Comments (7)
lmulroney
commented on August 28, 2024
Hi @kwonej0617,
Just a quick question,
In the eventalign_collapse.tsv snippet you shared, are the two data lines from the same file or the first data line from the two separate files with the same header? An eventalalign_collapse.tsv file should not have two lines for the same position for the same transcript. Could you also check if the eventalign_collapse.tsv files have index files?
Thanks,
Logan
from nanocompore.
kwonej0617
commented on August 28, 2024
Actually what I shared above is wt_eventalign.txt and ko_eventalign.txt, not wt_eventalign.txt and ko_eventalign.txt.
Here is eventalalign_collapse.tsv. As you mentioned, each line has a distinct position within a transcript.
#71576efc-add3-4fc3-823c-05628a65a835 ENST00000361390
ref_pos ref_kmer num_events num_signals dwell_time NNNNN_dwell_time mismatch_dwell_time status median mad
1 TACCC 3 85 0.028220000211149454 0.0 0.0 valid 78.497 1.0115051
2 ACCCA 3 66 0.021919999504461884 0.0 0.0 valid 64.625 1.0115013
3 CCCAT 2 40 0.013280000304803252 0.0 0.0 valid 72.78925 1.0114975
4 CCATG 4 37 0.012279999908059835 0.0 0.0 valid 80.9535 1.7340012
5 CATGG 1 44 0.01460999995470047 0.0 0.0 valid 81.31475 1.0114975
6 ATGGC 1 8 0.0026599999982863665 0.0 0.0 valid 95.62025 2.8899956
7 TGGCC 1 24 0.007969999685883522 0.0 0.0 valid 101.256 2.0229988
8 GGCCA 3 61 0.02025000029243529 0.0 0.0 valid 101.184 1.8789978
9 GCCAA 2 32 0.010620000073686242 0.0 0.0 valid 73.006 1.5894966
10 CCAAC 3 43 0.014269999926909804 0.0 0.0 valid 85.5775 1.1559982
11 CAACC 1 22 0.007300000172108412 0.0 0.0 valid 89.69575 1.300499
12 AACCT 2 19 0.006310000084340572 0.0 0.0 valid 78.786 2.312004
13 ACCTC 2 42 0.01394000044092536 0.0 0.0 valid 70.116 0.7947502
14 CCTCC 1 20 0.006639999803155661 0.0 0.0 valid 66.28675 1.0114975
15 CTCCT 1 12 0.003980000037699938 0.0 0.0 valid 69.9715 0.8670006
16 TCCTA 1 42 0.013939999975264072 0.0 0.0 valid 72.139 1.083747
This is eventalign_collapse.tsv.idx file.
ref_id ref_start ref_end read_id num_events num_signals dwell_time kmers missing_kmers NNNNN_kmers mismatch_kmers valid_kmers
byte_offset byte_len
ENST00000361390 1 951 71576efc-add3-4fc3-823c-05628a65a835 1887 35626 11.827349983388558 951 47 25 0 879 0
61727
ENST00000361390 1 951 2ffef773-aba8-4661-99ce-3450bf9b281e 2782 51606 17.132349965977482 951 55 40 0 856 61728 61735
ENST00000361390 1 951 946d14af-3aaa-4207-adaa-8f59e603f756 1776 33154 11.00635999662336 951 42 27 0 882 123464 62335
ENST00000361390 1 935 6d97273d-5b12-444b-a735-38742b318747 2203 39707 13.181959986453876 935 44 23 0 868 185800 61013
ENST00000361390 1 951 a37a7b71-6ae3-4ad2-8b3b-1a7b27c3bc73 1609 27803 9.230239991564304 951 33 25 0 893 246814 62787
ENST00000361390 1 950 b3f6ee4c-8ce8-494f-96ad-3108dae3d30a 1748 32259 10.709549980936572 950 27 21 0 902 309602 63017
ENST00000361390 1 951 282c768d-35db-4a0c-ba32-b3e0d3c40aa8 1886 38191 12.678779986687005 951 34 21 0 896 372620 62635
ENST00000361390 1 951 fdde1767-74fb-48f5-8d13-6f5bfefbb0eb 2023 38461 12.768609974300489 951 44 31 0 876 435256 62274
Please let me know if you need more information. Thank you so much for your time!
from nanocompore.
lmulroney
commented on August 28, 2024
Hi @kwonej0617,
Do you get the same "SystemError: null argument to internal routine" error if you try to run Nanocompore sampcomp outside of your script?
I did a little digging into the error "SystemError: null argument to internal routine", and it appears that might be an internal python error and not an error specific to Nanocompore. How did you install python and nanocompore on your system?
Thanks,
Logan
from nanocompore.
kwonej0617
commented on August 28, 2024
@lmulroney Thank you for your response.
I installed nanocompore using conda.
I will try to run nanocompore sampcomp outside of the script, instead of submitting a job to the cluster. Also, I will try to install it again.
from nanocompore.
lmulroney
commented on August 28, 2024
I recommend checking your python installation in addition to your nanocompore installation.
Logan
from nanocompore.
kwonej0617
commented on August 28, 2024
@lmulroney
Thank you for your advice. I have installed nanocompore and checked python installation again.
After doing that, I didn't have "SystemError: null argument to internal routine" during running nanocompore. However, I got another error as below and the job was killed.
2023-06-22T08:57:36.115574-0400 WARNING - MainProcess | Running Eventalign_collapse
2023-06-22T08:57:36.116017-0400 INFO - MainProcess | Checking and initialising Eventalign_collapse
2023-06-22T08:57:36.117289-0400 INFO - MainProcess | Starting data processing
2023-06-22T19:28:53.406933-0400 INFO - Process-40 | Output reads written:837586
2023-06-22T19:28:59.128338-0400 WARNING - MainProcess | Running Eventalign_collapse
2023-06-22T19:28:59.128862-0400 INFO - MainProcess | Checking and initialising Eventalign_collapse
2023-06-22T19:28:59.130137-0400 INFO - MainProcess | Starting data processing
2023-06-22T22:36:14.728180-0400 ERROR - Process-40 | Error in Writer
2023-06-22T22:36:14.755494-0400 ERROR - Process-40 | Traceback (most recent call last):
File "/share/pkg/conda/nanocompore/1.0.4/lib/python3.6/site-packages/nanocompore/Eventalign_collapse.py", line 266, in __write_output
data_fp.write(data_str)
OSError: [Errno 5] Input/output error
During handling of the above exception, another exception occurred:
OSError: [Errno 5] Input/output error
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/share/pkg/conda/nanocompore/1.0.4/lib/python3.6/site-packages/nanocompore/Eventalign_collapse.py", line 280, in __write_output
data_fp.write ("#\n")
OSError: [Errno 5] Input/output error
Traceback (most recent call last):
File "/share/pkg/conda/nanocompore/1.0.4/bin/nanocompore", line 8, in <module>
2023-06-22T22:36:14.756267-0400 INFO - Process-40 | Output reads written:254087
2023-06-22T22:36:14.756337-0400 ERROR - MainProcess | Traceback (most recent call last):
File "/share/pkg/conda/nanocompore/1.0.4/lib/python3.6/site-packages/nanocompore/Eventalign_collapse.py", line 266, in __write_output
data_fp.write(data_str)
OSError: [Errno 5] Input/output error
During handling of the above exception, another exception occurred:
OSError: [Errno 5] Input/output error
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/share/pkg/conda/nanocompore/1.0.4/lib/python3.6/site-packages/nanocompore/Eventalign_collapse.py", line 280, in __write_output
data_fp.write ("#\n")
OSError: [Errno 5] Input/output error
2023-06-22T22:36:14.756909-0400 ERROR - MainProcess | Traceback (most recent call last):
File "/share/pkg/conda/nanocompore/1.0.4/lib/python3.6/site-packages/nanocompore/Eventalign_collapse.py", line 266, in __write_output
data_fp.write(data_str)
OSError: [Errno 5] Input/output error
During handling of the above exception, another exception occurred:
OSError: [Errno 5] Input/output error
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/share/pkg/conda/nanocompore/1.0.4/lib/python3.6/site-packages/nanocompore/Eventalign_collapse.py", line 280, in __write_output
data_fp.write ("#\n")
OSError: [Errno 5] Input/output error
2023-06-22T22:36:14.757184-0400 ERROR - MainProcess | An error occured. Killing all processes and closing queues
sys.exit(main())
File "/share/pkg/conda/nanocompore/1.0.4/lib/python3.6/site-packages/nanocompore/__main__.py", line 175, in main
args.func(args)
File "/share/pkg/conda/nanocompore/1.0.4/lib/python3.6/site-packages/nanocompore/__main__.py", line 258, in eventalign_collapse_main
e()
File "/share/pkg/conda/nanocompore/1.0.4/lib/python3.6/site-packages/nanocompore/Eventalign_collapse.py", line 131, in __call__
raise E
File "/share/pkg/conda/nanocompore/1.0.4/lib/python3.6/site-packages/nanocompore/Eventalign_collapse.py", line 108, in __call__
raise NanocomporeError(tb)
nanocompore.common.NanocomporeError: Traceback (most recent call last):
File "/share/pkg/conda/nanocompore/1.0.4/lib/python3.6/site-packages/nanocompore/Eventalign_collapse.py", line 266, in __write_output
data_fp.write(data_str)
OSError: [Errno 5] Input/output error
During handling of the above exception, another exception occurred:
OSError: [Errno 5] Input/output error
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/share/pkg/conda/nanocompore/1.0.4/lib/python3.6/site-packages/nanocompore/Eventalign_collapse.py", line 280, in __write_output
data_fp.write ("#\n")
OSError: [Errno 5] Input/output error
2023-06-22T22:36:21.650259-0400 WARNING - MainProcess | Running SampComp
2023-06-22T22:36:21.650716-0400 INFO - MainProcess | Checking and initialising SampComp
2023-06-22T22:36:21.653479-0400 INFO - MainProcess | Only 1 replicate found for condition wt
2023-06-22T22:36:21.653646-0400 INFO - MainProcess | This is not recommended. The statistics will be calculated with the logit method
2023-06-22T22:36:21.653810-0400 INFO - MainProcess | Only 1 replicate found for condition ko
2023-06-22T22:36:21.654022-0400 INFO - MainProcess | This is not recommended. The statistics will be calculated with the logit method
2023-06-22T22:36:25.091263-0400 INFO - MainProcess | Reading eventalign index files
2023-06-22T22:36:57.640431-0400 INFO - MainProcess | References found in index: 25646
2023-06-22T22:36:57.641048-0400 INFO - MainProcess | Filtering out references with low coverage
2023-06-22T22:37:00.087471-0400 INFO - MainProcess | References remaining after reference coverage filtering: 1769
2023-06-22T22:37:00.536628-0400 INFO - MainProcess | Starting data processing
2023-06-23T07:58:42.307276-0400 ERROR - Process-9 | Index and data files are not matching:
['']
OrderedDict([('ref_id', 'ENST00000398073'), ('ref_start', 1), ('ref_end', 806), ('read_id', '25c275fd-e3e2-44ae-a985-c7a921008786'), ('num_events', 2528), ('num_signals', 54601), ('dwell_time', 18.126699992455542), ('kmers', 806), ('missing_kmers', 35), ('NNNNN_kmers', 26), ('mismatch_kmers', 0), ('valid_kmers', 745), ('byte_offset', 11815044271), ('byte_len', 52838)])
2023-06-23T07:58:42.307653-0400 ERROR - Process-9 | Error in Worker
2023-06-23T07:58:42.342012-0400 ERROR - Process-9 | Traceback (most recent call last):
File "/share/pkg/conda/nanocompore/1.0.4/lib/python3.6/site-packages/nanocompore/SampComp.py", line 305, in __process_references
raise NanocomporeError("Index and data files are not matching:\n{}\n{}".format(header, read))
nanocompore.common.NanocomporeError: Index and data files are not matching:
['']
OrderedDict([('ref_id', 'ENST00000398073'), ('ref_start', 1), ('ref_end', 806), ('read_id', '25c275fd-e3e2-44ae-a985-c7a921008786'), ('num_events', 2528), ('num_signals', 54601), ('dwell_time', 18.126699992455542), ('kmers', 806), ('missing_kmers', 35), ('NNNNN_kmers', 26), ('mismatch_kmers', 0), ('valid_kmers', 745), ('byte_offset', 11815044271), ('byte_len', 52838)])
2023-06-23T07:58:42.342946-0400 ERROR - MainProcess | Traceback (most recent call last):
File "/share/pkg/conda/nanocompore/1.0.4/lib/python3.6/site-packages/nanocompore/SampComp.py", line 305, in __process_references
raise NanocomporeError("Index and data files are not matching:\n{}\n{}".format(header, read))
nanocompore.common.NanocomporeError: Index and data files are not matching:
['']
OrderedDict([('ref_id', 'ENST00000398073'), ('ref_start', 1), ('ref_end', 806), ('read_id', '25c275fd-e3e2-44ae-a985-c7a921008786'), ('num_events', 2528), ('num_signals', 54601), ('dwell_time', 18.126699992455542), ('kmers', 806), ('missing_kmers', 35), ('NNNNN_kmers', 26), ('mismatch_kmers', 0), ('valid_kmers', 745), ('byte_offset', 11815044271), ('byte_len', 52838)])
2023-06-23T07:58:42.343941-0400 ERROR - MainProcess | Traceback (most recent call last):
File "/share/pkg/conda/nanocompore/1.0.4/lib/python3.6/site-packages/nanocompore/SampComp.py", line 305, in __process_references
raise NanocomporeError("Index and data files are not matching:\n{}\n{}".format(header, read))
nanocompore.common.NanocomporeError: Index and data files are not matching:
['']
OrderedDict([('ref_id', 'ENST00000398073'), ('ref_start', 1), ('ref_end', 806), ('read_id', '25c275fd-e3e2-44ae-a985-c7a921008786'), ('num_events', 2528), ('num_signals', 54601), ('dwell_time', 18.126699992455542), ('kmers', 806), ('missing_kmers', 35), ('NNNNN_kmers', 26), ('mismatch_kmers', 0), ('valid_kmers', 745), ('byte_offset', 11815044271), ('byte_len', 52838)])
Traceback (most recent call last):
File "/share/pkg/conda/nanocompore/1.0.4/bin/nanocompore", line 8, in <module>
2023-06-23T07:58:42.344284-0400 ERROR - MainProcess | An error occured. Killing all processes and closing queues
sys.exit(main())
File "/share/pkg/conda/nanocompore/1.0.4/lib/python3.6/site-packages/nanocompore/__main__.py", line 175, in main
args.func(args)
File "/share/pkg/conda/nanocompore/1.0.4/lib/python3.6/site-packages/nanocompore/__main__.py", line 213, in sampcomp_main
db = s()
File "/share/pkg/conda/nanocompore/1.0.4/lib/python3.6/site-packages/nanocompore/SampComp.py", line 251, in __call__
raise E
File "/share/pkg/conda/nanocompore/1.0.4/lib/python3.6/site-packages/nanocompore/SampComp.py", line 221, in __call__
raise NanocomporeError(tb)
nanocompore.common.NanocomporeError: Traceback (most recent call last):
File "/share/pkg/conda/nanocompore/1.0.4/lib/python3.6/site-packages/nanocompore/SampComp.py", line 305, in __process_references
raise NanocomporeError("Index and data files are not matching:\n{}\n{}".format(header, read))
nanocompore.common.NanocomporeError: Index and data files are not matching:
['']
OrderedDict([('ref_id', 'ENST00000398073'), ('ref_start', 1), ('ref_end', 806), ('read_id', '25c275fd-e3e2-44ae-a985-c7a921008786'), ('num_events', 2528), ('num_signals', 54601), ('dwell_time', 18.126699992455542), ('kmers', 806), ('missing_kmers', 35), ('NNNNN_kmers', 26), ('mismatch_kmers', 0), ('valid_kmers', 745), ('byte_offset', 11815044271), ('byte_len', 52838)])
Because I got my first error in nanocompore eventalign_collapse process saying OSError: [Errno 5] Input/output error, , firstly I checked wt_eventalign.txt and ko_eventalign.txt which were generated from the previous step, nanopolish eventalign. However, I am not sure if there's any issue in the output.
wt_eventalign.txt
contig position reference_kmer read_name strand event_index event_level_mean event_stdv event_length model_kmer model_mean model_stdv standardized_level samples
ENST00000361390 1 TACCC 71576efc-add3-4fc3-823c-05628a65a835 t 1506 78.95 1.122 0.00930 TACCC 78.84 2.81 0.03 77.4855,77.7745,80.52,78.0635,79.7975,77.4855,77.919,78.0635,79.2195,78.9305,78.208,77.63,77.341,80.809,77.63,78.6415,79.2195,79.075,78.6415,79.942,80.3755,79.653,79.7975,79.075,78.3525,81.8205,78.497,80.6645
ENST00000361390 1 TACCC 71576efc-add3-4fc3-823c-05628a65a835 t 1507 78.83 1.662 0.01494 TACCC 78.84 2.81 -0.01 76.763,76.9075,79.364,79.653,76.9075,79.075,77.1965,77.7745,77.919,72.717,78.3525,76.6185,78.786,78.497,78.208,79.364,78.6415,77.4855,77.7745,78.497,78.3525,78.6415,78.0635,80.809,77.919,79.2195,78.497,79.942,77.1965,81.387,78.208,80.3755,78.9305,79.5085,81.2425,81.2425,79.653,78.6415,80.0865,79.5085,78.497,83.5545,78.786,80.231,82.254
ko_eventalign.txt.
contig position reference_kmer read_name strand event_index event_level_mean event_stdv event_length model_kmer model_mean model_stdv standardized_level samples
ENST00000361390 1 TACCC 38cc1b08-a86d-4e1b-92d6-18e7506a3eee t 310 78.13 2.096 0.00266 TACCC 78.84 2.81 -0.23 75.3311,76.4227,78.8787,79.6973,79.6973,78.06,81.3346,75.604
ENST00000361390 1 TACCC 38cc1b08-a86d-4e1b-92d6-18e7506a3eee t 311 74.57 1.585 0.00232 TACCC 78.84 2.81 -1.37 74.376,76.5591,76.832,74.376,74.1032,72.0565,73.6938
ENST00000361390 2 ACCCA 38cc1b08-a86d-4e1b-92d6-18e7506a3eee t 312 64.76 1.395 0.00299 ACCCA 66.30 2.07 -0.67 67.281,65.0979,63.4606,66.5988,64.2792,65.2344,63.1877,64.2792,63.4606
ENST00000361390 3 CCCAT 38cc1b08-a86d-4e1b-92d6-18e7506a3eee t 313 71.24 2.687 0.00232 CCCAT 73.36 2.11 -0.91 71.6472,73.6938,74.9218,71.5107,71.7836,67.5539,67.5539
The following is the output from wt/out_eventalign_collapse.tsv.
#71576efc-add3-4fc3-823c-05628a65a835 ENST00000361390
ref_pos ref_kmer num_events num_signals dwell_time NNNNN_dwell_time mismatch_dwell_time status median mad
1 TACCC 3 85 0.028220000211149454 0.0 0.0 valid 78.497 1.0115051
2 ACCCA 3 66 0.021919999504461884 0.0 0.0 valid 64.625 1.0115013
3 CCCAT 2 40 0.013280000304803252 0.0 0.0 valid 72.78925 1.0114975
4 CCATG 4 37 0.012279999908059835 0.0 0.0 valid 80.9535 1.7340012
5 CATGG 1 44 0.01460999995470047 0.0 0.0 valid 81.31475 1.0114975
6 ATGGC 1 8 0.0026599999982863665 0.0 0.0 valid 95.62025 2.8899956
7 TGGCC 1 24 0.007969999685883522 0.0 0.0 valid 101.256 2.0229988
8 GGCCA 3 61 0.02025000029243529 0.0 0.0 valid 101.184 1.8789978
9 GCCAA 2 32 0.010620000073686242 0.0 0.0 valid 73.006 1.5894966
10 CCAAC 3 43 0.014269999926909804 0.0 0.0 valid 85.5775 1.1559982
11 CAACC 1 22 0.007300000172108412 0.0 0.0 valid 89.69575 1.300499
12 AACCT 2 19 0.006310000084340572 0.0 0.0 valid 78.786 2.312004
13 ACCTC 2 42 0.01394000044092536 0.0 0.0 valid 70.116 0.7947502
14 CCTCC 1 20 0.006639999803155661 0.0 0.0 valid 66.28675 1.0114975
15 CTCCT 1 12 0.003980000037699938 0.0 0.0 valid 69.9715 0.8670006
16 TCCTA 1 42 0.013939999975264072 0.0 0.0 valid 72.139 1.0837479
17 CCTAC 2 44 0.014610000187531114 0.0 0.0 valid 79.43625 1.1559982
18 CTACT 13 514 0.17063999944366515 0.0 0.0 valid 84.4215 1.4449997
19 TACTC 1 7 0.002319999970495701 0.0 0.0 valid 88.323 1.0114975
20 ACTCC 1 12 0.003980000037699938 0.0 0.0 valid 85.144 0.8670006
21 CTCCT 3 48 0.015940000070258975 0.0 0.0 valid 71.85 1.5895004
22 TCCTC 2 14 0.004650000017136335 0.0 0.0 valid 71.19975 0.6502495
23 CCTCA 4 41 0.013609999907203019 0.0 0.0 valid 74.74 0.86699677
24 CTCAT 2 18 0.005979999899864197 0.0 0.0 valid 82.3985 0.93925476
25 TCATT 2 35 0.011619999771937728 0.0 0.0 valid 84.7105 1.1560059
26 CATTG 1 12 0.003980000037699938 0.0 0.0 valid 85.21625 1.0115013
27 ATTGT 6 134 0.044490000465884805 0.016270000487565994 0.0 NNNNN 87.38375 4.1904984
30 GTACC 1 20 0.006639999803155661 0.0 0.0 valid 73.65625 0.6502533
31 TACCC 1 12 0.003980000037699938 0.0 0.0 valid 78.786 0.7947464
The following is the output from ko/out_eventalign_collapse.tsv.
#38cc1b08-a86d-4e1b-92d6-18e7506a3eee ENST00000361390
ref_pos ref_kmer num_events num_signals dwell_time NNNNN_dwell_time mismatch_dwell_time status median mad
1 TACCC 2 15 0.004979999968782067 0.0 0.0 valid 76.4227 2.0466995
2 ACCCA 1 9 0.0029899999499320984 0.0 0.0 valid 64.2792 0.8187027
3 CCCAT 1 7 0.002319999970495701 0.0 0.0 valid 71.6472 2.0466003
4 CCATG 4 38 0.012610000092536211 0.0 0.0 valid 82.7673 1.5008965
5 CATGG 1 25 0.008299999870359898 0.0 0.0 valid 81.0618 0.955101
6 ATGGC 1 18 0.005979999899864197 0.0 0.0 valid 95.3201 1.7737503
7 TGGCC 1 27 0.008960000239312649 0.0 0.0 valid 103.438 2.3199997
8 GGCCA 1 22 0.007300000172108412 0.0 0.0 valid 98.45825 3.8204002
9 GCCAA 1 7 0.002319999970495701 0.0 0.0 valid 73.148 0.8186035
10 CCAAC 1 8 0.0026599999982863665 0.0 0.0 valid 84.7457 0.54574966
11 CAACC 2 44 0.014599999878555536 0.0 0.0 valid 89.58945 1.1597443
12 AACCT 3 39 0.012950000120326877 0.0 0.0 valid 81.6075 2.4560013
13 ACCTC 3 61 0.02025999967008829 0.0 0.0 valid 69.737 1.0914993
14 CCTCC 1 7 0.002319999970495701 0.0 0.0 valid 72.0565 1.5009003
15 CTCCT 1 8 0.0026599999982863665 0.0 0.0 valid 69.5323 0.6140022
16 TCCTA 1 13 0.00431999983265996 0.0 0.0 valid 73.4209 1.5009003
17 CCTAC 2 110 0.03651999915018678 0.0 0.0 valid 79.288 0.88690186
18 CTACT 1 52 0.017260000109672546 0.0 0.0 valid 83.3813 1.2279968
19 TACTC 2 30 0.009959999937564135 0.0 0.0 valid 86.38305 1.2280006
20 ACTCC 1 14 0.004650000017136335 0.0 0.0 valid 75.8087 1.0915489
21 CTCCT 5 55 0.018269999884068966 0.0 0.0 valid 72.0565 1.2279968
22 TCCTC 1 6 0.001990000018849969 0.0 0.0 valid 72.0565 0.6140022
23 CCTCA 3 67 0.022240000311285257 0.0 0.0 valid 74.5125 1.2280045
24 CTCAT 1 18 0.005979999899864197 0.0 0.0 valid 84.0635 0.682251
25 TCATT 1 6 0.001990000018849969 0.0 0.0 valid 88.49795 0.68224716
26 CATTG 1 10 0.0033199999015778303 0.0 0.0 valid 89.521255 0.9550934
Could you please give me advice to solve the error? Thank you so much for your help.
from nanocompore.
lmulroney
commented on August 28, 2024
Hi @kwonej0617,
It looks like all of the I/O errors happened during a write command, and not a read command. First thing I would do is make sure you didn't run out of disc space... Based on the comments you're leaving on other rna modification detection tools, it seems like you might be processing the data a lot, and these files can get really big really fast.
If it's not that, and you wrote the output of nanopolish eventalign to stdout during an HPC job, you might have written the job summary stats to the eventalign output. Write a parser script to make sure that every line is formatted as you expect. I'm assuming that what you posted is not the entire file, but just the first 5-30 lines.
If it's not that, I'd recommend starting over from nanopolish index in an interactive job instead of a bash script. That way you can be sure and respond to errors more readily and explore the problems as they come up.
Logan
from nanocompore.
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