I have gone throught the steps of SplitNCigarReads and flagCorrection.r. When trying to call variants using DeepVariant, I came across the following error mesage.
2024-06-11 01:56:30.095375: F deepvariant/allelecounter.cc:204] Check failed: offset + len <= read.aligned_quality_size() (1 vs. 0)
Fatal Python error: Aborted
Current thread 0x00002b8bf9b76b80 (most recent call first):
File "/tmp/Bazel.runfiles_4uwuinr3/runfiles/com_google_deepvariant/deepvariant/make_examples_core.py", line 2040 in candidates_in_region
File "/tmp/Bazel.runfiles_4uwuinr3/runfiles/com_google_deepvariant/deepvariant/make_examples_core.py", line 1734 in process
File "/tmp/Bazel.runfiles_4uwuinr3/runfiles/com_google_deepvariant/deepvariant/make_examples_core.py", line 2838 in make_examples_runner
File "/tmp/Bazel.runfiles_4uwuinr3/runfiles/com_google_deepvariant/deepvariant/make_examples.py", line 224 in main
File "/tmp/Bazel.runfiles_4uwuinr3/runfiles/absl_py/absl/app.py", line 258 in _run_main
File "/tmp/Bazel.runfiles_4uwuinr3/runfiles/absl_py/absl/app.py", line 312 in run
File "/tmp/Bazel.runfiles_4uwuinr3/runfiles/com_google_deepvariant/deepvariant/make_examples.py", line 234 in <module>
parallel: This job failed:
It seems to be related to a similar issue, where the base quality is missing. Could you advise on this issue?
Hi lrRNAseqVariantCalling team,
I have gone throught the steps of SplitNCigarReads and flagCorrection.r. When trying to call variants using DeepVariant, I came across the following error mesage.
It seems to be related to a similar issue, where the base quality is missing. Could you advise on this issue?
Thanks.