99it/s]rm: cannot remove './TMHMM_*': No such file or directory
^M 30%|???       | 16/54 [00:02<00:06,  6.03it/s]rm: cannot remove './TMHMM_*': No such file or directory
^M 31%|????      | 17/54 [00:02<00:06,  6.07it/s]rm: cannot remove './TMHMM_*': No such file or directory
^M 33%|????      | 18/54 [00:03<00:05,  6.10it/s]rm: cannot remove './TMHMM_*': No such file or directory
^M 35%|????      | 19/54 [00:03<00:05,  5.92it/s]rm: cannot remove './TMHMM_*': No such file or directory
^M 37%|????      | 20/54 [00:03<00:05,  5.81it/s]rm: cannot remove './TMHMM_*': No such file or directory
^M 39%|????      | 21/54 [00:03<00:05,  5.90it/s]rm: cannot remove './TMHMM_*': No such file or directory
^M 41%|????      | 22/54 [00:03<00:05,  5.79it/s]^M 43%|?????     | 23/54 [00:05<00:17,  1.81it/s]rm: cannot remove './TMHMM_*': No such file or directory
^M 44%|?????     | 24/54 [00:05<00:13,  2.29it/s]rm: cannot remove './TMHMM_*': No such file or directory
^M 46%|?????     | 25/54 [00:05<00:10,  2.83it/s]rm: cannot remove './TMHMM_*': No such file or directory
^M 48%|?????     | 26/54 [00:05<00:08,  3.36it/s]^M 50%|?????     | 27/54 [00:06<00:09,  2.72it/s]rm: cannot remove './TMHMM_*': No such file or directory
^M 52%|??????    | 28/54 [00:06<00:07,  3.26it/s]rm: cannot remove './TMHMM_*': No such file or directory
^M 54%|??????    | 29/54 [00:06<00:06,  3.80it/s]rm: cannot remove './TMHMM_*': No such file or directory
^M 56%|??????    | 30/54 [00:06<00:05,  4.28it/s]rm: cannot remove './TMHMM_*': No such file or directory
^M 57%|??????    | 31/54 [00:06<00:04,  4.72it/s]rm: cannot remove './TMHMM_*': No such file or directory
^M 59%|??????    | 32/54 [00:07<00:04,  5.08it/s]rm: cannot remove './TMHMM_*': No such file or directory
^M 61%|??????    | 33/54 [00:07<00:04,  5.21it/s]^M 63%|???????   | 34/54 [00:07<00:04,  4.16it/s]rm: cannot remove './TMHMM_*': No such file or directory
^M 65%|???????   | 35/54 [00:07<00:04,  4.60it/s]rm: cannot remove './TMHMM_*': No such file or directory
^M 67%|???????   | 36/54 [00:07<00:03,  4.98it/s]rm: cannot remove './TMHMM_*': No such file or directory
^M 69%|???????   | 37/54 [00:08<00:03,  5.27it/s]rm: cannot remove './TMHMM_*': No such file or directory
^M 70%|???????   | 38/54 [00:08<00:02,  5.51it/s]^M 72%|????????  | 39/54 [00:09<00:09,  1.65it/s]rm: cannot remove './TMHMM_*': No such file or directory
^M 74%|????????  | 40/54 [00:09<00:06,  2.11it/s]rm: cannot remove './TMHMM_*': No such file or directory
^M 76%|????????  | 41/54 [00:10<00:04,  2.63it/s]rm: cannot remove './TMHMM_*': No such file or directory
^M 78%|????????  | 42/54 [00:10<00:03,  3.18it/s]rm: cannot remove './TMHMM_*': No such file or directory
^M 80%|????????  | 43/54 [00:10<00:03,  3.64it/s]rm: cannot remove './TMHMM_*': No such file or directory
^M 81%|????????? | 44/54 [00:10<00:02,  4.06it/s]^M 83%|????????? | 45/54 [00:13<00:08,  1.02it/s]rm: cannot remove './TMHMM_*': No such file or directory
^M 85%|????????? | 46/54 [00:13<00:05,  1.36it/s]^M 87%|????????? | 47/54 [00:15<00:07,  1.03s/it]^M 89%|????????? | 48/54 [00:15<00:04,  1.20it/s]rm: cannot remove './TMHMM_*': No such file or directory
^M 91%|????????? | 49/54 [00:15<00:03,  1.59it/s]rm: cannot remove './TMHMM_*': No such file or directory
^M 93%|??????????| 50/54 [00:15<00:01,  2.04it/s]rm: cannot remove './TMHMM_*': No such file or directory
^M 94%|??????????| 51/54 [00:16<00:01,  2.52it/s]rm: cannot remove './TMHMM_*': No such file or directory
^M 96%|??????????| 52/54 [00:16<00:00,  3.06it/s]rm: cannot remove './TMHMM_*': No such file or directory
^M 98%|??????????| 53/54 [00:16<00:00,  3.60it/s]rm: cannot remove './TMHMM_*': No such file or directory
^M100%|??????????| 54/54 [00:16<00:00,  4.11it/s]^M100%|??????????| 54/54 [00:16<00:00,  3.26it/s]
Input sequence provided is already in string format. No operation performed
^M  0%|          | 0/1 [00:00<?, ?it/s]^M100%|??????????| 1/1 [00:00<00:00, 42.29it/s]
Input sequence provided is already in string format. No operation performed
^M  0%|          | 0/1 [00:00<?, ?it/s]^M100%|??????????| 1/1 [00:00<00:00, 42.10it/s]
Input sequence provided is already in string format. No operation performed
^M  0%|          | 0/1 [00:00<?, ?it/s]^M100%|??????????| 1/1 [00:00<00:00, 41.38it/s]
Input sequence provided is already in string format. No operation performed
^M  0%|          | 0/1 [00:00<?, ?it/s]^M100%|??????????| 1/1 [00:00<00:00, 42.81it/s]
Input sequence provided is already in string format. No operation performed
^M  0%|          | 0/1 [00:00<?, ?it/s]^M100%|??????????| 1/1 [00:00<00:00, 40.24it/s]
Input sequence provided is already in string format. No operation performed
1 input query terms found dup hits:     [('ENSG00000173698', 2)]
^M  0%|          | 0/2 [00:00<?, ?it/s]^M100%|??????????| 2/2 [00:00<00:00, 44.94it/s]
Input sequence provided is already in string format. No operation performed
1 input query terms found dup hits:     [('ENSG00000173698', 2)]
^M  0%|          | 0/3 [00:00<?, ?it/s]^M100%|??????????| 3/3 [00:00<00:00, 46.64it/s]
Input sequence provided is already in string format. No operation performed
1 input query terms found dup hits:     [('ENSG00000173698', 2)]
^M  0%|          | 0/2 [00:00<?, ?it/s]^M100%|??????????| 2/2 [00:00<00:00, 46.10it/s]
Input sequence provided is already in string format. No operation performed
1 input query terms found dup hits:     [('ENSG00000173698', 2)]
^M  0%|          | 0/3 [00:00<?, ?it/s]^M100%|??????????| 3/3 [00:00<00:00, 47.60it/s]
Input sequence provided is already in string format. No operation performed
^M  0%|          | 0/1 [00:00<?, ?it/s]^M100%|??????????| 1/1 [00:00<00:00, 43.90it/s]
^M  0%|          | 0/54 [00:00<?, ?it/s]^M  2%|?         | 1/54 [00:00<00:22,  2.38it/s]rm: cannot remove './TMHMM_*': No such file or directory
^M  4%|?         | 2/54 [00:00<00:13,  3.72it/s]^M  6%|?         | 3/54 [00:00<00:16,  3.09it/s]^M  7%|?         | 4/54 [00:04<01:14,  1.49s/it]^M  9%|?         | 5/54 [00:04<00:54,  1.12s/it]^M 11%|?         | 6/54 [00:10<02:14,  2.81s/it]^M 13%|??        | 7/54 [00:11<01:39,  2.11s/it]^M 15%|??        | 8/54 [00:12<01:16,  1.66s/it]rm: cannot remove './TMHMM_*': No such file or directory
^M 17%|??        | 9/54 [00:12<00:53,  1.19s/it]rm: cannot remove './TMHMM_*': No such file or directory
^M 19%|??        | 10/54 [00:12<00:38,  1.15it/s]rm: cannot remove './TMHMM_*': No such file or directory
^M 20%|??        | 11/54 [00:12<00:28,  1.52it/s]rm: cannot remove './TMHMM_*': No such file or directory
^M 22%|???       | 12/54 [00:12<00:21,  1.97it/s]rm: cannot remove './TMHMM_*': No such file or directory
^M 24%|???       | 13/54 [00:12<00:16,  2.48it/s]^M 26%|???       | 14/54 [00:15<00:47,  1.18s/it]^M 28%|???       | 15/54 [00:22<01:53,  2.92s/it]rm: cannot remove './TMHMM_*': No such file or directory
^M 30%|???       | 16/54 [00:23<01:19,  2.09s/it]^M 31%|????      | 17/54 [00:23<00:58,  1.58s/it]rm: cannot remove './TMHMM_*': No such file or directory
^M 33%|????      | 18/54 [00:23<00:41,  1.16s/it]^M 35%|????      | 19/54 [00:24<00:32,  1.08it/s]^M 37%|????      | 20/54 [00:24<00:26,  1.28it/s]^M 39%|????      | 21/54 [00:24<00:22,  1.50it/s]rm: cannot remove './TMHMM_*': No such file or directory
^M 41%|????      | 22/54 [00:25<00:16,  1.93it/s]rm: cannot remove './TMHMM_*': No such file or directory
^M 43%|?????     | 23/54 [00:25<00:12,  2.42it/s]rm: cannot remove './TMHMM_*': No such file or directory
^M 44%|?????     | 24/54 [00:25<00:10,  2.96it/s]^M 46%|?????     | 25/54 [00:32<01:09,  2.39s/it]rm: cannot remove './TMHMM_*': No such file or directory
^M 48%|?????     | 26/54 [00:32<00:48,  1.73s/it]rm: cannot remove './TMHMM_*': No such file or directory
^M 50%|?????     | 27/54 [00:32<00:34,  1.26s/it]^M 52%|??????    | 28/54 [00:35<00:39,  1.51s/it]rm: cannot remove './TMHMM_*': No such file or directory
^M 54%|??????    | 29/54 [00:35<00:27,  1.11s/it]^M 56%|??????    | 30/54 [00:36<00:26,  1.09s/it]^M 57%|??????    | 31/54 [00:37<00:27,  1.21s/it]rm: cannot remove './TMHMM_*': No such file or directory
^M 59%|??????    | 32/54 [00:37<00:19,  1.12it/s]rm: cannot remove './TMHMM_*': No such file or directory
^M 61%|??????    | 33/54 [00:38<00:14,  1.48it/s]rm: cannot remove './TMHMM_*': No such file or directory
^M 63%|???????   | 34/54 [00:38<00:10,  1.90it/s]rm: cannot remove './TMHMM_*': No such file or directory
^M 65%|???????   | 35/54 [00:38<00:07,  2.40it/s]rm: cannot remove './TMHMM_*': No such file or directory
^M 67%|???????   | 36/54 [00:38<00:06,  2.92it/s]^M 69%|???????   | 37/54 [00:39<00:10,  1.70it/s]^M 70%|???????   | 38/54 [00:40<00:09,  1.74it/s]rm: cannot remove './TMHMM_*': No such file or directory
^M 72%|????????  | 39/54 [00:40<00:06,  2.22it/s]^M 74%|????????  | 40/54 [00:40<00:06,  2.28it/s]^M 76%|????????  | 41/54 [00:42<00:12,  1.07it/s]^M 78%|????????  | 42/54 [00:50<00:36,  3.05s/it]^M 80%|????????  | 43/54 [00:54<00:34,  3.10s/it]rm: cannot remove './TMHMM_*': No such file or directory
^M 81%|????????? | 44/54 [00:54<00:22,  2.22s/it]rm: cannot remove './TMHMM_*': No such file or directory
^M 83%|????????? | 45/54 [00:54<00:14,  1.60s/it]rm: cannot remove './TMHMM_*': No such file or directory
^M 85%|????????? | 46/54 [00:54<00:09,  1.17s/it]^M 87%|????????? | 47/54 [00:56<00:09,  1.35s/it]^M 89%|????????? | 48/54 [00:56<00:06,  1.07s/it]rm: cannot remove './TMHMM_*': No such file or directory
^M 91%|????????? | 49/54 [00:56<00:03,  1.25it/s]^M 93%|??????????| 50/54 [01:14<00:23,  5.92s/it]rm: cannot remove './TMHMM_*': No such file or directory
^M 94%|??????????| 51/54 [01:15<00:12,  4.20s/it]^M 96%|??????????| 52/54 [01:16<00:06,  3.28s/it]^M 98%|??????????| 53/54 [01:28<00:06,  6.14s/it]^M100%|??????????| 54/54 [01:30<00:00,  4.79s/it]^M100%|??????????| 54/54 [01:30<00:00,  1.68s/it]
Input sequence provided is already in string format. No operation performed
3 input query terms found dup hits:     [('ENSG00000187266', 2), ('ENSG00000166736', 2), ('ENSG00000006118', 3)]
^M  0%|          | 0/10 [00:00<?, ?it/s]^M100%|??????????| 10/10 [00:00<00:00, 10702.49it/s]
Input sequence provided is already in string format. No operation performed
4 input query terms found dup hits:     [('ENSG00000086159', 2), ('ENSG00000006118', 6), ('ENSG00000187266', 2), ('ENSG00000166736', 2)]
^M  0%|          | 0/23 [00:00<?, ?it/s]^M100%|??????????| 23/23 [00:00<00:00, 17137.86it/s]
Input sequence provided is already in string format. No operation performed
3 input query terms found dup hits:     [('ENSG00000187266', 2), ('ENSG00000166736', 2), ('ENSG00000006118', 3)]
^M  0%|          | 0/10 [00:00<?, ?it/s]^M100%|??????????| 10/10 [00:00<00:00, 12803.13it/s]
Input sequence provided is already in string format. No operation performed
4 input query terms found dup hits:     [('ENSG00000086159', 2), ('ENSG00000006118', 5), ('ENSG00000187266', 2), ('ENSG00000166736', 2)]
^M  0%|          | 0/22 [00:00<?, ?it/s]^M100%|??????????| 22/22 [00:00<00:00, 11424.38it/s]
Input sequence provided is already in string format. No operation performed
^M  0%|          | 0/1 [00:00<?, ?it/s]^M100%|??????????| 1/1 [00:00<00:00, 7695.97it/s]
Input sequence provided is already in string format. No operation performed
1 input query terms found dup hits:     [('ENSG00000006118', 4)]
^M  0%|          | 0/4 [00:00<?, ?it/s]^M100%|??????????| 4/4 [00:00<00:00, 14768.68it/s]
Traceback (most recent call last):
  File "analysis.py", line 68, in <module>
    surface.run_dash_B_antigen(pkl='result/surface_antigen_lr.p',candidates='result/surface/candidates_3_lr_None.txt',prediction_mode='long_read', python_executable='/scratch/work/malonzm1/.conda_envs/snaf-env/bin/python')
  File "/scratch/work/malonzm1/.conda_envs/snaf-env/lib/python3.7/site-packages/snaf/surface/main.py", line 279, in run_dash_B_antigen
    _run_dash_long_read_mode(pkl,candidates,python_executable,host=host,port=port)
  File "/scratch/work/malonzm1/.conda_envs/snaf-env/lib/python3.7/site-packages/snaf/surface/main.py", line 156, in _run_dash_long_read_mode
    with open(pkl,'rb') as f1:
FileNotFoundError: [Errno 2] No such file or directory: 'result/surface_antigen_lr.p'
Error in atexit._run_exitfuncs:
Traceback (most recent call last):
  File "/scratch/work/malonzm1/.conda_envs/snaf-env/lib/python3.7/site-packages/snaf/dash_app/app.py", line 20, in clear_assets
    imgs = os.listdir('assets')
FileNotFoundError: [Errno 2] No such file or directory: 'assets'

Please advise. The installation of SNAF via pip didn't encounter any problems.

Thanks and good day.
@frankligy
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Owner

Hi @malonzm1,

Sorry for the inconvenience, I want to verify a few things:

[1] Particularly, you ran into issue when testing the B-cell pipeline, the other parts are ok and ran smoothly on your end?
[2] After the failed job as you showed, how did your result folder look like?
[3] Did you also install TMHMM (https://snaf.readthedocs.io/en/latest/installation.html#step-4-optional-install-netmhcpan4-1-and-tmhmm2-0)

Thank you,
Frank

@malonzm1
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Author

Hi @frankligy,

Thanks.

The following is the output before the error:

2025-02-11 00:41:59 starting initialization
Current loaded gtex cohort with shape (12827, 2629)
Adding cohort tcga_control with shape (12902, 705) to the database
now the shape of control db is (12908, 3334)
Adding cohort gtex_skin with shape (12098, 313) to the database
now the shape of control db is (12908, 3647)
2025-02-11 00:42:43 finishing initialization
-------------pass initiate test----------------
2025-02-11 00:42:43 starting surface antigen initialization
2025-02-11 00:43:05 finished surface antigen initialization
-------------pass B antigen initiate test----------------
reduce valid NeoJunction from 12927 to 840 because they are present in GTEx
reduce valid Neojunction from 840 to 668 because they are present in added control tcga_control
reduce valid Neojunction from 668 to 597 because they are present in added control gtex_skin
junction_count_matrix: (12927, 2)
cores: 24
valid: 597
invalid: 12330
cond_df: (12927, 2)
subset: (597, 2)
translated: list of None nj objects
cond_subset_df: (597, 2)
results: list of length None
no candidates for strigency 5 style None overlap_extracellular True
no candidates for strigency 5 style deletion overlap_extracellular True
no candidates for strigency 5 style insertion overlap_extracellular True
no candidates for strigency 5 style insertion overlap_extracellular False
no candidates for strigency 4 style None overlap_extracellular True
no candidates for strigency 4 style deletion overlap_extracellular True
no candidates for strigency 4 style insertion overlap_extracellular True
no candidates for strigency 3 style insertion overlap_extracellular True
-------------pass B antigen short read mode test----------------
-------------pass B antigen short long mode test----------------
-------------SNAF-B viewer will be launched, follow prompt, once finished, you can close the session----------------

The result/surface folder was modified:

(/scratch/work/malonzm1/.conda_envs/snaf-env) [malonzm1@pe21]/scratch/cs/pan-autoimmune/data/tumor_project/utilities/snaf% ls -ltr result/s
urface
total 6772
drwxr-sr-x 2 malonzm1 pan-autoimmune    4096 Feb 10 08:07 B_candidates
-rw-r--r-- 1 malonzm1 pan-autoimmune 2104222 Feb 11 01:01 NeoJunction_statistics_maxmin.txt
-rw-r--r-- 1 malonzm1 pan-autoimmune 1553114 Feb 11 01:01 surface_antigen_sr.p
-rw-r--r-- 1 malonzm1 pan-autoimmune      49 Feb 11 01:02 validation_5_sr_None_False.txt
-rw-r--r-- 1 malonzm1 pan-autoimmune     478 Feb 11 01:02 candidates_5_sr_None_False.txt
-rw-r--r-- 1 malonzm1 pan-autoimmune      49 Feb 11 01:02 validation_5_sr_deletion_False.txt
-rw-r--r-- 1 malonzm1 pan-autoimmune     478 Feb 11 01:02 candidates_5_sr_deletion_False.txt
-rw-r--r-- 1 malonzm1 pan-autoimmune      49 Feb 11 01:03 validation_4_sr_None_False.txt
-rw-r--r-- 1 malonzm1 pan-autoimmune     481 Feb 11 01:03 candidates_4_sr_None_False.txt
-rw-r--r-- 1 malonzm1 pan-autoimmune      49 Feb 11 01:03 validation_4_sr_deletion_False.txt
-rw-r--r-- 1 malonzm1 pan-autoimmune     478 Feb 11 01:03 candidates_4_sr_deletion_False.txt
-rw-r--r-- 1 malonzm1 pan-autoimmune      49 Feb 11 01:03 validation_4_sr_insertion_False.txt
-rw-r--r-- 1 malonzm1 pan-autoimmune     475 Feb 11 01:03 candidates_4_sr_insertion_False.txt
-rw-r--r-- 1 malonzm1 pan-autoimmune      10 Feb 11 01:03 validation_3_sr_None_True.txt
-rw-r--r-- 1 malonzm1 pan-autoimmune    1011 Feb 11 01:03 candidates_3_sr_None_True.txt
-rw-r--r-- 1 malonzm1 pan-autoimmune      15 Feb 11 01:03 validation_3_sr_None_False.txt
-rw-r--r-- 1 malonzm1 pan-autoimmune    1492 Feb 11 01:03 candidates_3_sr_None_False.txt
-rw-r--r-- 1 malonzm1 pan-autoimmune      10 Feb 11 01:03 validation_3_sr_deletion_True.txt
-rw-r--r-- 1 malonzm1 pan-autoimmune    1011 Feb 11 01:03 candidates_3_sr_deletion_True.txt
-rw-r--r-- 1 malonzm1 pan-autoimmune      15 Feb 11 01:03 validation_3_sr_deletion_False.txt
-rw-r--r-- 1 malonzm1 pan-autoimmune    1489 Feb 11 01:03 candidates_3_sr_deletion_False.txt
-rw-r--r-- 1 malonzm1 pan-autoimmune       5 Feb 11 01:03 validation_3_sr_insertion_False.txt
-rw-r--r-- 1 malonzm1 pan-autoimmune     475 Feb 11 01:03 candidates_3_sr_insertion_False.txt
-rw-r--r-- 1 malonzm1 pan-autoimmune 3104619 Feb 11 01:05 surface_antigen_lr.p
-rw-r--r-- 1 malonzm1 pan-autoimmune      50 Feb 11 01:05 validation_3_lr_None_True.txt
-rw-r--r-- 1 malonzm1 pan-autoimmune    6841 Feb 11 01:05 candidates_3_lr_None_True.txt
-rw-r--r-- 1 malonzm1 pan-autoimmune     115 Feb 11 01:05 validation_3_lr_None_False.txt
-rw-r--r-- 1 malonzm1 pan-autoimmune   14415 Feb 11 01:05 candidates_3_lr_None_False.txt
-rw-r--r-- 1 malonzm1 pan-autoimmune      50 Feb 11 01:06 validation_3_lr_deletion_True.txt
-rw-r--r-- 1 malonzm1 pan-autoimmune    6829 Feb 11 01:06 candidates_3_lr_deletion_True.txt
-rw-r--r-- 1 malonzm1 pan-autoimmune     110 Feb 11 01:06 validation_3_lr_deletion_False.txt
-rw-r--r-- 1 malonzm1 pan-autoimmune   13902 Feb 11 01:06 candidates_3_lr_deletion_False.txt
-rw-r--r-- 1 malonzm1 pan-autoimmune       5 Feb 11 01:06 validation_3_lr_insertion_True.txt
-rw-r--r-- 1 malonzm1 pan-autoimmune       0 Feb 11 01:06 further.txt
-rw-r--r-- 1 malonzm1 pan-autoimmune    1022 Feb 11 01:06 candidates_3_lr_insertion_True.txt
-rw-r--r-- 1 malonzm1 pan-autoimmune      20 Feb 11 01:06 validation_3_lr_insertion_False.txt
-rw-r--r-- 1 malonzm1 pan-autoimmune    2764 Feb 11 01:06 candidates_3_lr_insertion_False.txt

but not the direct contents of result folder.

Yes, I installed TMHMM.

Thanks.

@frankligy
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Hi @malonzm1,

I will check it myself and get back to you in one day.

Best,
Frank

@frankligy frankligy changed the title Test error Testing example failed? Feb 11, 2025
@frankligy frankligy self-assigned this Feb 11, 2025
@frankligy
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Hi @malonzm1,

Sorry for the wait, from what I can see here, actually everything looks good. In your /result/surface folder, you have all the files generated, the error you encountered at the end, is when launching the B-antigen portal, it can not find the surface_antigen_lr.p, this is an error in my testing script, because the correct path to that file should be result/surface/surface_antigen_lr.p, if you change that, you should be able to run through. I've already updated the codes.

No need to worry about that No such file or directory: 'assets', it's not an error: #30

Best,
Frank

@malonzm1
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Thanks @frankligy,

I did that and got a different error:

Traceback (most recent call last):
  File "analysis.py", line 68, in <module>
    surface.run_dash_B_antigen(pkl='result/surface/surface_antigen_lr.p',candidates='result/surface/candidates_3_lr_None.txt',prediction_mode='long_read', python_executable='/scratch/work/malonzm1/.conda_envs/snaf-env/bin/python')
  File "/scratch/work/malonzm1/.conda_envs/snaf-env/lib/python3.7/site-packages/snaf/surface/main.py", line 279, in run_dash_B_antigen
    _run_dash_long_read_mode(pkl,candidates,python_executable,host=host,port=port)
  File "/scratch/work/malonzm1/.conda_envs/snaf-env/lib/python3.7/site-packages/snaf/surface/main.py", line 159, in _run_dash_long_read_mode
    with open(candidates,'r') as f2:
FileNotFoundError: [Errno 2] No such file or directory: 'result/surface/candidates_3_lr_None.txt'
Error in atexit._run_exitfuncs:
Traceback (most recent call last):
  File "/scratch/work/malonzm1/.conda_envs/snaf-env/lib/python3.7/site-packages/snaf/dash_app/app.py", line 20, in clear_assets
    imgs = os.listdir('assets')
FileNotFoundError: [Errno 2] No such file or directory: 'assets'

On the other hand, I've tried running the pipeline in the tutorial on my data and everything seemed to work fine.

@frankligy
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Sorry, right it was another typo, instead of result/surface/candidates_3_lr_None.txt, it should be result/surface/candidates_3_lr_None_False.txt, just updated it. The tutorial (https://snaf.readthedocs.io/en/latest/tutorial.html#id2) should be right.

Frank

@malonzm1
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Thanks! Another question, if I want to analyze data from different diseases, is it ok to analyze everything with SNAF, or does it make more sense to analyze per disease?

@frankligy
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Hi @malonzm1,

Just want to make sure I understand the question correctly, were you referring to the situation where, for instance, you have multiple cancers, and you want to know whether you can combine all cancers data together as a whole or you should do that one by one?

Since the program will report sample-level results anyway, so I think it won't hurt that much when it comes to combine or not. But some of the results automatically generated indeed summarize cohort-level statistics, in that sense, maybe analyzing per disease will make more sense and later to coalesce.

Best,
Frank

@malonzm1
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malonzm1 commented Feb 14, 2025 via email

@frankligy
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Yeah the concept should be the same, in autoimmune disease, the goal should be to eliminate auto-reactive B or T cells, similar to how people find blood cancer targets. I also applied SNAF on senescence as well, the only difference is probably to be cautious about the normal tissue expression, for instance, CD19 and BCMA will be highly expressed in blood, which should be fine in autoimmune disease. Other than that, I think from a characterization perspective, it makes no difference no matter which context people will be using the tools.

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