/var/spool/sge/scc-kb5/job_scripts/365156: line 239: intersectBed: command not found
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] invalid BAM binary header (this is not a BAM file).
/var/spool/sge/scc-kb5/job_scripts/365156: line 290: 19869 Segmentation fault      samtools sort -n ${INPUT_BAM} ${Sample_ID}'_sorted'
open: No such file or directory
[main_samview] fail to open "G123_M2_sorted.bam" for reading.
/restricted/projectnb/waxmanlab/environment/.conda/envs/new_env1/lib/python2.7/site-packages/HTSeq-0.6.1p1-py2.7-linux-x86_64.egg/HTSeq/__init__.py:9: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility
  from _HTSeq import *
100000 GFF lines processed.
200000 GFF lines processed.
212107 GFF lines processed.
Error occured when reading beginning of SAM/BAM file.
  
  [Exception type: StopIteration, raised in count.py:88]