[miso-users] error with miso run

[Fan Gao]

Dear MISO community,

I am a freshman to this software. Based on installation instruction, I installed MISO on my laptop that has been pre-installed with Ubuntu. I also installed bedtools and samtools as required.

I got the following error message when I tried to compute insert length. The bam file I used was from tophat.
Does anyone know what is the problem?

Thanks a lot.

Fan
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fan at fan-X45U:~/Meningiomas_RNAseq$ python ~fan/yarden-MISO-4f32ca4/misopy/pe_utils.py --compute-insert-len 010_bam/010_accepted_hits.bam /home/fan/Downloads/exon_hg19/Homo_sapiens.GRCh37.65.min_1000.const_exons.gff --output-dir 010_insert-dist/
Computing insert length distribution of 1 files:
  /home/fan/Meningiomas_RNAseq/010_bam/010_accepted_hits.bam
  - Using const. exons from: /home/fan/Downloads/exon_hg19/Homo_sapiens.GRCh37.65.min_1000.const_exons.gff
  - Outputting to: /home/fan/Meningiomas_RNAseq/010_insert-dist
  - Minimum exon size used: 500
Making directory: /home/fan/Meningiomas_RNAseq/010_insert-dist
Getting constitutive exons...
  - Input GFF: /home/fan/Downloads/exon_hg19/Homo_sapiens.GRCh37.65.min_1000.const_exons.gff
  - Output dir: /home/fan/Meningiomas_RNAseq/010_insert-dist
  - Output format: gff
  - Including only exons greater than or equal to 500-bp
Constitutive exons GFF was given, so not outputting another one.
Filtering BAM reads
Fetching reads in constitutive exons
Mapping BAM to GFF...
  - BAM: /home/fan/Meningiomas_RNAseq/010_bam/010_accepted_hits.bam
  - GFF: /home/fan/Downloads/exon_hg19/Homo_sapiens.GRCh37.65.min_1000.const_exons.gff
  - Output file: /home/fan/Meningiomas_RNAseq/010_insert-dist/bam2gff_Homo_sapiens.GRCh37.65.min_1000.const_exons.gff/010_accepted_hits.bam
Preparing to call bedtools 'tagBam'
tagBam -i /home/fan/Meningiomas_RNAseq/010_bam/010_accepted_hits.bam -files /home/fan/Downloads/exon_hg19/Homo_sapiens.GRCh37.65.min_1000.const_exons.gff -labels gff -intervals -f 1 | samtools view -h - | egrep '^@|:gff:' | samtools view -Shb -o /home/fan/Meningiomas_RNAseq/010_insert-dist/bam2gff_Homo_sapiens.GRCh37.65.min_1000.const_exons.gff/010_accepted_hits.bam - 
[samopen] SAM header is present: 25 sequences.
[sam_read1] reference 'ID:TopHat	CL:/home/fangao/tophat-2.0.4.Linux_x86_64/tophat -p 12 -o CGATGT_fusion_new2 --solexa1.3-quals --fusion-search --bowtie1 /home/fangao/seqlib/bowtie_index_hg19/hg19 s_1_1_CGATGT_sequence.txt s_1_2_CGATGT_sequence.txt	VN:2.0.4
' is recognized as '*'.
[main_samview] truncated file.
Traceback (most recent call last):
  File "/home/fan/yarden-MISO-4f32ca4/misopy/pe_utils.py", line 528, in <module>
    main()
  File "/home/fan/yarden-MISO-4f32ca4/misopy/pe_utils.py", line 525, in main
    sd_max=sd_max)
  File "/home/fan/yarden-MISO-4f32ca4/misopy/pe_utils.py", line 272, in compute_insert_len
    output_dir)
  File "/usr/local/lib/python2.7/dist-packages/misopy/exon_utils.py", line 187, in map_bam2gff
    raise Exception, "Error: tagBam call failed."
Exception: Error: tagBam call failed.

**************************************************
Fan Gao, Ph.D
Research Associate
Zilkha Neurogenetic Institute 
Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research
Keck School of Medicine
University of Southern California
1425 San Pablo Street, BCC 409B
Los Angeles, CA 90089
United States
Phone: 323-442-2497
Email: gaof at usc.edu
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