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PacificBiosciences / pbbioconda

PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.
BSD 3-Clause Clear License
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libgcc_s.so.1 must be installed for pthread_cancel to work #260

Closed ddEmoryU closed 4 years ago

ddEmoryU commented 4 years ago

I'm trying to run fc_run using HIFI pacbio data. I set input_type=preads, so I skip the 1-rawreads step, but when is running the second step 2-preads_oval, we are getting the following errors:

ERROR - Failed to submit Pbb24ee009d9f9a: 'bash -C /root/miniconda3/lib/python3.7/site-packages/pwatcher/mains/job_start.sh >| /data/1-preads_ovl/daligner-runs/j_0097/run-Pbb24ee009d9f9a.bash.stdout 2>| /data/1-preads_ovl/daligner-runs/j_0097/run-Pbb24ee009d9f9a.bash.stderr' Setting rc=42.

ERROR - Noop. We cannot kill blocked threads. Hopefully, everything will die on SIGTERM libgcc_s.so.1 must be installed for pthread_cancel to work

And then the process d_aligner keeps running for hours without a single new file being created.

I'm attaching the log file

all_nonstop.log

armintoepfer commented 4 years ago

Closing due to lack of activity.