Hello All,

This my first post here. I ran arrow in smrtlink (v6.0) with reference input file from the canu contig.fasta and merged bam file generated by bax2bam. The software gave me error as following and quit within a minute of runing:

Does anyone have experience with this error? Thank you.

my command:

variantCaller -j8 --algorithm=arrow --referenceFilename FN_CANU.contigs.fasta --outputFilename FN_CANU_ARROW.fasta --outputFilename FN_CANU_ARROW.fastq --outputFilename FN_CANU_ARROW.gff Raw_aligned.bam

[ERROR] 'M5'

Traceback (most recent call last):

File "/share/pacbio/smrtlink/install/smrtlink-release_6.0.0.47841/bundles/smrttools/install/smrttools-release_6.0.0.47835/private/thirdparty/python/python_2.7.9/site-packages/pbcommand/cli/core.py", line 138, in _pacbio_main_runner return_code = exe_main_func(args, *kwargs)

File "/share/pacbio/smrtlink/install/smrtlink-release_6.0.0.47841/bundles/smrttools/install/smrttools-release_6.0.0.47835/private/thirdparty/python/python_2.7.9/site-packages/GenomicConsensus/main.py", line 340, in args_runner return tr.main()

File "/share/pacbio/smrtlink/install/smrtlink-release_6.0.0.47841/bundles/smrttools/install/smrttools-release_6.0.0.47835/private/thirdparty/python/python_2.7.9/site-packages/GenomicConsensus/main.py", line 258, in main with AlignmentSet(options.inputFilename) as peekFile:

File "/share/pacbio/smrtlink/install/smrtlink-release_6.0.0.47841/bundles/smrttools/install/smrttools-release_6.0.0.47835/private/thirdparty/python/python_2.7.9/site-packages/pbcore/io/dataset/DataSetIO.py", line 2699, in __init__ super(AlignmentSet, self).__init__(files, *kwargs)

File "/share/pacbio/smrtlink/install/smrtlink-release_6.0.0.47841/bundles/smrttools/install/smrttools-release_6.0.0.47835/private/thirdparty/python/python_2.7.9/site-packages/pbcore/io/dataset/DataSetIO.py", line 1963, in __init__ super(ReadSet, self).__init__(files, *kwargs)

File "/share/pacbio/smrtlink/install/smrtlink-release_6.0.0.47841/bundles/smrttools/install/smrttools-release_6.0.0.47835/private/thirdparty/python/python_2.7.9/site-packages/pbcore/io/dataset/DataSetIO.py", line 450, in __init__ self.updateCounts()

File "/share/pacbio/smrtlink/install/smrtlink-release_6.0.0.47841/bundles/smrttools/install/smrttools-release_6.0.0.47835/private/thirdparty/python/python_2.7.9/site-packages/pbcore/io/dataset/DataSetIO.py", line 2517, in updateCounts self.assertIndexed()

File "/share/pacbio/smrtlink/install/smrtlink-release_6.0.0.47841/bundles/smrttools/install/smrttools-release_6.0.0.47835/private/thirdparty/python/python_2.7.9/site-packages/pbcore/io/dataset/DataSetIO.py", line 2347, in assertIndexed self._assertIndexed((IndexedBamReader, CmpH5Reader))

File "/share/pacbio/smrtlink/install/smrtlink-release_6.0.0.47841/bundles/smrttools/install/smrttools-release_6.0.0.47835/private/thirdparty/python/python_2.7.9/site-packages/pbcore/io/dataset/DataSetIO.py", line 1920, in _assertIndexed self._openFiles()

File "/share/pacbio/smrtlink/install/smrtlink-release_6.0.0.47841/bundles/smrttools/install/smrttools-release_6.0.0.47835/private/thirdparty/python/python_2.7.9/site-packages/pbcore/io/dataset/DataSetIO.py", line 2044, in _openFiles resource = IndexedBamReader(location)

File "/share/pacbio/smrtlink/install/smrtlink-release_6.0.0.47841/bundles/smrttools/install/smrttools-release_6.0.0.47835/private/thirdparty/python/python_2.7.9/site-packages/pbcore/io/align/BamIO.py", line 373, in __init__ super(IndexedBamReader, self).__init__(fname, referenceFastaFname)

File "/share/pacbio/smrtlink/install/smrtlink-release_6.0.0.47841/bundles/smrttools/install/smrttools-release_6.0.0.47835/private/thirdparty/python/python_2.7.9/site-packages/pbcore/io/align/BamIO.py", line 181, in __init__ self._loadReferenceInfo()

File "/share/pacbio/smrtlink/install/smrtlink-release_6.0.0.47841/bundles/smrttools/install/smrttools-release_6.0.0.47835/private/thirdparty/python/python_2.7.9/site-packages/pbcore/io/align/BamIO.py", line 49, in _loadReferenceInfo refMD5s = [r["M5"] for r in refRecords]

KeyError: 'M5'