alignPacBio.py error

[luping]

[luping@centos cluster]$ alignPacBio.py /disk/luping/bam/iso-bam/cluster/FG/ FG /disk/luping/bam/iso-bam/cluster/FG.RR.32.genome.fa /disk/luping/bam/iso-bam/cluster/all.consensus_isoforms.fasta 
cat: write error: Broken pipe
<Tue Nov  7 10:39:42 2017> Converting filtered/temp_dir/all_r1.sam to filtered/temp_dir/all_r1.bam
<Tue Nov  7 10:39:42 2017> Sorting BAM file
<Tue Nov  7 10:39:42 2017> Generating BAM index
<Tue Nov  7 10:39:42 2017> Elapsed time: 0.00 minutes.
Traceback (most recent call last):
  File "/disk/luping/tools/comp_bio-tapis-44cc05ebc78c/TAP/bin/cleanAlignments.py", line 81, in <module>
    bamfile = pysam.Samfile(args.bam_input , 'rb' )
  File "calignmentfile.pyx", line 302, in pysam.calignmentfile.AlignmentFile.__cinit__ (pysam/calignmentfile.c:4834)
  File "calignmentfile.pyx", line 485, in pysam.calignmentfile.AlignmentFile._open (pysam/calignmentfile.c:6789)
ValueError: file header is empty (mode='rb') - is it SAM/BAM format?
Traceback (most recent call last):
  File "/disk/luping/tools/comp_bio-tapis-44cc05ebc78c/TAP/bin/alignPacBio.py", line 75, in <module>
    if os.path.getsize(gmapIn) == 0:
  File "/disk/luping/tools/Python-2.7.9/lib/python2.7/genericpath.py", line 49, in getsize
    return os.stat(filename).st_size
OSError: [Errno 2] No such file or directory: 'filtered/temp_dir/all_fixed_r1.fa'

[mkdie]

I came across the same problem as yours , so how did you solve it ??? can you share it , thanks a lot!!

[MouYin]

Dear luping,

I have the same problem as you. How did you solve it? Would you mind telling me? Thank you very much!