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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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Isoseq3 cluster2 exits without error message #685

Closed sagnikbanerjee15 closed 3 months ago

sagnikbanerjee15 commented 5 months ago

Operating system Linux

Package name

isoseq 4.0.0 (commit v4.0.0)

Using: pbbam : 2.4.99 (commit v2.4.0-16-g5cc6e4b) pbcopper : 2.3.99 (commit v2.3.0-14-g5ac5693) pbmm2 : 1.11.99 (commit v1.11.0-1-g1b5a417) minimap2 : 2.15 parasail : 2.1.3 boost : 1.77 htslib : 1.17 zlib : 1.2.13

Describe the bug Executing --> nohup isoseq3 cluster2 --log-level TRACE --log-file $PWD/isoseq3_cluster.log --num-threads 64 $PWD/flnc_first2.fofn $PWD/first2.clustered.bam 1> $PWD/first2.clusterd.output 2> $PWD/first2.clustered.error &

Program exits without any error message but does not produce the intended results

Error message No error message

To Reproduce Works on small dataset. Exists without error on large datasets.

Expected behavior Produce clustered transcript file

armintoepfer commented 3 months ago

Were you able to succeed? What are your system specs? Where in the log is it stopping?

armintoepfer commented 3 months ago

I'll reopen once you provide a reproducible example