added first loom (MI2)

data/log_run10x.txt

+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