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CHEUI_preprocess_m5C.py give error
I successfully run the CHEUI_preprocess_m6A.py. but when I ran the CHEUI_preprocess_m5C.py script then the below error occurred. Can you please resolve this issue? Thanks in advance
Here is the command which I used:
nohup python3 /home/apps/CHEUI/scripts/CHEUI_preprocess_m5C.py -i /Drive7/CHEUI/nanopolish_out.txt -m /home/apps/CHEUI/kmer_models/model_kmer.csv -o out_C_signals -n 35 &
multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File "/usr/lib/python3.6/multiprocessing/pool.py", line 119, in worker
result = (True, func(*args, **kwds))
File "/usr/lib/python3.6/multiprocessing/pool.py", line 44, in mapstar
return list(map(*args))
File "/home/apps/CHEUI/scripts/CHEUI_preprocess_m5C.py", line 482, in parse_nanopolish
counter)
File "/home/apps/CHEUI/scripts/CHEUI_preprocess_m5C.py", line 160, in _parse_kmers
samples = [float(i) for i in checked_line[samples_idx].split(',')]
File "/home/apps/CHEUI/scripts/CHEUI_preprocess_m5C.py", line 160, in
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/home/apps/CHEUI/scripts/CHEUI_preprocess_m5C.py", line 560, in
Hi,
Sorry about the issue. Can you please share few lines of the nanopolish input file you used? Also, we recommend using the C++ version for faster preprocessing.
Thanks, Akanksha
here is the input file for your reference: contig position reference_kmer read_name strand event_index event_level_mean event_stdv event_length model_kmer model_ mean model_stdv standardized_level start_idx end_idx samples gene1 452 TTTAA 3a40d16c-e4fe-4e28-bc3c-7d31eabfdeb7 t 2 81.02 1.173 0.00398 TTTAA 84.44 2.46 -1.18 20956 20968 81.951 ,82.6334,82.0875,79.085,79.9039,80.3133,81.2686,82.0875,80.1768,79.2215,81.4051,82.0875 gene1 452 TTTAA 3a40d16c-e4fe-4e28-bc3c-7d31eabfdeb7 t 3 83.74 1.112 0.00498 TTTAA 84.44 2.46 -0.24 20941 20956 83.861 7,81.8145,84.1346,81.8145,82.9063,85.0899,83.8617,82.3604,83.4522,83.1793,84.1346,85.0899,84.544,85.4994,84.4076 gene1 452 TTTAA 3a40d16c-e4fe-4e28-bc3c-7d31eabfdeb7 t 4 85.62 1.945 0.02590 TTTAA 84.44 2.46 0.41 20863 20941 87.273 6,84.817,86.5912,87.1371,86.1817,86.1817,84.1346,85.6358,85.6358,85.6358,85.7723,85.6358,85.9088,85.6358,87.0006,88.5018,86.0453,85.2264,86.4547,86.5912,84.95 35,84.9535,85.4994,84.4076,86.3182,94.9162,82.7699,85.9088,83.3158,83.5887,87.0006,88.2289,86.1817,85.9088,76.0826,84.6805,85.7723,85.2264,86.3182,84.1346,86. 7276,84.9535,83.9981,85.2264,83.8617,85.4994,85.4994,83.7252,83.9981,83.5887,85.4994,86.5912,84.4076,84.1346,86.8641,84.9535,83.8617,83.9981,87.9559,85.9088,8 5.9088,86.5912,84.6805,86.8641,86.5912,85.7723,85.4994,86.8641,85.7723,85.9088,85.0899,87.5465,86.4547,88.6383,86.0453,83.1793,86.4547,85.2264 gene1 452 TTTAA 3a40d16c-e4fe-4e28-bc3c-7d31eabfdeb7 t 5 84.54 0.925 0.00232 TTTAA 84.44 2.46 0.04 20856 20863 85.362 9,83.9981,82.9063,85.6358,83.8617,84.6805,85.3629 gene1 453 TTAAA 3a40d16c-e4fe-4e28-bc3c-7d31eabfdeb7 t 6 94.67 3.645 0.01029 TTAAA 92.05 3.04 0.73 20825 20856 95.735 ,95.735,93.4149,93.5514,94.0973,95.735,96.5539,97.3727,95.735,96.8268,98.1916,95.8715,95.3256,95.3256,98.1916,76.492,94.5067,93.9609,91.9137,95.4621,94.3703,9 5.4621,96.6904,95.1891,92.869,95.1891,97.7822,92.5961,94.7797,95.0527,94.7797 gene1 453 TTAAA 3a40d16c-e4fe-4e28-bc3c-7d31eabfdeb7 t 7 96.60 1.775 0.00365 TTAAA 92.05 3.04 1.27 20814 20825 95.052 7,95.0527,94.7797,95.735,98.874,98.3281,95.4621,94.0973,98.601,98.601,98.0551 gene1 454 TAAAT 3a40d16c-e4fe-4e28-bc3c-7d31eabfdeb7 t 8 97.39 1.404 0.00432 TAAAT 108.51 2.68 -3.53 20801 20814 97.509 2,96.1445,97.7822,95.4621,95.1891,97.2363,99.4199,99.0104,97.0998,98.0551,96.9633,96.2809,99.9658 gene1 455 AAATG 3a40d16c-e4fe-4e28-bc3c-7d31eabfdeb7 t 9 110.97 3.286 0.02722 AAATG 110.67 3.11 0.08 20719 20801 104.06 ,97.2363,114.705,108.427,111.839,113.886,112.112,115.66,110.747,113.75,113.477,112.931,115.933,113.75,111.293,111.976,111.976,112.522,110.201,101.058,113.067, 105.971,112.931,111.43,116.206,102.695,116.889,110.611,108.837,108.837,115.66,113.75,111.703,108.837,113.204,114.705,110.065,111.703,109.519,109.519,103.378,1 13.34,112.385,107.881,114.159,111.839,113.477,109.11,111.02,110.747,112.794,114.296,111.43,108.973,110.065,111.293,109.792,110.884,112.249,111.43,113.75,112.7 94,112.249,108.291,114.023,110.474,110.884,113.204,106.653,114.432,110.884,112.658,109.792,109.792,109.656,109.519,109.656,109.792,110.338,109.519,108.291,108 .837 gene1 456 AATGC 3a40d16c-e4fe-4e28-bc3c-7d31eabfdeb7 t 10 80.66 7.228 0.00764 AATGC 81.80 3.87 -0.25 20696 20719 72.807 1,78.9485,75.6731,80.7227,72.5342,69.1223,78.8121,86.7276,69.6682,79.7674,75.9461,94.2338,77.0379,81.1321,79.6309,75.8096,88.7748,82.3604,84.2711,99.8293,85.4 994,79.4944,86.4547 gene1 456 AATGC 3a40d16c-e4fe-4e28-bc3c-7d31eabfdeb7 t 11 82.82 1.951 0.00432 AATGC 81.80 3.87 0.22 20683 20696 82.769 9,85.9088,81.5416,85.0899,82.9063,85.4994,83.7252,82.6334,81.2686,79.2215,83.8617,79.9039,82.3604 gene1 456 AATGC 3a40d16c-e4fe-4e28-bc3c-7d31eabfdeb7 t 12 79.87 3.572 0.00299 AATGC 81.80 3.87 -0.42 20674 20683 78.539 1,86.0453,73.7625,79.9039,77.3108,82.7699,76.3555,81.5416,82.6334 gene1 457 ATGCA 3a40d16c-e4fe-4e28-bc3c-7d31eabfdeb7 t 13 84.56 2.839 0.00598 ATGCA 84.45 3.13 0.03 20656 20674 85.908 8,83.3158,80.9957,89.3207,89.5936,84.6805,87.5465,83.4522,77.3108,85.0899,84.1346,86.3182,81.951,86.1817,83.7252,82.4969,84.817,85.2264 gene1 457 ATGCA 3a40d16c-e4fe-4e28-bc3c-7d31eabfdeb7 t 14 82.56 3.086 0.01029 ATGCA 84.45 3.13 -0.51 20625 20656 80.449 8,84.2711,84.6805,85.6358,79.7674,79.4944,76.492,77.4473,83.3158,80.7227,85.4994,86.1817,83.0428,84.6805,81.5416,82.3604,75.9461,86.1817,82.0875,82.2239,84.27 11,79.7674,86.5912,90.276,84.817,81.6781,82.7699,84.4076,81.6781,80.1768,80.8592 gene1 457 ATGCA 3a40d16c-e4fe-4e28-bc3c-7d31eabfdeb7 t 15 87.31 2.366 0.00332 ATGCA 84.45 3.13 0.78 20615 20625 88.365 3,89.1842,91.7772,88.2289,83.8617,85.2264,87.0006,83.7252,87.2736,88.5018 gene1 457 ATGCA 3a40d16c-e4fe-4e28-bc3c-7d31eabfdeb7 t 16 79.71 3.939 0.00232 ATGCA 84.45 3.13 -1.29 20608 20615 72.124 --More--(0%) Thanks in advance for resolving the issue.
Thanks, the format for nanopolish file looks ok. Can you please try 2 things:
- run the preprocessing code on the test file (https://github.com/comprna/CHEUI/blob/master/test/nanopolish_output_test.txt) to see if the installation is correct.
- Can you please try it with the C++ version of preprocessing? Otherwise, we might have to find a way to share the nanopolish file to debug. Thanks, Akanksha
1- run the preprocessing code on the test file:
The test run was completely successful. No error occurs. I used the command:
nohup ./CHEUI -i /home/aclab/apps/CHEUI/test/nanopolish_output_test.txt -o /home/aclab/apps/CHEUI/scripts/preprocessing_CPP/test/out_C_signals+IDs.p/ -m /home/aclab/apps/CHEUI/kmer_models/model_kmer.csv -n 50 --m5C &
2- I try the C++ version of preprocessing:
nohup ./CHEUI -i /Drive7/nanopolish_out.txt -o /Drive7/out_C_signals+IDs.p/ -m /home/aclab/apps/CHEUI/kmer_models/model_kmer.csv -n 50 --m5C &
But it also gives following error: terminate called after throwing an instance of 'std::invalid_argument' what(): stof
"please sort out this issue if possible, I want to run this pipeline. Thanks in advance
Thank you so much for running the 2 tests. Do you get the error message after some temp files are created or its straight away? We can look at our end if you are happy to share the nanopolish file. I know it can be huge though. Email:[email protected] Thanks, Akanksha
Do you get the error message after some temp files are created or is it straight away?
The temp file(51 in number) was made and also main output file(nanopolish_out_signals+IDS.p) has some data.
Here below the command is processed before getting error happens:
2500000 processed lines
3500000 processed lines
4000000 processed lines
5500000 processed lines
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500000 processed lines
1000000 processed lines
5000000 processed lines
2000000 processed lines
3500000 processed lines
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multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File "/usr/lib/python3.6/multiprocessing/pool.py", line 119, in worker
result = (True, func(*args, **kwds))
File "/usr/lib/python3.6/multiprocessing/pool.py", line 44, in mapstar
return list(map(*args))
File "/home/aclab/apps/CHEUI/scripts/CHEUI_preprocess_m5C.py", line 482, in parse_nanopolish
counter)
File "/home/aclab/apps/CHEUI/scripts/CHEUI_preprocess_m5C.py", line 160, in _parse_kmers
samples = [float(i) for i in checked_line[samples_idx].split(',')]
File "/home/aclab/apps/CHEUI/scripts/CHEUI_preprocess_m5C.py", line 160, in
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/home/aclab/apps/CHEUI/scripts/CHEUI_preprocess_m5C.py", line 560, in
Thanks. Just wondering is it possible to run the script without multiprocessing (n=1).
Also can you please share the number of lines in your nanopolish file.
Thanks, Akanksha
As you suggested I ran the the script with n=1 but it also not completed:
500000 processed lines
4000000 processed lines
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5500000 processed lines
6000000 processed lines
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Traceback (most recent call last):
File "/home/aclab/apps/CHEUI/scripts/CHEUI_preprocess_m5C.py", line 555, in
I run the command in nohup. I don't think its the issue. Is my nanopolish file is too large for the command running.
Thanks. Yes running in background should be fine. I think it gets stuck somewhere between line 253500000 to end of your file which is 254747839. Can you please cp the lines from 253000000 till end of your file into another file and then share with me. It seems like either the nanopolish file is corrupt or the preprocessing script is missing a check to handle the special case that might be in thenano polish file.
Also if you can share the output file that you got from the above run might be useful.
Thanks, Akanksha
Could you please take a moment to review the nanopolish out file I shared on May 4th? I'd appreciate it if you could identify any issues or problems. Thank you! in advance.
Hi, Sorry about the delay in reply. So if you look at last two lines of your file they look weird.
1747834 gene9 616.0 GCTGA c9ee63a7-28b7-40a9-a743-c0eccfba7f73 t 127.0 81.03 2.141 0.00996 GCTGA 89.96 2.85 -2.77 27749.0 27779.0 81.3491,85.069,81.2113,80.2469,79.1447,78.0425,78.4558,82.4513,80.1091,79.4202,80.3847,80.2469,82.0379,82.4513,75.9759,82.0379,79.9713,83.829,82.0379,87.5489,78.[post-run summary] total reads: 384066, unparseable: 0, qc fail: 6183, could not calibrate: 415, no alignment: 266, bad fast5: 0
1747835 0425,79.558,82.1757,80.9358,80.798,80.3847,81.9002,82.1757,81.0735,81.7624
```
That's where the preprocessing code will get stuck. If you remove these two lines. The issue should be resolved.
Also, If you already have the output from the preprocessing code I think it should be fine to run the next steps.
Thanks,
Akanskha
when I run the CHEUI model 1 code in nohup command then when i open nohup file then it shows this message. I want to know my file is run completely or not: This message occur in both command for m6A and m5C. Ran out of input All signals have been processed 44982579
whichever file is made in read level detection code, i procees it for site level detection:
The below output file for m6A site detection level. I want to understand the output file of the CHEUI model 2 code because if the second column is my m6A site like in 1st row it says 1495 is m6A site but at my sequence the 1495 doesn't contain m6A sites. likewise 1541 position is also don't contain m6A sites.
transcript.fa 1495 TAGCAGGAA 161 0.30434782608695654 0.30759284
transcript.fa 1502 AACTACTAG 167 0.10256410256410256 0.12798941
transcript.fa 1505 TACTAGTAC 158 0.36904761904761907 0.43889725
transcript.fa 1508 TAGTACCCT 149 0.16393442622950818 0.39143988
transcript.fa 1522 AACAAATAG 108 0.1368421052631579 0.2662186
transcript.fa 1523 ACAAATAGG 108 0.13402061855670103 0.49044427
transcript.fa 1525 AAATAGGAT 112 0.1625 0.4378153
transcript.fa 1539 ACACATAAT 161 0.547945205479452 0.5977786
transcript.fa 1541 ACATAATCC 156 0.3389830508474576 0.86891454
transcript.fa 1542 CATAATCCA 153 0.23622047244094488 0.74543554
transcript.fa 1546 ATCCACCTA 157 0.40963855421686746 0.49316177
transcript.fa 1555 TCCCAGTAG 134 0.17708333333333334 0.18778525
transcript.fa 1558 CAGTAGGAG 131 0.2948717948717949 0.54169106
Thanks in advance
Hi, If it says "All signals have been processed" that means its complete. To get the position of the center nucleotide you need to add +5. The position column gives the position of the first nucleotide of the 9mer sequence. I hope it helps.
Thanks, Akanksha