fail to open a sam file

[IEkAdN]

Hello.

FALCON_unzip fails with the error below(4-quiver/track_reads_h/pwatcher.dir/stderr). I think it failed to create a sam file for some reason. How can I avoid this problem ?

. . . samfile_fn:'/scratch/hoge/FU_1701151949/4-quiver/reads/000613F_002.sam' samfile_fn:'/scratch/hoge/FU_1701151949/4-quiver/reads/000053F_008.sam' samfile_fn:'/scratch/hoge/FU_1701151949/4-quiver/reads/000083F_022.sam' [E::hts_open_format] fail to open file '/scratch/hoge/FU_1701151949/4-quiver/reads/000083F_022.sam' /scratch/hoge/FU_1701151949/4-quiver/track_reads_h/track_reads_h.sh: line 9: 7124 segmentation fault fc_select_reads_from_bam.py --basedir ../.. /scratch/hoge/FU_1701151949/input_bam.fofn touch /scratch/hoge/FU_1701151949/4-quiver/track_reads_h/track_reads_h_done.exit

• touch /scratch/hoge/FU_1701151949/4-quiver/track_reads_h/track_reads_h_done.exit 2017-01-19 05:14:24,967 - root - DEBUG - CD: '/scratch/hoge/FU_1701151949/4-quiver/track_reads_h' -> '/scratch/hoge/FU_1701151949/4-quiver/track_reads_h' 2017-01-19 05:14:24,967 - root - DEBUG - CD: '/scratch/hoge/FU_1701151949/4-quiver/track_reads_h' -> '/scratch/hoge/FU_1701151949/4-quiver/track_reads_h' 2017-01-19 05:14:24,968 - root - CRITICAL - Error in /data/hoge/tools/FALCON-integrate/pypeFLOW/pypeflow/do_task.py with args="{'json_fn': '/scratch/hoge/FU_1701151949/4-quiver/track_reads_h/task.json',\n 'timeout': 60,\n 'tmpdir': None}" Traceback (most recent call last): File "/data/hoge/tools/Python-2.7.9_build/lib/python2.7/runpy.py", line 162, in _run_module_as_main "main", fname, loader, pkg_name) File "/data/hoge/tools/Python-2.7.9_build/lib/python2.7/runpy.py", line 72, in _run_code exec code in run_globals File "/data/hoge/tools/FALCON-integrate/pypeFLOW/pypeflow/do_task.py", line 190, in main() File "/data/hoge/tools/FALCON-integrate/pypeFLOW/pypeflow/do_task.py", line 182, in main run(**vars(parsed_args)) File "/data/hoge/tools/FALCON-integrate/pypeFLOW/pypeflow/do_task.py", line 136, in run run_cfg_in_tmpdir(cfg, tmpdir) File "/data/hoge/tools/FALCON-integrate/pypeFLOW/pypeflow/do_task.py", line 160, in run_cfg_in_tmpdir run_python_func(func, myinputs, myoutputs, parameters) File "/data/hoge/tools/FALCON-integrate/pypeFLOW/pypeflow/do_task.py", line 125, in run_python_func do_support.run_bash(script_fn) File "/data/hoge/tools/FALCON-integrate/pypeFLOW/pypeflow/do_support.py", line 51, in run_bash raise Exception('{} <- {!r}'.format(rc, cmd)) Exception: 35584 <- '/bin/bash -vex /scratch/hoge/FU_1701151949/4-quiver/track_reads_h/track_reads_h.sh'

real 234m16.529s user 931m6.059s sys 37m34.987s returned: 256

[pb-jchin]

You samtools or pysam installation may not be able to handle the files.

[IEkAdN]

Thank you for your quick reply. I added ${FALCON_unzip_38de578_install_dir}/lib/python2.7/site-packages to the top of PYTHONPATH, and assigned ${smrtlink_3.1.1_install_dir}/smrtcmds/bin to smrt_bin in fc_unzip.cfg. Doesn't it mean that I ran FALCON_unzip with the expected version of samtools and pysam ?

[IEkAdN]

In the directory ${FALCON_unzip_38de578_install_dir}/lib/python2.7/site-packages, there is a directory pysam-0.9.1.4-py2.7-linux-x86_64.egg/, so I thought pysam was automatically installed when I installed FALCON_unzip. Is it right ?

And when I installed FALCON_unzip, messages below were output. Are these related to this problem ?

package init file 'samtools/init.py' not found (or not a regular file) package init file 'bcftools/init.py' not found (or not a regular file) package init file 'samtools/win32/init.py' not found (or not a regular file) package init file 'htslib/init.py' not found (or not a regular file) package init file 'htslib/htslib/init.py' not found (or not a regular file)