velocyto run OSError: no BGZF EOF marker; file may be truncated

[shijianasdf]

when I run velocyto like this:

velocyto run -b /home/shijian/scvelo1/ESCA-5-post-T_.tsv -m /home/shijian/scvelo/human_rmsk.gtf /WFDATA/yang_res_z/0901cp/ESCA-5-post-T/outs/possorted_genome_bam.bam /home/shijian/scvelo/genes.gtf -o /WFDATA/yang_scvelo/ESCA-5-post-T

and I got error as follow:

Traceback (most recent call last):
 File "/home/shijian/anaconda3/bin/velocyto", line 8, in <module>
   sys.exit(cli())
 File "/home/shijian/anaconda3/lib/python3.8/site-packages/click/core.py", line 1137, in __call__
   return self.main(*args, **kwargs)
 File "/home/shijian/anaconda3/lib/python3.8/site-packages/click/core.py", line 1062, in main
   rv = self.invoke(ctx)
 File "/home/shijian/anaconda3/lib/python3.8/site-packages/click/core.py", line 1668, in invoke
   return _process_result(sub_ctx.command.invoke(sub_ctx))
 File "/home/shijian/anaconda3/lib/python3.8/site-packages/click/core.py", line 1404, in invoke
   return ctx.invoke(self.callback, **ctx.params)
 File "/home/shijian/anaconda3/lib/python3.8/site-packages/click/core.py", line 763, in invoke
   return __callback(*args, **kwargs)
 File "/home/shijian/anaconda3/lib/python3.8/site-packages/velocyto/commands/run.py", line 113, in run
  return _run(bamfile=bamfile, gtffile=gtffile, bcfile=bcfile, outputfolder=outputfolder,
 File "/home/shijian/anaconda3/lib/python3.8/site-packages/velocyto/commands/_run.py", line 229, in _run
   results = exincounter.count(bamfile_cellsorted, multimap=multimap)  # NOTE: we would avoid some millions of if >statements evaluations if we write two function count and count_with output
 File "/home/shijian/anaconda3/lib/python3.8/site-packages/velocyto/counter.py", line 756, in count
   for r in self.iter_alignments(bamfile, unique=not multimap):
 File "/home/shijian/anaconda3/lib/python3.8/site-packages/velocyto/counter.py", line 251, in iter_alignments
   fin = pysam.AlignmentFile(bamfile)  # type: pysam.AlignmentFile
 File "pysam/libcalignmentfile.pyx", line 742, in pysam.libcalignmentfile.AlignmentFile.__cinit__
 File "pysam/libcalignmentfile.pyx", line 952, in pysam.libcalignmentfile.AlignmentFile._open
 File "pysam/libchtslib.pyx", line 365, in pysam.libchtslib.HTSFile.check_truncation
OSError: no BGZF EOF marker; file may be truncated

[ShobiStassen]

@shijianasdf hi did you managed to solve this issue, I also get the EOF error

[GouQiao]

Hi did you find a solution about this matter?

[hyjforesight]

@GouQiao see here https://github.com/velocyto-team/velocyto.py/issues/250