search

tleonardi / nanocompore

RNA modifications detection from Nanopore dRNA-Seq data
https://nanocompore.rna.rocks
GNU General Public License v3.0
78 stars 12 forks source link

No progress in the data processing step #158

Closed ploy-np closed 3 years ago

ploy-np commented 3 years ago

Hi there, I installed NanoCompore successfully, but when I ran nanocompore sampcomp the program made no progress. Please see the figure below. I'm not sure if I missed any step.

figure

Thank you very much.

tleonardi commented 3 years ago

Hello, can you run the last version of Nanocompore with --log_level debug and post here the log file? thanks!

pabloacera commented 3 years ago

Hi, I am having the same issue: nanocompore sampcomp --file_list1 /media/labuser/Data/nanopore/m6A_classifier/benchmark/nanocompore/nanocompore_1/subset_chr1_1_eventalign_collapse.tsv --file_list2 /media/labuser/Data/nanopore/m6A_classifier/benchmark/nanocompore/nanocompore_2/subset_chr1_2_eventalign_collapse.tsv --label1 Subset_1 --label2 Subset_2 --fasta /media/labuser/Data/nanopore/m6A_classifier/benchmark/gencode.v36.transcripts_chr1.fa --outpath /media/labuser/Data/nanopore/m6A_classifier/benchmark/nanocompore/nanocompore_results --overwrite --log_level debug --max_invalid_kmers_freq 0.5 --min_coverage 10

This is my log 

2021-02-16T14:40:47.069152+1100 WARNING - MainProcess | Running SampComp
2021-02-16T14:40:47.069499+1100 INFO - MainProcess | Checking and initialising SampComp
2021-02-16T14:40:47.069642+1100 DEBUG - MainProcess |   package_name: nanocompore
2021-02-16T14:40:47.069767+1100 DEBUG - MainProcess |   package_version: 1.0.3
2021-02-16T14:40:47.069889+1100 DEBUG - MainProcess |   timestamp: 2021-02-16 14:40:47.069881
2021-02-16T14:40:47.070007+1100 DEBUG - MainProcess |   fasta_fn: /media/labuser/Data/nanopore/m6A_classifier/benchmark/gencode.v36.transcripts_chr1.fa
2021-02-16T14:40:47.070127+1100 DEBUG - MainProcess |   outpath: /media/labuser/Data/nanopore/m6A_classifier/benchmark/nanocompore/nanocompore_results
2021-02-16T14:40:47.070240+1100 DEBUG - MainProcess |   outprefix: out
2021-02-16T14:40:47.070481+1100 DEBUG - MainProcess |   overwrite: True
2021-02-16T14:40:47.070760+1100 DEBUG - MainProcess |   comparison_methods: GMM,KS
2021-02-16T14:40:47.070873+1100 DEBUG - MainProcess |   logit: True
2021-02-16T14:40:47.070984+1100 DEBUG - MainProcess |   anova: False
2021-02-16T14:40:47.071192+1100 DEBUG - MainProcess |   allow_warnings: False
2021-02-16T14:40:47.071379+1100 DEBUG - MainProcess |   sequence_context: 0
2021-02-16T14:40:47.071490+1100 DEBUG - MainProcess |   sequence_context_weights: uniform
2021-02-16T14:40:47.071616+1100 DEBUG - MainProcess |   min_coverage: 10
2021-02-16T14:40:47.071736+1100 DEBUG - MainProcess |   min_ref_length: 100
2021-02-16T14:40:47.071930+1100 DEBUG - MainProcess |   downsample_high_coverage: 5000
2021-02-16T14:40:47.072042+1100 DEBUG - MainProcess |   max_invalid_kmers_freq: 1.0
2021-02-16T14:40:47.072222+1100 DEBUG - MainProcess |   select_ref_id: []
2021-02-16T14:40:47.072406+1100 DEBUG - MainProcess |   exclude_ref_id: []
2021-02-16T14:40:47.072577+1100 DEBUG - MainProcess |   nthreads: 3
2021-02-16T14:40:47.072687+1100 DEBUG - MainProcess |   progress: False
2021-02-16T14:40:47.072802+1100 INFO - MainProcess | Only 1 replicate found for condition Subset_1
2021-02-16T14:40:47.072933+1100 INFO - MainProcess | This is not recommended. The statistics will be calculated with the logit method
2021-02-16T14:40:47.073161+1100 INFO - MainProcess | Only 1 replicate found for condition Subset_2
2021-02-16T14:40:47.073273+1100 INFO - MainProcess | This is not recommended. The statistics will be calculated with the logit method
2021-02-16T14:40:47.073790+1100 DEBUG - MainProcess | OrderedDict([('Subset_1', {'Subset_1_1': '/media/labuser/Data/nanopore/m6A_classifier/benchmark/nanocompore/nanocompore_1/subset_chr1_1_eventalign_collapse.tsv'}), ('Subset_2', {'Subset_2_1': '/media/labuser/Data/nanopore/m6A_classifier/benchmark/nanocompore/nanocompore_2/subset_chr1_2_eventalign_collapse.tsv'})])
2021-02-16T14:40:47.154178+1100 INFO - MainProcess | Reading eventalign index files
2021-02-16T14:40:47.250153+1100 ERROR - MainProcess | High fraction of invalid kmers (120.43%) for read 7836
2021-02-16T14:40:47.294915+1100 ERROR - MainProcess | High fraction of invalid kmers (112.95%) for read 11532
2021-02-16T14:40:47.402869+1100 ERROR - MainProcess | High fraction of invalid kmers (171.59%) for read 20388
2021-02-16T14:40:47.627540+1100 ERROR - MainProcess | High fraction of invalid kmers (109.5%) for read 32233
2021-02-16T14:40:47.854086+1100 ERROR - MainProcess | High fraction of invalid kmers (116.53%) for read 50867
2021-02-16T14:40:47.892107+1100 ERROR - MainProcess | High fraction of invalid kmers (111.94%) for read 54185
2021-02-16T14:40:47.930154+1100 ERROR - MainProcess | High fraction of invalid kmers (120.44%) for read 56680
2021-02-16T14:40:48.086751+1100 ERROR - MainProcess | High fraction of invalid kmers (165.85%) for read 68849
2021-02-16T14:40:48.095247+1100 ERROR - MainProcess | High fraction of invalid kmers (100.76%) for read 69495
2021-02-16T14:40:48.193309+1100 ERROR - MainProcess | High fraction of invalid kmers (104.86%) for read 76649
2021-02-16T14:40:48.264032+1100 ERROR - MainProcess | High fraction of invalid kmers (155.32%) for read 81577
2021-02-16T14:40:48.352444+1100 ERROR - MainProcess | High fraction of invalid kmers (108.11%) for read 88317
2021-02-16T14:40:48.384631+1100 ERROR - MainProcess | High fraction of invalid kmers (109.52%) for read 90523
2021-02-16T14:40:48.451753+1100 ERROR - MainProcess | High fraction of invalid kmers (103.88%) for read 95976
2021-02-16T14:40:48.506587+1100 ERROR - MainProcess | High fraction of invalid kmers (109.3%) for read 99953
2021-02-16T14:40:48.978562+1100 ERROR - MainProcess | High fraction of invalid kmers (102.15%) for read 125888
2021-02-16T14:40:49.002037+1100 ERROR - MainProcess | High fraction of invalid kmers (110.08%) for read 127753
2021-02-16T14:40:49.098436+1100 ERROR - MainProcess | High fraction of invalid kmers (112.42%) for read 135549
2021-02-16T14:40:49.152989+1100 ERROR - MainProcess | High fraction of invalid kmers (110.31%) for read 140048
2021-02-16T14:40:49.154153+1100 ERROR - MainProcess | High fraction of invalid kmers (103.09%) for read 140117
2021-02-16T14:40:49.354307+1100 ERROR - MainProcess | High fraction of invalid kmers (169.57%) for read 155857
2021-02-16T14:40:49.368393+1100 ERROR - MainProcess | High fraction of invalid kmers (143.9%) for read 156999
2021-02-16T14:40:49.430966+1100 ERROR - MainProcess | High fraction of invalid kmers (128.19%) for read 162197
2021-02-16T14:40:49.432388+1100 ERROR - MainProcess | High fraction of invalid kmers (102.46%) for read 162293
2021-02-16T14:40:49.432960+1100 ERROR - MainProcess | High fraction of invalid kmers (103.57%) for read 162337
2021-02-16T14:40:49.499741+1100 ERROR - MainProcess | High fraction of invalid kmers (101.91%) for read 167553
2021-02-16T14:40:49.523134+1100 ERROR - MainProcess | High fraction of invalid kmers (107.61%) for read 168945
2021-02-16T14:40:49.691718+1100 ERROR - MainProcess | High fraction of invalid kmers (104.35%) for read 182776
2021-02-16T14:40:49.836266+1100 ERROR - MainProcess | High fraction of invalid kmers (164.34%) for read 195166
2021-02-16T14:40:49.843062+1100 ERROR - MainProcess | High fraction of invalid kmers (104.0%) for read 195738
2021-02-16T14:40:50.180310+1100 ERROR - MainProcess | High fraction of invalid kmers (107.84%) for read 210313
2021-02-16T14:40:50.186028+1100 ERROR - MainProcess | High fraction of invalid kmers (169.39%) for read 210702
2021-02-16T14:40:50.241657+1100 ERROR - MainProcess | High fraction of invalid kmers (118.26%) for read 214637
2021-02-16T14:40:50.600653+1100 ERROR - MainProcess | High fraction of invalid kmers (102.44%) for read 244186
2021-02-16T14:40:50.612679+1100 ERROR - MainProcess | High fraction of invalid kmers (113.58%) for read 245142
2021-02-16T14:40:51.081683+1100 ERROR - MainProcess | High fraction of invalid kmers (117.07%) for read 283354
2021-02-16T14:40:51.109553+1100 ERROR - MainProcess | High fraction of invalid kmers (166.27%) for read 285640
2021-02-16T14:40:51.166432+1100 ERROR - MainProcess | High fraction of invalid kmers (123.77%) for read 290182
2021-02-16T14:40:51.173129+1100 DEBUG - MainProcess |   Condition:Subset_1 Sample:Subset_1_1    valid reads: 285,088    High fraction of invalid kmers (120.43%) for read 7836: 1   High fraction of invalid kmers (112.95%) for read 11532: 1  High fraction of invalid kmers (171.59%) for read 20388: 1  High fraction of invalid kmers (109.5%) for read 32233: 1   High fraction of invalid kmers (116.53%) for read 50867: 1  High fraction of invalid kmers (111.94%) for read 54185: 1  High fraction of invalid kmers (120.44%) for read 56680: 1  High fraction of invalid kmers (165.85%) for read 68849: 1  High fraction of invalid kmers (100.76%) for read 69495: 1  High fraction of invalid kmers (104.86%) for read 76649: 1  High fraction of invalid kmers (155.32%) for read 81577: 1  High fraction of invalid kmers (108.11%) for read 88317: 1  High fraction of invalid kmers (109.52%) for read 90523: 1  High fraction of invalid kmers (103.88%) for read 95976: 1  High fraction of invalid kmers (109.3%) for read 99953: 1   High fraction of invalid kmers (102.15%) for read 125888: 1 High fraction of invalid kmers (110.08%) for read 127753: 1 High fraction of invalid kmers (112.42%) for read 135549: 1 High fraction of invalid kmers (110.31%) for read 140048: 1 High fraction of invalid kmers (103.09%) for read 140117: 1 High fraction of invalid kmers (169.57%) for read 155857: 1 High fraction of invalid kmers (143.9%) for read 156999: 1  High fraction of invalid kmers (128.19%) for read 162197: 1 High fraction of invalid kmers (102.46%) for read 162293: 1 High fraction of invalid kmers (103.57%) for read 162337: 1 High fraction of invalid kmers (101.91%) for read 167553: 1 High fraction of invalid kmers (107.61%) for read 168945: 1 High fraction of invalid kmers (104.35%) for read 182776: 1 High fraction of invalid kmers (164.34%) for read 195166: 1 High fraction of invalid kmers (104.0%) for read 195738: 1  High fraction of invalid kmers (107.84%) for read 210313: 1 High fraction of invalid kmers (169.39%) for read 210702: 1 High fraction of invalid kmers (118.26%) for read 214637: 1 High fraction of invalid kmers (102.44%) for read 244186: 1 High fraction of invalid kmers (113.58%) for read 245142: 1 High fraction of invalid kmers (117.07%) for read 283354: 1 High fraction of invalid kmers (166.27%) for read 285640: 1 High fraction of invalid kmers (123.77%) for read 290182: 1
2021-02-16T14:40:51.651190+1100 ERROR - MainProcess | High fraction of invalid kmers (203.23%) for read 24261
2021-02-16T14:40:51.655546+1100 ERROR - MainProcess | High fraction of invalid kmers (140.91%) for read 24584
2021-02-16T14:40:51.834811+1100 ERROR - MainProcess | High fraction of invalid kmers (100.67%) for read 39154
2021-02-16T14:40:51.835213+1100 ERROR - MainProcess | High fraction of invalid kmers (176.32%) for read 39161
2021-02-16T14:40:52.020832+1100 ERROR - MainProcess | High fraction of invalid kmers (108.62%) for read 54334
2021-02-16T14:40:52.144866+1100 ERROR - MainProcess | High fraction of invalid kmers (106.56%) for read 63957
2021-02-16T14:40:52.317103+1100 ERROR - MainProcess | High fraction of invalid kmers (104.51%) for read 78121
2021-02-16T14:40:52.318162+1100 ERROR - MainProcess | High fraction of invalid kmers (107.59%) for read 78187
2021-02-16T14:40:52.372141+1100 ERROR - MainProcess | High fraction of invalid kmers (120.83%) for read 82390
2021-02-16T14:40:52.427328+1100 ERROR - MainProcess | High fraction of invalid kmers (106.61%) for read 86947
2021-02-16T14:40:52.539875+1100 ERROR - MainProcess | High fraction of invalid kmers (106.02%) for read 96087
2021-02-16T14:40:52.645384+1100 ERROR - MainProcess | High fraction of invalid kmers (129.55%) for read 104695
2021-02-16T14:40:52.705069+1100 ERROR - MainProcess | High fraction of invalid kmers (100.76%) for read 109457
2021-02-16T14:40:52.780607+1100 ERROR - MainProcess | High fraction of invalid kmers (102.01%) for read 115625
2021-02-16T14:40:53.098357+1100 ERROR - MainProcess | High fraction of invalid kmers (126.18%) for read 122318
2021-02-16T14:40:53.171042+1100 ERROR - MainProcess | High fraction of invalid kmers (125.0%) for read 128412
2021-02-16T14:40:53.277857+1100 ERROR - MainProcess | High fraction of invalid kmers (101.89%) for read 137444
2021-02-16T14:40:53.310339+1100 ERROR - MainProcess | High fraction of invalid kmers (101.85%) for read 140071
2021-02-16T14:40:53.311375+1100 ERROR - MainProcess | High fraction of invalid kmers (102.2%) for read 140148
2021-02-16T14:40:53.316262+1100 ERROR - MainProcess | High fraction of invalid kmers (116.35%) for read 140541
2021-02-16T14:40:53.341819+1100 ERROR - MainProcess | High fraction of invalid kmers (106.98%) for read 142801
2021-02-16T14:40:53.578526+1100 ERROR - MainProcess | High fraction of invalid kmers (102.48%) for read 162302
2021-02-16T14:40:53.582287+1100 ERROR - MainProcess | High fraction of invalid kmers (120.0%) for read 162575
2021-02-16T14:40:53.703572+1100 ERROR - MainProcess | High fraction of invalid kmers (103.28%) for read 172307
2021-02-16T14:40:53.777280+1100 ERROR - MainProcess | High fraction of invalid kmers (122.29%) for read 178689
2021-02-16T14:40:53.924568+1100 ERROR - MainProcess | High fraction of invalid kmers (109.83%) for read 191152
2021-02-16T14:40:53.933878+1100 ERROR - MainProcess | High fraction of invalid kmers (120.11%) for read 191910
2021-02-16T14:40:53.979276+1100 ERROR - MainProcess | High fraction of invalid kmers (111.05%) for read 195847
2021-02-16T14:40:54.011195+1100 ERROR - MainProcess | High fraction of invalid kmers (102.2%) for read 198421
2021-02-16T14:40:54.034614+1100 ERROR - MainProcess | High fraction of invalid kmers (139.86%) for read 200364
2021-02-16T14:40:54.048146+1100 ERROR - MainProcess | High fraction of invalid kmers (100.66%) for read 201556
2021-02-16T14:40:54.327534+1100 ERROR - MainProcess | High fraction of invalid kmers (183.86%) for read 224703
2021-02-16T14:40:54.405245+1100 ERROR - MainProcess | High fraction of invalid kmers (114.29%) for read 230898
2021-02-16T14:40:54.669480+1100 ERROR - MainProcess | High fraction of invalid kmers (107.26%) for read 252850
2021-02-16T14:40:54.754320+1100 ERROR - MainProcess | High fraction of invalid kmers (117.65%) for read 258864
2021-02-16T14:40:55.378249+1100 ERROR - MainProcess | High fraction of invalid kmers (208.33%) for read 283340
2021-02-16T14:40:55.448488+1100 ERROR - MainProcess | High fraction of invalid kmers (117.2%) for read 288710
2021-02-16T14:40:55.478523+1100 DEBUG - MainProcess |   Condition:Subset_2 Sample:Subset_2_1    valid reads: 285,296    High fraction of invalid kmers (203.23%) for read 24261: 1  High fraction of invalid kmers (140.91%) for read 24584: 1  High fraction of invalid kmers (100.67%) for read 39154: 1  High fraction of invalid kmers (176.32%) for read 39161: 1  High fraction of invalid kmers (108.62%) for read 54334: 1  High fraction of invalid kmers (106.56%) for read 63957: 1  High fraction of invalid kmers (104.51%) for read 78121: 1  High fraction of invalid kmers (107.59%) for read 78187: 1  High fraction of invalid kmers (120.83%) for read 82390: 1  High fraction of invalid kmers (106.61%) for read 86947: 1  High fraction of invalid kmers (106.02%) for read 96087: 1  High fraction of invalid kmers (129.55%) for read 104695: 1 High fraction of invalid kmers (100.76%) for read 109457: 1 High fraction of invalid kmers (102.01%) for read 115625: 1 High fraction of invalid kmers (126.18%) for read 122318: 1 High fraction of invalid kmers (125.0%) for read 128412: 1  High fraction of invalid kmers (101.89%) for read 137444: 1 High fraction of invalid kmers (101.85%) for read 140071: 1 High fraction of invalid kmers (102.2%) for read 140148: 1  High fraction of invalid kmers (116.35%) for read 140541: 1 High fraction of invalid kmers (106.98%) for read 142801: 1 High fraction of invalid kmers (102.48%) for read 162302: 1 High fraction of invalid kmers (120.0%) for read 162575: 1  High fraction of invalid kmers (103.28%) for read 172307: 1 High fraction of invalid kmers (122.29%) for read 178689: 1 High fraction of invalid kmers (109.83%) for read 191152: 1 High fraction of invalid kmers (120.11%) for read 191910: 1 High fraction of invalid kmers (111.05%) for read 195847: 1 High fraction of invalid kmers (102.2%) for read 198421: 1  High fraction of invalid kmers (139.86%) for read 200364: 1 High fraction of invalid kmers (100.66%) for read 201556: 1 High fraction of invalid kmers (183.86%) for read 224703: 1 High fraction of invalid kmers (114.29%) for read 230898: 1 High fraction of invalid kmers (107.26%) for read 252850: 1 High fraction of invalid kmers (117.65%) for read 258864: 1 High fraction of invalid kmers (208.33%) for read 283340: 1 High fraction of invalid kmers (117.2%) for read 288710: 1
2021-02-16T14:40:55.485791+1100 INFO - MainProcess |    References found in index: 3643
2021-02-16T14:40:55.486079+1100 INFO - MainProcess | Filtering out references with low coverage
2021-02-16T14:40:55.661787+1100 DEBUG - MainProcess |   Subset_2 Subset_2_1 Reads: 256,666  Subset_1 Subset_1_1 Reads: 256,494  invalid_ref_id: 2,800   valid_ref_id: 843
2021-02-16T14:40:55.662073+1100 INFO - MainProcess |    References remaining after reference coverage filtering: 843
2021-02-16T14:40:55.713078+1100 INFO - MainProcess | Starting data processing
2021-02-16T14:40:55.743835+1100 DEBUG - Process-1 | Adding ENST00000623083.4|ENSG00000279457.4|OTTHUMG00000191963|OTTHUMT00000491421.1|WASH9P-201|WASH9P|1397|unprocessed_pseudogene| to in_q
2021-02-16T14:40:55.745317+1100 DEBUG - Process-1 | Adding ENST00000416931.1|ENSG00000225972.1|OTTHUMG00000002338|OTTHUMT00000006720.1|MTND1P23-201|MTND1P23|372|unprocessed_pseudogene| to in_q
2021-02-16T14:40:55.746053+1100 DEBUG - Process-1 | Adding ENST00000457540.1|ENSG00000225630.1|OTTHUMG00000002336|OTTHUMT00000006718.1|MTND2P28-201|MTND2P28|1044|unprocessed_pseudogene| to in_q
2021-02-16T14:40:55.746340+1100 DEBUG - Process-1 | Adding ENST00000414273.1|ENSG00000237973.1|OTTHUMG00000002333|OTTHUMT00000006715.1|MTCO1P12-201|MTCO1P12|1543|unprocessed_pseudogene| to in_q
2021-02-16T14:40:55.746574+1100 DEBUG - Process-1 | Adding ENST00000427426.1|ENSG00000229344.1|OTTHUMG00000002334|OTTHUMT00000006716.1|MTCO2P12-201|MTCO2P12|682|unprocessed_pseudogene| to in_q
2021-02-16T14:40:55.746806+1100 DEBUG - Process-1 | Adding ENST00000514057.1|ENSG00000248527.1|OTTHUMG00000002335|OTTHUMT00000006717.1|MTATP6P1-201|MTATP6P1|681|unprocessed_pseudogene| to in_q
2021-02-16T14:40:55.747035+1100 DEBUG - Process-1 | Adding ENST00000416718.2|ENSG00000198744.5|OTTHUMG00000002337|OTTHUMT00000006719.1|MTCO3P12-201|MTCO3P12|547|unprocessed_pseudogene| to in_q
2021-02-16T14:40:55.758043+1100 DEBUG - Process-1 | Adding ENST00000415481.1|ENSG00000234711.1|OTTHUMG00000002470|OTTHUMT00000007024.1|TUBB8P11-201|TUBB8P11|1058|unprocessed_pseudogene| to in_q
2021-02-16T14:40:55.758254+1100 DEBUG - Process-1 | Adding ENST00000649529.1|ENSG00000187608.10|OTTHUMG00000040777|OTTHUMT00000501480.1|ISG15-203|ISG15|637|protein_coding| to in_q
2021-02-16T14:40:55.758446+1100 DEBUG - Process-1 | Adding ENST00000379198.5|ENSG00000176022.7|OTTHUMG00000001813|OTTHUMT00000005071.1|B3GALT6-201|B3GALT6|2805|protein_coding| to in_q
2021-02-16T14:40:55.758636+1100 DEBUG - Process-1 | Adding ENST00000338338.9|ENSG00000175756.13|OTTHUMG00000001413|OTTHUMT00000004082.1|AURKAIP1-202|AURKAIP1|1047|protein_coding| to in_q
2021-02-16T14:40:55.758802+1100 DEBUG - Process-1 | Adding ENST00000344843.12|ENSG00000242485.6|OTTHUMG00000002916|OTTHUMT00000008139.1|MRPL20-201|MRPL20|700|protein_coding| to in_q
2021-02-16T14:40:55.758973+1100 DEBUG - Process-1 | Adding ENST00000291386.4|ENSG00000160075.12|OTTHUMG00000000576|OTTHUMT00000001366.1|SSU72-201|SSU72|1284|protein_coding| to in_q
2021-02-16T14:40:55.759140+1100 DEBUG - Process-1 | Adding ENST00000378609.9|ENSG00000078369.18|OTTHUMG00000000940|OTTHUMT00000002762.1|GNB1-201|GNB1|3163|protein_coding| to in_q
2021-02-16T14:40:55.759321+1100 DEBUG - Process-1 | Adding ENST00000378546.9|ENSG00000162585.17|OTTHUMG00000001404|OTTHUMT00000316541.1|FAAP20-202|FAAP20|727|protein_coding| to in_q
2021-02-16T14:40:55.759494+1100 DEBUG - Process-1 | Adding ENST00000378536.5|ENSG00000157933.10|OTTHUMG00000001407|OTTHUMT00000004070.1|SKI-201|SKI|6083|protein_coding| to in_q
2021-02-16T14:40:55.759677+1100 DEBUG - Process-1 | Adding ENST00000605895.6|ENSG00000157916.20|OTTHUMG00000001403|OTTHUMT00000004061.1|RER1-209|RER1|3028|protein_coding| to in_q
2021-02-16T14:40:55.759845+1100 DEBUG - Process-1 | Adding ENST00000449232.1|ENSG00000229280.1|OTTHUMG00000000732|OTTHUMT00000001813.1|EEF1DP6-201|EEF1DP6|372|processed_pseudogene| to in_q
2021-02-16T14:40:55.760009+1100 DEBUG - Process-1 | Adding ENST00000234875.9|ENSG00000116251.11|OTTHUMG00000193375|OTTHUMT00000002830.1|RPL22-201|RPL22|2061|protein_coding| to in_q
2021-02-16T14:40:55.760214+1100 DEBUG - Process-1 | Adding ENST00000343813.10|ENSG00000116237.16|OTTHUMG00000001254|OTTHUMT00000003681.1|ICMT-201|ICMT|4795|protein_coding| to in_q
2021-02-16T14:40:55.760407+1100 DEBUG - Process-1 | Adding ENST00000377705.6|ENSG00000162408.11|OTTHUMG00000000904|OTTHUMT00000002625.1|NOL9-201|NOL9|6627|protein_coding| to in_q
2021-02-16T14:40:55.760596+1100 DEBUG - Process-1 | Adding ENST00000377648.5|ENSG00000116273.6|OTTHUMG00000001439|OTTHUMT00000004201.1|PHF13-201|PHF13|3632|protein_coding| to in_q
2021-02-16T14:40:55.760788+1100 DEBUG - Process-1 | Adding ENST00000473578.5|ENSG00000171735.19|OTTHUMG00000001212|OTTHUMT00000003597.1|CAMTA1-208|CAMTA1|567|protein_coding| to in_q
2021-02-16T14:40:55.760979+1100 DEBUG - Process-1 | Adding ENST00000054666.11|ENSG00000049245.13|OTTHUMG00000001225|OTTHUMT00000003625.1|VAMP3-201|VAMP3|2178|protein_coding| to in_q
2021-02-16T14:40:55.761175+1100 DEBUG - Process-1 | Adding ENST00000493678.5|ENSG00000116288.13|OTTHUMG00000001210|OTTHUMT00000003577.1|PARK7-209|PARK7|1088|protein_coding| to in_q
2021-02-16T14:40:55.761379+1100 DEBUG - Process-1 | Adding ENST00000338639.10|ENSG00000116288.13|OTTHUMG00000001210|OTTHUMT00000003578.1|PARK7-201|PARK7|1127|protein_coding| to in_q
2021-02-16T14:40:55.761616+1100 DEBUG - Process-1 | Adding ENST00000377482.10|ENSG00000116285.13|OTTHUMG00000001221|OTTHUMT00000003617.1|ERRFI1-201|ERRFI1|3097|protein_coding| to in_q
2021-02-16T14:40:55.761823+1100 DEBUG - Process-1 | Adding ENST00000445254.1|ENSG00000226545.1|OTTHUMG00000001776|OTTHUMT00000004951.1|AL357552.1-201|AL357552.1|415|unprocessed_pseudogene| to in_q
2021-02-16T14:40:55.762044+1100 DEBUG - Process-1 | Adding ENST00000234590.10|ENSG00000074800.16|OTTHUMG00000001773|OTTHUMT00000497295.1|ENO1-201|ENO1|1781|protein_coding| to in_q
2021-02-16T14:40:55.762266+1100 DEBUG - Process-1 | Adding ENST00000645609.1|ENSG00000074800.16|OTTHUMG00000001773|OTTHUMT00000494648.1|ENO1-210|ENO1|1819|retained_intron| to in_q
2021-02-16T14:40:55.762455+1100 DEBUG - Process-1 | Adding ENST00000424862.2|ENSG00000232208.2|OTTHUMG00000001759|OTTHUMT00000004907.1|AL139415.1-201|AL139415.1|352|processed_pseudogene| to in_q
2021-02-16T14:40:55.762649+1100 DEBUG - Process-1 | Adding ENST00000583026.2|ENSG00000265141.2|-|-|RN7SL451P-201|RN7SL451P|299|misc_RNA| to in_q
2021-02-16T14:40:55.762874+1100 DEBUG - Process-1 | Adding ENST00000302692.7|ENSG00000171612.7|OTTHUMG00000001322|OTTHUMT00000003851.1|SLC25A33-201|SLC25A33|3865|protein_coding| to in_q
2021-02-16T14:40:55.763065+1100 DEBUG - Process-1 | Adding ENST00000435277.1|ENSG00000231181.1|OTTHUMG00000001323|OTTHUMT00000003852.1|AL954705.1-201|AL954705.1|559|processed_pseudogene| to in_q
2021-02-16T14:40:55.763278+1100 DEBUG - Process-1 | Adding ENST00000603781.1|ENSG00000271264.1|OTTHUMG00000184268|OTTHUMT00000468523.1|MZT1P1-201|MZT1P1|246|processed_pseudogene| to in_q
2021-02-16T14:40:55.763478+1100 DEBUG - Process-1 | Adding ENST00000377223.6|ENSG00000162441.12|OTTHUMG00000001804|OTTHUMT00000005037.1|LZIC-202|LZIC|4989|protein_coding| to in_q
2021-02-16T14:40:55.763698+1100 DEBUG - Process-1 | Adding ENST00000377205.6|ENSG00000173614.14|OTTHUMG00000001799|OTTHUMT00000005029.1|NMNAT1-201|NMNAT1|3734|protein_coding| to in_q
2021-02-16T14:40:55.763907+1100 DEBUG - Process-1 | Adding ENST00000365545.1|ENSG00000202415.1|-|-|RN7SKP269-201|RN7SKP269|319|misc_RNA| to in_q
2021-02-16T14:40:55.764108+1100 DEBUG - Process-1 | Adding ENST00000294435.8|ENSG00000162444.12|OTTHUMG00000001798|OTTHUMT00000005027.1|RBP7-201|RBP7|625|protein_coding| to in_q
2021-02-16T14:40:55.764307+1100 DEBUG - Process-1 | Adding ENST00000377093.8|ENSG00000054523.18|OTTHUMG00000001817|OTTHUMT00000005104.1|KIF1B-205|KIF1B|7565|protein_coding| to in_q
2021-02-16T14:40:55.764512+1100 DEBUG - Process-1 | Adding ENST00000362692.1|ENSG00000199562.1|-|-|RNU6-37P-201|RNU6-37P|107|snRNA| to in_q
2021-02-16T14:40:55.764716+1100 DEBUG - Process-1 | Adding ENST00000270776.13|ENSG00000142657.21|OTTHUMG00000001905|OTTHUMT00000005398.1|PGD-201|PGD|2268|protein_coding| to in_q
2021-02-16T14:40:55.764917+1100 DEBUG - Process-1 | Adding ENST00000309048.8|ENSG00000175279.22|OTTHUMG00000059085|OTTHUMT00000130797.1|CENPS-201|CENPS|905|protein_coding| to in_q
2021-02-16T14:40:55.765161+1100 DEBUG - Process-1 | Adding ENST00000377038.8|ENSG00000160049.12|OTTHUMG00000001909|OTTHUMT00000005418.1|DFFA-202|DFFA|6035|protein_coding| to in_q
2021-02-16T14:40:55.765365+1100 DEBUG - Process-1 | Adding ENST00000377036.2|ENSG00000160049.12|OTTHUMG00000001909|OTTHUMT00000005419.1|DFFA-201|DFFA|1403|protein_coding| to in_q
2021-02-16T14:40:55.765534+1100 DEBUG - Process-1 | Adding ENST00000356607.9|ENSG00000142655.13|OTTHUMG00000001908|OTTHUMT00000005414.1|PEX14-201|PEX14|1922|protein_coding| to in_q
2021-02-16T14:40:55.765728+1100 DEBUG - Process-1 | Adding ENST00000240185.8|ENSG00000120948.18|OTTHUMG00000002120|OTTHUMT00000006063.1|TARDBP-201|TARDBP|4185|protein_coding| to in_q
2021-02-16T14:40:55.765931+1100 DEBUG - Process-1 | Adding ENST00000376957.7|ENSG00000116649.10|OTTHUMG00000002119|OTTHUMT00000006056.1|SRM-201|SRM|1260|protein_coding| to in_q
2021-02-16T14:40:55.766124+1100 DEBUG - Process-1 | Adding ENST00000376810.6|ENSG00000120942.14|OTTHUMG00000002075|OTTHUMT00000005773.1|UBIAD1-202|UBIAD1|3654|protein_coding| to in_q
2021-02-16T14:40:55.774728+1100 DEBUG - Process-2 | Worker thread started
2021-02-16T14:40:55.810341+1100 DEBUG - Process-1 | Adding ENST00000433562.1|ENSG00000238199.1|OTTHUMG00000002077|OTTHUMT00000005778.1|UBE2V2P3-201|UBE2V2P3|437|processed_pseudogene| to in_q
2021-02-16T14:40:55.810567+1100 DEBUG - Process-1 | Adding ENST00000314340.10|ENSG00000177674.16|OTTHUMG00000002230|OTTHUMT00000006335.1|AGTRAP-201|AGTRAP|1130|protein_coding| to in_q
2021-02-16T14:40:55.810846+1100 DEBUG - Process-1 | Adding ENST00000376572.8|ENSG00000116685.16|OTTHUMG00000002391|OTTHUMT00000006858.1|KIAA2013-201|KIAA2013|2819|protein_coding| to in_q
2021-02-16T14:40:55.811021+1100 DEBUG - Process-1 | Adding ENST00000196061.5|ENSG00000083444.17|OTTHUMG00000002393|OTTHUMT00000006865.1|PLOD1-201|PLOD1|2976|protein_coding| to in_q
2021-02-16T14:40:55.811192+1100 DEBUG - Process-1 | Adding ENST00000317869.7|ENSG00000179172.10|OTTHUMG00000001931|OTTHUMT00000005462.1|HNRNPCL1-201|HNRNPCL1|1134|protein_coding| to in_q
2021-02-16T14:40:55.811123+1100 DEBUG - Process-2 | Worker thread processing new item from in_q: ENST00000623083.4|ENSG00000279457.4|OTTHUMG00000191963|OTTHUMT00000491421.1|WASH9P-201|WASH9P|1397|unprocessed_pseudogene|
2021-02-16T14:40:55.811784+1100 DEBUG - Process-1 | Adding ENST00000323770.8|ENSG00000179412.11|OTTHUMG00000189238|OTTHUMT00000479154.1|HNRNPCL4-201|HNRNPCL4|1718|protein_coding| to in_q
2021-02-16T14:40:55.811992+1100 DEBUG - Process-1 | Adding ENST00000416175.1|ENSG00000235829.1|OTTHUMG00000037853|OTTHUMT00000092384.1|TBCAP2-201|TBCAP2|326|processed_pseudogene| to in_q
2021-02-16T14:40:55.812449+1100 DEBUG - Process-1 | Adding ENST00000400795.3|ENSG00000215720.4|OTTHUMG00000002045|OTTHUMT00000005697.1|MFFP1-201|MFFP1|710|processed_pseudogene| to in_q
2021-02-16T14:40:55.812615+1100 DEBUG - Process-1 | Adding ENST00000375980.9|ENSG00000142634.13|OTTHUMG00000002254|OTTHUMT00000006433.1|EFHD2-201|EFHD2|2422|protein_coding| to in_q
2021-02-16T14:40:55.812787+1100 DEBUG - Process-1 | Adding ENST00000454346.1|ENSG00000235084.3|OTTHUMG00000002360|OTTHUMT00000006774.1|CHCHD2P6-201|CHCHD2P6|447|processed_pseudogene| to in_q
2021-02-16T14:40:55.813231+1100 DEBUG - Process-1 | Adding ENST00000431782.1|ENSG00000224321.1|OTTHUMG00000003108|OTTHUMT00000008572.1|RPL12P14-201|RPL12P14|490|processed_pseudogene| to in_q
2021-02-16T14:40:55.813397+1100 DEBUG - Process-1 | Adding ENST00000321418.6|ENSG00000178715.8|OTTHUMG00000003169|OTTHUMT00000008737.1|AL450998.1-201|AL450998.1|438|processed_pseudogene| to in_q
2021-02-16T14:40:55.813564+1100 DEBUG - Process-1 | Adding ENST00000375759.8|ENSG00000065526.12|OTTHUMG00000009376|OTTHUMT00000025993.1|SPEN-201|SPEN|12385|protein_coding| to in_q
2021-02-16T14:40:55.813843+1100 DEBUG - Process-1 | Adding ENST00000358432.8|ENSG00000142627.13|OTTHUMG00000009527|OTTHUMT00000026322.1|EPHA2-201|EPHA2|3946|protein_coding| to in_q
2021-02-16T14:40:55.814004+1100 DEBUG - Process-1 | Adding ENST00000421314.1|ENSG00000233929.1|OTTHUMG00000037883|OTTHUMT00000092471.1|MT1XP1-201|MT1XP1|186|processed_pseudogene| to in_q
2021-02-16T14:40:55.814174+1100 DEBUG - Process-1 | Adding ENST00000419267.1|ENSG00000236698.1|OTTHUMG00000002579|OTTHUMT00000007333.1|EIF1AXP1-201|EIF1AXP1|435|processed_pseudogene| to in_q
2021-02-16T14:40:55.814357+1100 DEBUG - Process-1 | Adding ENST00000375499.8|ENSG00000117118.10|OTTHUMG00000002289|OTTHUMT00000006603.1|SDHB-201|SDHB|1015|protein_coding| to in_q
2021-02-16T14:40:55.814526+1100 DEBUG - Process-1 | Adding ENST00000375436.9|ENSG00000179051.14|OTTHUMG00000002513|OTTHUMT00000007144.1|RCC2-202|RCC2|4040|protein_coding| to in_q
2021-02-16T14:40:55.814692+1100 DEBUG - Process-1 | Adding ENST00000400664.2|ENSG00000179023.8|OTTHUMG00000002431|OTTHUMT00000006923.1|KLHDC7A-201|KLHDC7A|5145|protein_coding| to in_q
2021-02-16T14:40:55.815577+1100 DEBUG - Process-1 | Adding ENST00000596113.1|ENSG00000235282.3|OTTHUMG00000002435|OTTHUMT00000006930.1|DYNLL1P3-201|DYNLL1P3|266|processed_pseudogene| to in_q
2021-02-16T14:40:55.815774+1100 DEBUG - Process-1 | Adding ENST00000455833.7|ENSG00000169991.11|OTTHUMG00000002499|OTTHUMT00000007099.1|IFFO2-203|IFFO2|6179|protein_coding| to in_q
2021-02-16T14:40:55.815959+1100 DEBUG - Process-1 | Adding ENST00000375254.8|ENSG00000127481.15|OTTHUMG00000002498|OTTHUMT00000007085.1|UBR4-204|UBR4|15892|protein_coding| to in_q
2021-02-16T14:40:55.816301+1100 DEBUG - Process-1 | Adding ENST00000330263.5|ENSG00000053372.5|OTTHUMG00000002496|OTTHUMT00000007075.1|MRTO4-201|MRTO4|2049|protein_coding| to in_q
2021-02-16T14:40:55.816484+1100 DEBUG - Process-1 | Adding ENST00000235835.7|ENSG00000053371.12|OTTHUMG00000002522|OTTHUMT00000007165.1|AKR7A2-201|AKR7A2|1362|protein_coding| to in_q
2021-02-16T14:40:55.816669+1100 DEBUG - Process-1 | Adding ENST00000264202.8|ENSG00000077549.19|OTTHUMG00000002556|OTTHUMT00000476514.1|CAPZB-201|CAPZB|1675|protein_coding| to in_q
2021-02-16T14:40:55.816894+1100 DEBUG - Process-1 | Adding ENST00000481521.3|ENSG00000240490.3|-|-|RN7SL277P-201|RN7SL277P|288|misc_RNA| to in_q
2021-02-16T14:40:55.817092+1100 DEBUG - Process-1 | Adding ENST00000617872.4|ENSG00000173436.15|OTTHUMG00000002712|-|MICOS10-210|MICOS10|3678|protein_coding| to in_q
2021-02-16T14:40:55.817300+1100 DEBUG - Process-1 | Adding ENST00000322753.7|ENSG00000173436.15|OTTHUMG00000002712|OTTHUMT00000007697.1|MICOS10-201|MICOS10|3723|protein_coding| to in_q
2021-02-16T14:40:55.817488+1100 DEBUG - Process-1 | Adding ENST00000467029.5|ENSG00000173436.15|OTTHUMG00000002712|OTTHUMT00000007698.1|MICOS10-203|MICOS10|583|processed_transcript| to in_q
2021-02-16T14:40:55.817682+1100 DEBUG - Process-1 | Adding ENST00000457263.1|ENSG00000226396.1|OTTHUMG00000002695|OTTHUMT00000007654.1|AL031727.1-201|AL031727.1|455|processed_pseudogene| to in_q
2021-02-16T14:40:55.817866+1100 DEBUG - Process-1 | Adding ENST00000375078.4|ENSG00000162545.6|OTTHUMG00000002837|OTTHUMT00000007949.1|CAMK2N1-201|CAMK2N1|2326|protein_coding| to in_q
2021-02-16T14:40:55.818062+1100 DEBUG - Process-1 | Adding ENST00000443195.1|ENSG00000215520.3|OTTHUMG00000002839|OTTHUMT00000007952.1|RPS4XP4-201|RPS4XP4|763|processed_pseudogene| to in_q
2021-02-16T14:40:55.818250+1100 DEBUG - Process-1 | Adding ENST00000321556.5|ENSG00000158828.8|OTTHUMG00000002841|OTTHUMT00000007954.1|PINK1-201|PINK1|2657|protein_coding| to in_q
2021-02-16T14:40:55.818436+1100 DEBUG - Process-1 | Adding ENST00000415136.6|ENSG00000244038.11|OTTHUMG00000002844|-|DDOST-201|DDOST|2126|protein_coding| to in_q
2021-02-16T14:40:55.818641+1100 DEBUG - Process-1 | Adding ENST00000374695.8|ENSG00000142798.20|OTTHUMG00000002674|OTTHUMT00000007598.1|HSPG2-203|HSPG2|14341|protein_coding| to in_q
2021-02-16T14:40:55.818826+1100 DEBUG - Process-1 | Adding ENST00000656825.1|ENSG00000070831.17|OTTHUMG00000002753|OTTHUMT00000504537.1|CDC42-209|CDC42|10503|protein_coding| to in_q
2021-02-16T14:40:55.819011+1100 DEBUG - Process-1 | Adding ENST00000442089.1|ENSG00000215381.3|OTTHUMG00000003221|OTTHUMT00000008883.1|AL109936.1-201|AL109936.1|460|processed_pseudogene| to in_q
2021-02-16T14:40:55.819199+1100 DEBUG - Process-1 | Adding ENST00000478691.5|ENSG00000125944.21|OTTHUMG00000003224|OTTHUMT00000008890.1|HNRNPR-210|HNRNPR|7646|protein_coding| to in_q
2021-02-16T14:40:55.819384+1100 DEBUG - Process-1 | Adding ENST00000445848.2|ENSG00000232482.2|OTTHUMG00000003230|OTTHUMT00000008906.1|AL357134.1-201|AL357134.1|426|processed_pseudogene| to in_q
2021-02-16T14:40:55.819573+1100 DEBUG - Process-1 | Adding ENST00000374561.6|ENSG00000117318.9|OTTHUMG00000003229|OTTHUMT00000008904.1|ID3-201|ID3|950|protein_coding| to in_q
2021-02-16T14:40:55.819804+1100 DEBUG - Process-1 | Adding ENST00000374550.8|ENSG00000142676.14|OTTHUMG00000002926|OTTHUMT00000494315.1|RPL11-201|RPL11|660|protein_coding| to in_q
2021-02-16T14:40:55.819990+1100 DEBUG - Process-1 | Adding ENST00000643754.2|ENSG00000142676.14|OTTHUMG00000002926|OTTHUMT00000008168.1|RPL11-206|RPL11|1017|protein_coding| to in_q
2021-02-16T14:40:55.820173+1100 DEBUG - Process-1 | Adding ENST00000246151.9|ENSG00000057757.10|OTTHUMG00000002960|OTTHUMT00000008243.1|PITHD1-201|PITHD1|1590|protein_coding| to in_q
2021-02-16T14:40:55.820458+1100 DEBUG - Process-1 | Adding ENST00000374514.8|ENSG00000011009.11|OTTHUMG00000002961|OTTHUMT00000008245.1|LYPLA2-205|LYPLA2|1635|protein_coding| to in_q
2021-02-16T14:40:55.820644+1100 DEBUG - Process-1 | Adding ENST00000374490.8|ENSG00000117305.15|OTTHUMG00000002963|OTTHUMT00000008253.1|HMGCL-203|HMGCL|1570|protein_coding| to in_q
2021-02-16T14:40:55.820829+1100 DEBUG - Process-1 | Adding ENST00000374479.4|ENSG00000179163.12|OTTHUMG00000002965|OTTHUMT00000008259.1|FUCA1-201|FUCA1|2043|protein_coding| to in_q
2021-02-16T14:40:55.821340+1100 DEBUG - Process-1 | Adding ENST00000334351.8|ENSG00000189266.13|OTTHUMG00000013891|OTTHUMT00000038946.1|PNRC2-201|PNRC2|2400|protein_coding| to in_q
2021-02-16T14:40:55.821525+1100 DEBUG - Process-1 | Adding ENST00000344989.10|ENSG00000188529.15|OTTHUMG00000013893|OTTHUMT00000038951.1|SRSF10-204|SRSF10|3487|protein_coding| to in_q
2021-02-16T14:40:55.821711+1100 DEBUG - Process-1 | Adding ENST00000442164.2|ENSG00000215905.4|OTTHUMG00000013926|OTTHUMT00000039095.1|AL590609.1-201|AL590609.1|328|processed_pseudogene| to in_q
2021-02-16T14:40:55.821958+1100 DEBUG - Process-1 | Adding ENST00000468822.5|ENSG00000133226.17|OTTHUMG00000003320|OTTHUMT00000009300.1|SRRM1-207|SRRM1|768|processed_transcript| to in_q
2021-02-16T14:40:55.822143+1100 DEBUG - Process-1 | Adding ENST00000488683.1|ENSG00000169504.15|OTTHUMG00000003327|OTTHUMT00000009333.1|CLIC4-202|CLIC4|2723|nonsense_mediated_decay| to in_q
2021-02-16T14:40:55.822327+1100 DEBUG - Process-1 | Adding ENST00000374379.9|ENSG00000169504.15|OTTHUMG00000003327|OTTHUMT00000009332.1|CLIC4-201|CLIC4|4253|protein_coding| to in_q
2021-02-16T14:40:55.822512+1100 DEBUG - Process-1 | Adding ENST00000413189.1|ENSG00000233419.3|OTTHUMG00000003319|OTTHUMT00000009291.1|IFITM3P7-201|IFITM3P7|402|processed_pseudogene| to in_q
2021-02-16T14:40:55.919335+1100 ERROR - Process-2 | Required fields not found in the data file: ['ref_pos', 'ref_kmer', 'num_events', 'dwell_time', 'NNNNN_dwell_time', 'mismatch_dwell_time', 'start_idx', 'end_idx']
2021-02-16T14:40:55.919674+1100 ERROR - Process-2 | Error in Worker
2021-02-16T14:40:55.920315+1100 ERROR - Process-2 | Traceback (most recent call last):
  File "/home/labuser/anaconda3/envs/nanopore/lib/python3.7/site-packages/nanocompore/SampComp.py", line 305, in __process_references
    raise NanocomporeError("Required fields not found in the data file: {}".format(col_names))
nanocompore.common.NanocomporeError: Required fields not found in the data file: ['ref_pos', 'ref_kmer', 'num_events', 'dwell_time', 'NNNNN_dwell_time', 'mismatch_dwell_time', 'start_idx', 'end_idx']

2021-02-16T14:40:55.920893+1100 DEBUG - Process-2 | Processed Transcrits:0 Reads:0 Lines:0
2021-02-16T14:40:55.921050+1100 DEBUG - Process-2 | Adding poison pill to out_q
2021-02-16T14:40:55.921688+1100 ERROR - MainProcess | Traceback (most recent call last):
  File "/home/labuser/anaconda3/envs/nanopore/lib/python3.7/site-packages/nanocompore/SampComp.py", line 305, in __process_references
    raise NanocomporeError("Required fields not found in the data file: {}".format(col_names))
nanocompore.common.NanocomporeError: Required fields not found in the data file: ['ref_pos', 'ref_kmer', 'num_events', 'dwell_time', 'NNNNN_dwell_time', 'mismatch_dwell_time', 'start_idx', 'end_idx']

2021-02-16T14:40:55.922666+1100 ERROR - MainProcess | Traceback (most recent call last):
  File "/home/labuser/anaconda3/envs/nanopore/lib/python3.7/site-packages/nanocompore/SampComp.py", line 305, in __process_references
    raise NanocomporeError("Required fields not found in the data file: {}".format(col_names))
nanocompore.common.NanocomporeError: Required fields not found in the data file: ['ref_pos', 'ref_kmer', 'num_events', 'dwell_time', 'NNNNN_dwell_time', 'mismatch_dwell_time', 'start_idx', 'end_idx']

2021-02-16T14:40:55.923205+1100 ERROR - MainProcess | An error occured. Killing all processes and closing queues

It says that Required fields not found in the data file and I found that median column is not in my tsv files.

#5      ENST00000488147.1|ENSG00000227232.5|OTTHUMG00000000958|OTTHUMT00000002839.1|WASH7P-201|WASH7P|1351|unprocessed_pseudogene|
ref_pos ref_kmer        num_events      dwell_time      NNNNN_dwell_time        mismatch_dwell_time     start_idx       end_idx
1261    GGGGG   2       0.01693 0.0     0.0     11283   11334
1262    GGGGA   8       0.04283 0.0     0.0     11154   11283
1263    GGGAC   1       0.00598 0.0     0.0     11136   11154
1264    GGACG   2       0.0073  0.0     0.0     11114   11136
1265    GACGG   2       0.01925 0.01029 0.0     11056   11114
1267    CGGCT   1       0.00863 0.0     0.0     11030   11056
1268    GGCTC   3       0.01826 0.0     0.0     10975   11030
1269    GCTCC   1       0.00498 0.0     0.0     10960   10975
1270    CTCCA   1       0.00465 0.0     0.0     10946   10960
1271    TCCAC   1       0.00564 0.0     0.0     10929   10946
1272    CCACC   1       0.00365 0.0     0.0     10918   10929
1273    CACCC   18      0.07998999999999999     0.0     0.0     10677   10918
1274    ACCCA   6       0.023899999999999998    0.0     0.0     10605   10677

I assume I have to re-run nanopolish using the flag --samples? Thanks!

tleonardi commented 3 years ago

Hi @pabloacera, yes exactly. As specified in Nanocompore's documentation you need run Nanopolish with these options: --print-read-names --scale-events --samples