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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