Endless running Tombo resuiggle, reached to 100% in resuiggle but doesn't go to next step, generate output files

[kwonej0617]

Hello! @marcus1487

I have run Tombo successfully with my dataset earlier. However, I used the same data and run the same pipeline again (I might add some options in resquiggle like corrected-group RawGenomeCorrected_000 --basecall-group Basecall_1D_000 --fit-global-scale --include-event-stdev --ignore-read-locks ), but it didn't work this time. In my error log file, it looks like the resquiggle process was successfully running and reached 100%, but it didn't go to the next step, which are tombs detet_modification step and text_output browser_files. No stats files, wig, bedgraph files generated. Could you please help me with how to solve this problem? Thank you so much!

#preprocess
#singularity exec /share/pkg/containers/tombo/tombo_1.5.1.sif tombo preprocess annotate_raw_with_fastqs --fast5-basedir ${wt_fast5} --fastq-filenames ${wt_fastq} --overwrite --processes 40

#resquiggling
singularity exec /share/pkg/containers/tombo/tombo_1.5.1.sif tombo resquiggle ${wt_fast5} ${ref} --rna --corrected-group RawGenomeCorrected_000 --basecall-group Basecall_1D_000 --overwrite --processes 40 --fit-global-scale --include-event-stdev --ignore-read-locks

#detect modifications
singularity exec /share/pkg/containers/tombo/tombo_1.5.1.sif tombo detect_modifications de_novo --fast5-basedirs ${wt_fast5} --statistics-file-basename wt --corrected-group RawGenomeCorrected_000 --processes 40

#output statistical results
singularity exec /share/pkg/containers/tombo/tombo_1.5.1.sif tombo text_output browser_files --fast5-basedirs ${wt_fast5} --statistics-filename wt.tombo.stats --browser-file-basename wt_rrach --genome-fasta ${ref} --motif-descriptions RRACH:3:m6A --file-types coverage dampened_fraction fraction --corrected-group RawGenomeCorrected_00

[12:18:53] Re-squiggling reads (raw signal to genomic sequence alignment).
^M 0%| | 0/1294636 [00:00<?, ?it/s]^M 0%| | 4/1294636 [00:01<90:04:40, 3.99it/s]^M 0%| | 16/1294636 [00:01<33:47:03, 10.64it/s]^M 0%| | 32/1294636 [00:02<22:31:29, 15.97it/s]^M 0%| | 59/1294636 [00:03<18:19:25, 19.62it/s]^M 0%| | 89/1294636 [00:04<16:11:43, 22.20it/s]^M 0%| | 131/1294636 [00:05<15:07:39, 23.77it/s]^M 0%| | 176/1294636 [00:07<14:19:49, 25.09it/s]^M 0%| | 232/1294636 [00:09<13:58:35, 25.73it/s]^M 0%| | 290/1294636 [00:11<13:39:54, 26.31it/s]^M 0%| | 358/1294636 [00:13<13:35:
...
[11:20:16<04:30, 31.51it/s]^M 99%|█████████▉| 1286300/1294636 [11:20:25<04:24, 31.51it/s]^M 99%|█████████▉| 1286400/1294636 [11:20:40<04:21,
31.50it/s]^M 99%|█████████▉| 1286500/1294636 [11:20:42<04:18, 31.50it/s]^M 99%|█████████▉| 1286600/1294636 [11:20:48<04:15, 31.50it/s]^M 99%|█████████▉| 1286700/1294636 [
11:20:49<04:11, 31.50it/s]^M 99%|█████████▉| 1286800/1294636 [11:20:56<04:08, 31.50it/s]^M 99%|█████████▉| 1286900/1294636 [11:20:57<04:05, 31.50it/s]^M 99%|█████████▉| 12
87100/1294636 [11:20:58<03:59, 31.50it/s]^M 99%|█████████▉| 1287300/1294636 [11:21:01<03:52, 31.50it/s]^M 99%|█████████▉| 1287500/1294636 [11:21:10<03:46, 31.50it/s]^M 99%
|█████████▉| 1287800/1294636 [11:21:12<03:36, 31.51it/s]^M 99%|█████████▉| 1288000/1294636 [11:21:30<03:30, 31.50it/s]^M 99%|█████████▉| 1288100/1294636 [11:21:31<03:27, 3
1.50it/s]^M100%|█████████▉| 1288200/1294636 [11:21:32<03:24, 31.50it/s]^M100%|█████████▉| 1288400/1294636 [11:21:36<03:17, 31.50it/s]^M100%|█████████▉| 1288600/1294636 [11
:21:40<03:11, 31.51it/s]^M100%|█████████▉| 1288800/1294636 [11:21:46<03:05, 31.51it/s]^M100%|█████████▉| 1289000/1294636 [11:21:48<02:58, 31.51it/s]^M100%|█████████▉| 1289
200/1294636 [11:21:55<02:52, 31.51it/s]^M100%|█████████▉| 1289400/1294636 [11:22:03<02:46, 31.51it/s]^M100%|█████████▉| 1289600/1294636 [11:22:08<02:39, 31.51it/s]^M100%|█
████████▉| 1289800/1294636 [11:22:14<02:33, 31.51it/s]^M100%|█████████▉| 1290000/1294636 [11:22:25<02:27, 31.51it/s]^M100%|█████████▉| 1290100/1294636 [11:22:36<02:24, 31.
50it/s]^M100%|█████████▉| 1290200/1294636 [11:22:39<02:20, 31.50it/s]^M100%|█████████▉| 1290400/1294636 [11:22:46<02:14, 31.50it/s]^M100%|█████████▉| 1290600/1294636 [11:2
2:47<02:08, 31.50it/s]^M100%|█████████▉| 1290800/1294636 [11:22:50<02:01, 31.51it/s]^M100%|█████████▉| 1291000/1294636 [11:22:56<01:55, 31.51it/s]^M100%|█████████▉| 129120
0/1294636 [11:23:04<01:49, 31.50it/s]^M100%|█████████▉| 1291400/1294636 [11:23:10<01:42, 31.50it/s]^M100%|█████████▉| 1291600/1294636 [11:23:13<01:36, 31.51it/s]^M100%|███
██████▉| 1291800/1294636 [11:23:24<01:30, 31.50it/s]^M100%|█████████▉| 1291900/1294636 [11:23:28<01:26, 31.50it/s]^M100%|█████████▉| 1292000/1294636 [11:23:30<01:23, 31.50
it/s]^M100%|█████████▉| 1292100/1294636 [11:23:39<01:20, 31.50it/s]^M100%|█████████▉| 1292200/1294636 [11:23:41<01:17, 31.50it/s]^M100%|█████████▉| 1292300/1294636 [11:23:
42<01:14, 31.50it/s]^M100%|█████████▉| 1292400/1294636 [11:23:46<01:10, 31.50it/s]^M100%|█████████▉| 1292500/1294636 [11:23:47<01:07, 31.50it/s]^M100%|█████████▉| 1292623/
1294636 [11:23:47<01:03, 31.51it/s]^M100%|█████████▉| 1293854/1294636 [11:23:48<00:24, 31.54it/s]^M100%|█████████▉| 1294325/1294636 [11:24:00<00:09, 31.54it/s]

[haowBio]

I encountered the same problem when running with docker. After installing it with conda, it ran normally.