[miso-users] miso file format
mykhwab
mykhwab at gmail.com
Thu Dec 20 22:05:14 EST 2012
Bam file …............
FCC16UKACXX:6:1101:15756:2521#TATTCGCG 77 * 0 0 * * 0 0
CGGGCATTGAGAAGGAAGGACGCTTTCAGAGGCGAAAGGCCATGGGGAGATACCGTCTGTGATCCATGGATCTCCGATCGGGAAACCGTA
CCCFFFFFHFHGHJJIIIGIJJJJJIIJIJIIGDDHHIGEIJJJJIHHFFDBCCCBBDDDDECDDDDDCDDDDDD>BDDDD3<BBCDDBB
XM:i:0
FCC16UKACXX:6:1101:15756:2521#TATTCGCG 141 * 0 0 * * 0 0
GCCGCTACTAACGGGGTCTCGGTTGATTTCCCTTCCTTTAGCTACTTAGATGTTTCAGTTCGCTAAGTTTTCAAAGTCCAAAGAGCGCAG
CCCFFFFFHHHHHIGIGGGIIJ;FHHEGIIGI>EGIIJIEGG at HIICGGB@>C9FHIEHGIJHHFBFCDFEEDCC;;>CDDADDDDDDDB
XM:i:0
FCC16UKACXX:6:1101:15886:2524#TATTCGCG 163 AT2G34420.1 458 255 90M = 573
205
CAGATCTTCAGCGACGGAGGATTGGACTACTTGGGCAACCCGAGCTTGGTCCACGCTCAGAGCATCTTAGCCATTTGGGCTACTCAAGTT
C at CFFFFFHHHGFIGIIEHIGIIIGIJJJJJJIGGIJJCHIGBAEFHHFCDFFEDD
:BDCDDCDDDDDEDCDDDDDACDDCBCCCC>A at A XA:i:0 MD:Z:90 NM:i:0
FCC16UKACXX:6:1101:15886:2524#TATTCGCG 83 AT2G34420.1 573 255 90M = 458
-205
ACAGAGTCGCCGGAGATGGTCCATTGGGAGAAGCAGAGGACTTGCTTTACCCAGGTGGCAGCTTCGACCCATTGGGCCTCGCTACTGACC
CACDDDDDDDDDDDCDBDDDDDECC@
>7DFFFCCGHHHHEDGGHAGGF at JIEHHIGIGIIGHIGIHHJIIJJJIJJJHHHHDEEFFFCCB XA:i:0
MD:Z:90 NM:i:0
FCC16UKACXX:6:1101:15872:2533#TATTCGCG 99 AT4G30950.1 1027 255 90M = 1154
217
GGTAAAATTCTGGTTAATGCCATGGTTGGGCTATCACTTCTGGATGAGCACATTCACAATGGTTCATCATACGGCTCCGCATATACCTTT
CC at FFFDFGHGHHEHHJIGIGGCGIFFGIIFCHIGGIGHCGEHIIGHGHEDBFHHEGICGHE@FHIJIGEIJGGEE?D8=A8=@C>@CCD
XA:i:0 MD:Z:90 NM:i:0
FCC16UKACXX:6:1101:15872:2533#TATTCGCG 147 AT4G30950.1 1154 255 90M = 1027
-217
CTGAATGGAACTGTTCATTGTGACTACCCTAGTTGGATTGAAATTCTCTGCCATGATATCAACGTTCACATCCCGCATCATATTAGCCCA
:ABBB>@@3CA>A@;:CEFEBDEDHC;EJJGIHEGHHIIGD at 9GFDFGGEB<EIG@>EB at GGEGIGFF
;ADGGGBHGBFAHFDAEBB@?? XA:i:0 MD:Z:90 NM:i:0
FCC16UKACXX:6:1101:15953:2595#TATTCGCG 163 AT4G38040.1 21 255 90M = 122
191
GCAAAAAGAGCTAAATGCAGAGAGCTTCAGATCCGACCAAACAATGACGATCGTTAAACCGTCGCAGTTCTCATTCTCCGGCGGCGGATC
B@@DDDFFD?FFDGGGIJIEHGIGIIIJJGJIJGICGGGHIJGEDACGIIGIIGIGEHAHHFFDDD>=CCCCDEEEDCDDBD9>BB>599
XA:i:0 MD:Z:90 NM:i:0
+++++++++++++++++++++++++++++++++++++++++++++++++++
GFF.........
chr1 TAIR10 chromosome 1 30427671 . . . ID=chr1;Name=chr1
chr1 TAIR10 gene 3631 5899 . + .
ID=AT1G01010;Note=protein_coding_gene;Name=AT1G01010
chr1 TAIR10 mRNA 3631 5899 . + .
ID=AT1G01010.1;Parent=AT1G01010;Name=AT1G01010.1;Index=1
chr1 TAIR10 protein 3760 5630 . + .
ID=AT1G01010.1-Protein;Name=AT1G01010.1;Derives_from=AT1G01010.1
chr1 TAIR10 exon 3631 3913 . + . Parent=AT1G01010.1
chr1 TAIR10 five_prime_UTR 3631 3759 . + . Parent=AT1G01010.1
chr1 TAIR10 CDS 3760 3913 . + 0 Parent=AT1G01010.1,AT1G01010.1-Protein;
chr1 TAIR10 exon 3996 4276 . + . Parent=AT1G01010.1
chr1 TAIR10 CDS 3996 4276 . + 2 Parent=AT1G01010.1,AT1G01010.1-Protein;
chr1 TAIR10 exon 4486 4605 . + . Parent=AT1G01010.1
chr1 TAIR10 CDS 4486 4605 . + 0 Parent=AT1G01010.1,AT1G01010.1-Protein;
chr1 TAIR10 exon 4706 5095 . + . Parent=AT1G01010.1
chr1 TAIR10 CDS 4706 5095 . + 0 Parent=AT1G01010.1,AT1G01010.1-Protein;
chr1 TAIR10 exon 5174 5326 . + . Parent=AT1G01010.1
chr1 TAIR10 CDS 5174 5326 . + 0 Parent=AT1G01010.1,AT1G01010.1-Protein;
chr1 TAIR10 exon 5439 5899 . + . Parent=AT1G01010.1
chr1 TAIR10 CDS 5439 5630 . + 0 Parent=AT1G01010.1,AT1G01010.1-Protein;
chr1 TAIR10 three_prime_UTR 5631 5899 . + . Parent=AT1G01010.1
chr1 TAIR10 gene 5928 8737 . - .
ID=AT1G01020;Note=protein_coding_gene;Name=AT1G01020
chr1 TAIR10 mRNA 5928 8737 . - .
ID=AT1G01020.1;Parent=AT1G01020;Name=AT1G01020.1;Index=1
chr1 TAIR10 protein 6915 8666 . - .
ID=AT1G01020.1-Protein;Name=AT1G01020.1;Derives_from=AT1G01020.1
chr1 TAIR10 five_prime_UTR 8667 8737 . - . Parent=AT1G01020.1
chr1 TAIR10 CDS 8571 8666 . - 0 Parent=AT1G01020.1,AT1G01020.1-Protein;
chr1 TAIR10 exon 8571 8737 . - . Parent=AT1G01020.1
chr1 TAIR10 CDS 8417 8464 . - 0 Parent=AT1G01020.1,AT1G01020.1-Protein;
chr1 TAIR10 exon 8417 8464 . - . Parent=AT1G01020.1
chr1 TAIR10 CDS 8236 8325 . - 0 Parent=AT1G01020.1,AT1G01020.1-Protein;
chr1 TAIR10 exon 8236 8325 . - . Parent=AT1G01020.1
chr1 TAIR10 CDS 7942 7987 . - 0 Parent=AT1G01020.1,AT1G01020.1-Protein;
chr1 TAIR10 exon 7942 7987 . - . Parent=AT1G01020.1
chr1 TAIR10 CDS 7762 7835 . - 2 Parent=AT1G01020.1,AT1G01020.1-Protein;
,++++++++++++++++++++++++++++++++++++++++++++
On Fri, Dec 21, 2012 at 12:00 PM, Yarden Katz <yarden at mit.edu> wrote:
> I still need to see parts of the original GFF and parts of the BAM (i.e.
> "samtools view yourfile.bam | head -n 20") to see what is going on. It
> still looks like a headers mismatch.
>
> --Yarden
>
>
>
>
> On Dec 20, 2012, at 9:55 PM, mykhwab wrote:
>
> > yes Yarden you are right, I changed the Chr to chr. but got another
> issue. :(
> >
> > I am also attaching a file...
> > .......................................................
> > Loading settings from:
> /usr/local/lib/python2.7/dist-packages/misopy/settings/miso_settings.txt
> > Settings:
> > filter_results True
> > min_event_reads 20
> > cluster_command qsub
> > long_queue_name long
> > short_queue_name quick
> > burn_in 500
> > lag 10
> > num_iters 5000
> > num_chains 6
> > Computing Psi for 1 genes...
> > - AT3G15020
> > - GFF filename:
> /BiO2/ilyas/Fahim/misopy-0.4.6/misopy/indexed_SE_events/chr3/AT3G15020.pickle
> > - BAM:
> /BiO2/ilyas/Fahim/Data/F12FTSAPHK0171_ARAtitT/bam/Col-O.gene.sorted.bam
> > - Outputting to: /BiO2/ilyas/Fahim/misopy-0.4.6/misopy/fahim_output1
> > Loading genes from indexed GFF...
> > - Loading took: 0.00 seconds
> > Loading BAM filename from:
> /BiO2/ilyas/Fahim/Data/F12FTSAPHK0171_ARAtitT/bam/Col-O.gene.sorted.bam
> > Loading took 0.07 seconds
> > Cannot fetch reads in region: 3:5056068-5058248
> > Only 0 reads in gene, skipping (needed >= 20 reads)
> > - Executing: python /BiO2/ilyas/Fahim/misopy-0.4.6/misopy/run_miso.py
> --compute-gene-psi "AT5G01650"
> "/BiO2/ilyas/Fahim/misopy-0.4.6/misopy/indexed_SE_events/chr5/AT5G01650.pickle"
> /BiO2/ilyas/Fahim/Data/F12FTSAPHK0171_ARAtitT/bam/Col-O.gene.sorted.bam
> /BiO2/ilyas/Fahim/misopy-0.4.6/misopy/fahim_output1 --read-len 36
> --overhang-len 1 --settings-filename
> /usr/local/lib/python2.7/dist-packages/misopy/settings/miso_settings.txt
> >
> >
> > Regards
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > On Fri, Dec 21, 2012 at 11:38 AM, Yarden Katz <yarden at mit.edu> wrote:
> > Could you please show the first 10-20 lines of your GFF and the first
> 10-20 lines of your BAM file? That will help tell what is happening.
> >
> > It sounds like a mismatch between the GFF chromosome naming conventions
> and the BAM file.
> > When you index GFFs, miso adds a "chr" prefix to directories if they
> don't have it already.
> >
> > Since it created "fahim_events/chrChr2", it means that your chromosome
> in the GFF is named "Chr2" (note capital C). Your BAMs were most likely
> not aligned to a genome where the chromosomes are named this way. If
> "Chr2" is really "chr2" or "2" in your BAM, then that could generate the
> error.
> >
> > The current version in GitHub has more elaborate error checking so it
> catches this and produces a more reasonable error, but the latest stable
> version of MISO does not.
> >
> > --Yarden
> >
> > On Dec 20, 2012, at 11:09 AM, mykhwab wrote:
> >
> > > Thank you Yarden,
> > >
> > > here is the next problem :) Can you please tell me what is the
> possible solution...
> > >
> > > Loading settings from:
> /usr/local/lib/python2.7/dist-packages/misopy/settings/miso_settings.txt
> > > Settings:
> > > filter_results True
> > > min_event_reads 20
> > > cluster_command qsub
> > > long_queue_name long
> > > short_queue_name quick
> > > burn_in 500
> > > lag 10
> > > num_iters 5000
> > > num_chains 6
> > > Computing Psi for 1 genes...
> > > - AT2G43010
> > > - GFF filename:
> /BiO2/ilyas/Fahim/misopy-0.4.6/misopy/fahim_events/chrChr2/AT2G43010.pickle
> > > - BAM:
> /BiO2/ilyas/Fahim/Data/F12FTSAPHK0171_ARAtitT/bam/Col-O.gene.bam
> > > - Outputting to: /BiO2/ilyas/Fahim/misopy-0.4.6/misopy/fahim_out1
> > > Loading genes from indexed GFF...
> > > - Loading took: 0.00 seconds
> > > Loading BAM filename from:
> /BiO2/ilyas/Fahim/Data/F12FTSAPHK0171_ARAtitT/bam/Col-O.gene.bam
> > > Loading took 0.02 seconds
> > > Traceback (most recent call last):
> > > File "/BiO2/ilyas/Fahim/misopy-0.4.6/misopy/run_miso.py", line 615,
> in <module>
> > > main()
> > > File "/BiO2/ilyas/Fahim/misopy-0.4.6/misopy/run_miso.py", line 564,
> in main
> > > event_type=options.event_type)
> > > File "/BiO2/ilyas/Fahim/misopy-0.4.6/misopy/run_miso.py", line 310,
> in compute_gene_psi
> > > gene_obj)
> > > File "/usr/local/lib/python2.7/dist-packages/misopy/sam_utils.py",
> line 211, in fetch_bam_reads_in_gene
> > > chrom = chrom.split("chr")[1]
> > > IndexError: list index out of range
> > > - Executing: python
> /BiO2/ilyas/Fahim/misopy-0.4.6/misopy/run_miso.py --compute-gene-psi
> "AT1G49040"
> "/BiO2/ilyas/Fahim/misopy-0.4.6/misopy/fahim_events/chrChr1/AT1G49040.pickle"
> /BiO2/ilyas/Fahim/Data/F12FTSAPHK0171_ARAtitT/bam/Col-O.gene.bam
> /BiO2/ilyas/Fahim/misopy-0.4.6/misopy/fahim_out1 --read-len 36
> --overhang-len 1 --settings-filename
> /usr/local/lib/python2.7/dist-packages/misopy/settings/miso_settings.txt
> > >
> > >
> > >
> > > Regards
> > >
> > >
> > >
> > > On Thu, Dec 20, 2012 at 1:36 PM, Yarden Katz <yarden at mit.edu> wrote:
> > > It sounds like your cluster system does not support the queue name
> "long". You can change that in your MISO settings file, under the
> "[cluster]" section, to be a valid queue name. The queue names are system
> specific so you'll have to find out what yours are.
> > >
> > > --Yarden
> > >
> > >
> > >
> > >
> > > On Dec 19, 2012, at 11:33 PM, mykhwab wrote:
> > >
> > > >
> > > >
> > > > Dear MISO
> > > >
> > > > I am trying to make sashimi plot using Arabidopsis genome.
> > > > but i am acing problem in making .miso files.
> > > > i can run the test data for making plot but even not able to make
> .miso for test data.
> > > > what could be the possible reason.?
> > > >
> > > > when i run this command
> > > >
> > > > python run_events_analysis.py --compute-genes-psi indexed_SE_events/
> my_sample1.bam --output-dir my_output1/ --read-len 36 --use-cluster
> > > >
> > > >
> > > >
> > > > the errors.....
> > > >
> > > >
> > > > Running batch 39 (batch size = 199)
> > > > Submitting job: gene_psi_batch_39
> > > > Loading settings from:
> /usr/local/lib/python2.7/dist-packages/misopy/settings/miso_settings.txt
> > > > Settings:
> > > > filter_results True
> > > > min_event_reads 20
> > > > cluster_command qsub
> > > > long_queue_name long
> > > > short_queue_name quick
> > > > burn_in 500
> > > > lag 10
> > > > num_iters 5000
> > > > num_chains 6
> > > > cls.global_settings: {'cluster_command': 'qsub', 'filter_results':
> True, 'num_iters': 5000, 'lag': 10, 'long_queue_name': 'long', 'burn_in':
> 500, 'num_chains': 6, 'short_queue_name': 'quick', 'min_event_reads': 20}
> > > > - queue: long, using queue name long
> > > > Unable to run job: Colon (':') not allowed in objectname
> > > > Job was rejected because job requests unknown queue "long".
> > > > Exiting.
> > > > _______________________________________________
> > > > miso-users mailing list
> > > > miso-users at mit.edu
> > > > http://mailman.mit.edu/mailman/listinfo/miso-users
> > >
> > >
> >
> >
> > <files.doc>
>
>
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