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--></style></head><body lang=KO link=blue vlink="#954F72"><div class=WordSection1><p class=MsoNormal><span lang=EN-US style='font-size:12.0pt;font-family:"굴림",sans-serif'>Hi,<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:12.0pt;font-family:"굴림",sans-serif'><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:12.0pt;font-family:"굴림",sans-serif'>An error occurred when using pe_utils.<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:12.0pt;font-family:"굴림",sans-serif'><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:12.0pt;font-family:"굴림",sans-serif'>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.<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:12.0pt;font-family:"굴림",sans-serif'><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:12.0pt;font-family:"굴림",sans-serif'>At first I thought it was a problem of </span><span style='font-size:12.0pt;font-family:"굴림",sans-serif'>‘<span lang=EN-US>chr</span>’<span lang=EN-US><o:p></o:p></span></span></p><p class=MsoNormal><span lang=EN-US style='font-size:12.0pt;font-family:"굴림",sans-serif'><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:12.0pt;font-family:"굴림",sans-serif'>So I removed </span><span style='font-size:12.0pt;font-family:"굴림",sans-serif'>‘<span lang=EN-US>chr</span>’<span lang=EN-US> from ensGene.gff3 and ran exon_utils.<o:p></o:p></span></span></p><p class=MsoNormal><span lang=EN-US style='font-size:12.0pt;font-family:"굴림",sans-serif'><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:12.0pt;font-family:"굴림",sans-serif'>After then, I ran pe_utils, but I got the following error message:<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:12.0pt;font-family:"굴림",sans-serif'><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:12.0pt;font-family:"굴림",sans-serif;color:red'>File "/usr/local/bin/pe_utils", line 11, in <module><o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:12.0pt;font-family:"굴림",sans-serif;color:red'> sys.exit(main())<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:12.0pt;font-family:"굴림",sans-serif;color:red'> File "/usr/local/lib/python2.7/dist-packages/misopy/pe_utils.py", line 548, in main<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:12.0pt;font-family:"굴림",sans-serif;color:red'> sd_max=sd_max)<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:12.0pt;font-family:"굴림",sans-serif;color:red'> File "/usr/local/lib/python2.7/dist-packages/misopy/pe_utils.py", line 283, in compute_insert_len<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:12.0pt;font-family:"굴림",sans-serif;color:red'> mapped_bam = pysam.Samfile(mapped_bam_filename, "rb")<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:12.0pt;font-family:"굴림",sans-serif;color:red'> File "pysam/libcalignmentfile.pyx", line 401, in pysam.libcalignmentfile.AlignmentFile.__cinit__ (pysam/libcalignmentfile.c:5835)<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:12.0pt;font-family:"굴림",sans-serif;color:red'> File "pysam/libcalignmentfile.pyx", line 576, in pysam.libcalignmentfile.AlignmentFile._open (pysam/libcalignmentfile.c:7699)<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:12.0pt;font-family:"굴림",sans-serif;color:red'> File "pysam/libchtslib.pyx", line 331, in pysam.libchtslib.HTSFile.check_truncation (pysam/libchtslib.c:7195)<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:12.0pt;font-family:"굴림",sans-serif;color:red'>OSError: no BGZF EOF marker; file may be truncated<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:12.0pt;font-family:"굴림",sans-serif;color:red'><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:12.0pt;font-family:"굴림",sans-serif;color:black'>I tried to check the header using the following command, but found no difference.<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:11.5pt;font-family:"Arial",sans-serif;color:#222222'>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:'<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:11.5pt;font-family:"Arial",sans-serif;color:#222222'>samtools view -H /directories/insert-dist/bam2gff_Homo_sapiens.GRCh37.65.min_1000.const_exons.gff/control.bam<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:12.0pt;font-family:"굴림",sans-serif;color:black'><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:12.0pt;font-family:"굴림",sans-serif;color:black'>I don</span><span style='font-size:12.0pt;font-family:"굴림",sans-serif;color:black'>’<span lang=EN-US>t know what the problem is..<o:p></o:p></span></span></p></div></body></html>