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PacificBiosciences / kineticsTools

Tools for detecting DNA modifications from single molecule, real-time sequencing data
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ipdSummary: AssertionError Child process exited with exitcode=1 #92

Open anikajohn opened 2 years ago

anikajohn commented 2 years ago

Hi,

I am having trouble running ipdSummary (SMRTLINK version 11.0.0146107) although I am (presumingly) using all the right inputs. Reads were produced with Sequel II sequencer.

This is the command I am running: /usr/prog/GX/tools/src/pacbio/smrtlink/v11.0/smrtcmds/bin/ipdSummary aligned.bam --reference reference.fa --identify m6A --gff basemods.gff

Which gives me the following error: Process KineticWorkerProcess-1: Traceback (most recent call last): File "/usr/prog/GX/tools/src/pacbio/smrtlink/v11.0/install/smrtlink-release_11.0.0.146107/bundles/smrttools/install/smrttools-release_11.0.0.146107/private/thirdparty/python3/python3_3.9.6/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap self.run() File "/usr/prog/GX/tools/src/pacbio/smrtlink/v11.0/install/smrtlink-release_11.0.0.146107/bundles/smrttools/install/smrttools-release_11.0.0.146107/private/thirdparty/python3/python3_3.9.6/site-packages/kineticsTools/WorkerProcess.py", line 151, in run self._run() File "/usr/prog/GX/tools/src/pacbio/smrtlink/v11.0/install/smrtlink-release_11.0.0.146107/bundles/smrttools/install/smrttools-release_11.0.0.146107/private/thirdparty/python3/python3_3.9.6/site-packages/kineticsTools/WorkerProcess.py", line 127, in _run result = self.onChunk( # pylint: disable=assignment-from-none File "/usr/prog/GX/tools/src/pacbio/smrtlink/v11.0/install/smrtlink-release_11.0.0.146107/bundles/smrttools/install/smrttools-release_11.0.0.146107/private/thirdparty/python3/python3_3.9.6/site-packages/kineticsTools/KineticWorker.py", line 121, in onChunk perSiteResults = self._summarizeReferenceRegion( File "/usr/prog/GX/tools/src/pacbio/smrtlink/v11.0/install/smrtlink-release_11.0.0.146107/bundles/smrttools/install/smrttools-release_11.0.0.146107/private/thirdparty/python3/python3_3.9.6/site-packages/kineticsTools/KineticWorker.py", line 230, in _summarizeReferenceRegion (caseChunks, capValue) = self._fetchChunks( File "/usr/prog/GX/tools/src/pacbio/smrtlink/v11.0/install/smrtlink-release_11.0.0.146107/bundles/smrttools/install/smrttools-release_11.0.0.146107/private/thirdparty/python3/python3_3.9.6/site-packages/kineticsTools/KineticWorker.py", line 449, in _fetchChunks rawIpds = self._loadRawIpds(hits, start, end, factor) File "/usr/prog/GX/tools/src/pacbio/smrtlink/v11.0/install/smrtlink-release_11.0.0.146107/bundles/smrttools/install/smrttools-release_11.0.0.146107/private/thirdparty/python3/python3_3.9.6/site-packages/kineticsTools/KineticWorker.py", line 484, in _loadRawIpds rawIpd = aln.IPD() * factor File "/usr/prog/GX/tools/src/pacbio/smrtlink/v11.0/install/smrtlink-release_11.0.0.146107/bundles/smrttools/install/smrttools-release_11.0.0.146107/private/thirdparty/python3/python3_3.9.6/site-packages/pbcore/io/align/BamAlignment.py", line 49, in f return self.baseFeature(featureName, aligned, orientation) File "/usr/prog/GX/tools/src/pacbio/smrtlink/v11.0/install/smrtlink-release_11.0.0.146107/bundles/smrttools/install/smrttools-release_11.0.0.146107/private/thirdparty/python3/python3_3.9.6/site-packages/pbcore/io/align/BamAlignment.py", line 536, in baseFeature assert len(data) == self.peer.rlen AssertionError Child process exited with exitcode=1. Aborting. [ERROR] 2022-04-28 10:55:32,038Z [root monitorChildProcesses 592] Child process exited with exitcode=1. Aborting.

I alinged my reads using pbmm2: pbmm2 align reference.fa kinetic_reads.bam aligned.bam --sort

I also tried it with a 0.3 subset of my bam files, but it still gave the same error message. Feedback would be much appreciated, thanks already!

anikajohn commented 2 years ago

In case my set up is not suitable for this ipdSummary, I would also be happy about suggestions for alternative/better tools with similar functionalities. I am mainly interested in the detection of 6mA modified bases.