Commit f7cce0e1 authored by joweb106's avatar joweb106
Browse files

added first loom (MI2)

parent 4e1f100f
2019-12-14 01:22:41,925 - DEBUG - Using logic: Default
2019-12-14 01:22:41,960 - INFO - Read 15539 cell barcodes from /gpfs/scratch/joweb106/rna_velocity/data/52_NGS_EPDC_aggr/outs/filtered_feature_bc_matrix/barcodes.tsv.gz
2019-12-14 01:22:41,960 - DEBUG - Example of barcode: AAACCTGAGACAGAGA and cell_id: 52_NGS_EPDC_aggr:AAACCTGAGACAGAGA-1
2019-12-14 01:22:41,973 - DEBUG - Peeking into /gpfs/scratch/joweb106/rna_velocity/data/52_NGS_EPDC_aggr/outs/possorted_genome_bam.bam
[E::hts_open_format] Failed to open file /gpfs/scratch/joweb106/rna_velocity/data/52_NGS_EPDC_aggr/outs/possorted_genome_bam.bam
Traceback (most recent call last):
File "/software/velocyto/0.17.17/ivybridge/bin/velocyto", line 11, in <module>
sys.exit(cli())
File "/software/velocyto/0.17.17/ivybridge/lib/python3.6/site-packages/click/core.py", line 764, in __call__
return self.main(*args, **kwargs)
File "/software/velocyto/0.17.17/ivybridge/lib/python3.6/site-packages/click/core.py", line 717, in main
rv = self.invoke(ctx)
File "/software/velocyto/0.17.17/ivybridge/lib/python3.6/site-packages/click/core.py", line 1137, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/software/velocyto/0.17.17/ivybridge/lib/python3.6/site-packages/click/core.py", line 956, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/software/velocyto/0.17.17/ivybridge/lib/python3.6/site-packages/click/core.py", line 555, in invoke
return callback(*args, **kwargs)
File "/software/velocyto/0.17.17/ivybridge/lib/python3.6/site-packages/velocyto/commands/run10x.py", line 115, in run10x
samtools_memory=samtools_memory, dump=dump, loom_numeric_dtype=dtype, verbose=verbose, additional_ca=additional_ca)
File "/software/velocyto/0.17.17/ivybridge/lib/python3.6/site-packages/velocyto/commands/_run.py", line 159, in _run
exincounter.peek(bamfile[0])
File "/software/velocyto/0.17.17/ivybridge/lib/python3.6/site-packages/velocyto/counter.py", line 135, in peek
fin = pysam.AlignmentFile(bamfile) # type: pysam.AlignmentFile
File "pysam/libcalignmentfile.pyx", line 741, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 940, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/gpfs/scratch/joweb106/rna_velocity/data/52_NGS_EPDC_aggr/outs/possorted_genome_bam.bam`: No such file or directory
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