[miso-users] pe_utils error

[장재영]

Hi,

An error occurred when using pe_utils.

There was no problem when using UCSC reference and gff, but there was a problem when I replaced it with an ensembl reference for a variety of reasons.

At first I thought it was a problem of ‘chr’

So I removed ‘chr’ from ensGene.gff3 and ran exon_utils.

After then, I ran pe_utils, but I got the following error message:

File "/usr/local/bin/pe_utils", line 11, in <module>
    sys.exit(main())
  File "/usr/local/lib/python2.7/dist-packages/misopy/pe_utils.py", line 548, in main
    sd_max=sd_max)
  File "/usr/local/lib/python2.7/dist-packages/misopy/pe_utils.py", line 283, in compute_insert_len
    mapped_bam = pysam.Samfile(mapped_bam_filename, "rb")
  File "pysam/libcalignmentfile.pyx", line 401, in pysam.libcalignmentfile.AlignmentFile.__cinit__ (pysam/libcalignmentfile.c:5835)
  File "pysam/libcalignmentfile.pyx", line 576, in pysam.libcalignmentfile.AlignmentFile._open (pysam/libcalignmentfile.c:7699)
  File "pysam/libchtslib.pyx", line 331, in pysam.libchtslib.HTSFile.check_truncation (pysam/libchtslib.c:7195)
OSError: no BGZF EOF marker; file may be truncated

I tried to check the header using the following command, but found no difference.
tagBam -i control.bam -files /directories/exons/Homo_sapiens.GRCh37.65.min_1000.const_exons.gff -labels gff -intervals -f 1 | samtools view - -h | egrep '^@|:gff:'
samtools view -H /directories/insert-dist/bam2gff_Homo_sapiens.GRCh37.65.min_1000.const_exons.gff/control.bam

I don’t know what the problem is..
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