another run_tapis.py error

Hi,

I am trying to use TAPIS with this command

run_tapis.py -v -p -o test myannotation.gtf subreads_GMAP_alignment.bam

I got this error

Traceback (most recent call last):
  File "run_tapis.py", line 945, in <module>
    clusterReads(args.bamfile, cluster_treesP, cluster_treesN, readDict)
  File "run_tapis.py", line 223, in clusterReads
    chrom = bamfile.getrname(read.tid)
  File "pysam/libcalignmentfile.pyx", line 1609, in pysam.libcalignmentfile.AlignmentFile.getrname (pysam/libcalignmentfile.c:18459)
  File "pysam/libcalignmentfile.pyx", line 672, in pysam.libcalignmentfile.AlignmentFile.get_reference_name (pysam/libcalignmentfile.c:9423)
ValueError: reference_id -1 out of range 0<=tid<93

Could you please help me?

Thanks,

Maria Angela

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