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GenomeRIK / tama

Transcriptome Annotation by Modular Algorithms (for long read RNA sequencing data)
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Error, no groups found! #111

Open priyanka5795 opened 11 months ago

priyanka5795 commented 11 months ago

Hi Rik, I am using tama_collapse on small data (~400 reads) from nanopore sequencing and I see a lot of different transcripts. But when I used tama_collapse, it had a no groups found error. I don't understand that. My code- python2 $HOME/tama/tama_collapse.py -s $HOME/P2plas.sam -f $HOME/GRC39m.genome.fa -p tama

I used minimap to align.

Thanks! Priyanka

GenomeRIK commented 10 months ago

Hello Priyanka,

Could you copy paste a few lines form the SAM file?

Thank you, Richard

wangchi6748 commented 4 months ago

Hi Rechard， I am also using tama_collapse.py .I am using a bam file (output of minimap2),but I got the same error: tc_version_date_2023_03_28 Default collapse exon ends flag will be used: common_ends Default coverage: 99 Default identity: 85 Default identity calculation method: ident_cov Default 5 prime threshold: 10 Default exon/splice junction threshold: 10 Default 3 prime threshold: 10 Default splice junction priority: nopriority Default splice junction error threshold: 10 Default splice junction local density error threshold: 1000 Default simple error symbol for matches is the underscore "" . Using BAM format for reading in. Default log output on Default run mode original Default 5 read threshold time taken since last check: 0:0:0 time taken since beginning: 0:0:0 going through fasta time taken since last check: 0:3:12 time taken since beginning: 0:3:12 going through sam file 1 time taken since last check: 0:0:45 time taken since beginning: 0:3:57 going through groups: 0 Error, no groups found!

Here is some lines form the bam file: m64268e_240319_223038/140249903/ccs 0 Chr01A 59808 1 3S15=1I10=1X15=1I20=1I4=3I11=2I76=1I14=1I11=1I33=888N1=1I23=1I25=1I10=1I3=1I14=1I7=1I12=1I5=1I16=1I12=1I5=1I5=3I7=2I9=1I29=2I17=3I6=1I6=1I9=1I7=1I38=1I41=1I7=1I41=2I2=1I18=1I6=531N63=78N1I42=1I49=1I5=100N17=1I23=1I9=1I44=458N4=1I48=1I6=1I3=1I9=1I46=1I31=1I44=70N1I31=1I6=1I4=1I17=1I33=1I12=1I80=1I50=1I5=782N9=1I7=1I18=1I5=2I25=1I9=1I11=1I12=1724N7=1I10=1I3=1I8=1I53=134N11=1I17=1I5=1I16=2I38=1I18=2I6=1I4=1I27=2I10=1I19=1I9=1I17=1I36=1I9=1I20=1I13=1I15=1I14=1I4=1I81=1I43=1I7=1I23=123N1=1I8=1I11=1I23=1I9=1I10=1I14=1I62=1I7=1I19=1I46=1I7=1I3=1I9=1I9=2I32=1I14=73N28=1I13=1I9=1I8=1I16=1I14=86N28=1I6=1I33=2I12=1I19=1I20=1I4=1I11=1I21=1I24=1I8=1I14=1I4=169N4=1I11=1I10=1I32=2I41=2I10=1I15=1I4=1I5=1I18=1I18=1I8=3D19=1I4=1I11=1I2=1I13=1I10=1I11=1I29=1I15=1I11=1I6=1I3=1I6=1I14=1I27=1I9=1I19=1I28=2I22=1I2=1I3=1I4=1I12=1I13=1I8=1I8=1I1=1I13=1I16=1I21=1I21=1I6=1I4=2I32=1I17=1I10=1I2=1I11=1I8=1I16=2I3=1123N10=1I5=1I44=1I20=1I27=1I11=1I8=1I14=1I3=218N26=1I60=1I10=1I9=1I21=1I24=114N23=1I33=70N17=1I38=1I7=1I2=1I25=1I8=1I18=1I13=1I10=1I16=1I27=1I24=1I23=1I6=1I12=1I10=2I34=1I8=827N2=1I38=2I7=1I22=1I26=2I16=1I20=1I5=115N27=1I23=1I6=1740N16=1I18=2I31=3I7=2I20=1I6=1I26=1I11=1I17=1I10=1I11=1I28=1I22=1I10=985N1=1I4=1I71=1I17=1I14=1I97=87N1=1I22=1I24=1I14=1I29=1I47=1I20=1I41=1I5=1I7=1X1=1I12=1I45=2I11=1I5=2I23=1I12=1I17=1I5=2I9=1I3=1I11=2I4=1I11=1I17=1I27=1I7=665N17=1I8=2I16=1I12=1I6=1I4=1I5=1I25=1I16=2I29=1I7=1I9=1I9=2I7=1I25=1I3=1I17=1I24=1I47=1I3=1I62=1I13=1I11=1I48=1I1=3D46=1I7=1I37=1I44=1I23=1S * 0 16606 GGGGAATCGGACGAGCGTAAAAAGTTGAGAGGTCGAGAGCACTTATTTTCCTTCACTGAATTACGGTTTCATACTCCCGGCGTGGGCGCGCTCCTTCCCTCCCTCCCTCCCCCCCTCTCTCTCCCCCTCTTTCTGCGACGAACTGGGTGGGCTACCGCCGCCGCCCCTAAGCCAGGTGCCCAAGGCGAGGTTTGGTCTCTTCGCCGGCCACGAGCACCCACTAGTAAAAATAGTTAATGTATGCAAAGGATGGAACCAGATGTATTTCTGTAGAATGTAAATGATATTAACTACTAGATGATTAGAATATGAATTAAGGATGGAATAATTGTCCTGATGATAAGATGGCAAAAGATGGGATCTTGTTCAAACCAAACAATGGACGAAGCTAGTAGAATATAATAATCATTGACTCTCAAAGTGATGAGAAAATAAAATTTGTGTCTGGGAAACTTAGCATAAAGAGACAGTTTCCTTGAAAGGAGCATAAGGAGCCTCCATGCACAACAATGGACAACTAATGCGAATGAAGAAACATCCATTACTGATGATGATTCAGAAGGCCGATTTCATATGAATTCTCTCTCCGAGAATCAGATAATGAACAAGTATTCTCAGCATCCGAGGAAGGCAACTGAGGTACCTCTGACTGAGGAAGAAGTTGAAGAATTGGTTGCTGAATTCCTCGAAGTCGAGAGCAAAAGCAGCTCAAGCGCAAGAGTCACTTGAAAAGGAGTCACTGGACAAAAATTGAAACTGAAGTAAGATTGGAGTTATCTGAGAGGCTTCAAGGAGAATGAGTTAGAATCAGCTGTGTCAAACTGAGATGGAGCAATTCCAGATTGCAATGGGAAAAATGAACTTGATGATCTAGAGATCCGTAGTTCTATTCTGTTGGAACAAACTTGATGCTGCTGGAATTGAACTTCCCAGACTCTATAAGTCAATTGAAAAGTCAAAGTTTCCAAGTGTTTTGTGAAACTGAAGCATGGAAGAGCAGGACGCATTGGGCTGGTTCGTCAAGTGCCTGAAGAAGCTAACCGATCCATTAAAAAATGCTGATGAATACCTCCAGTCTTGCAGACCTGTACGGAGAAAAACACGGGAGGTTGCTGGAGGAAGGTGCTAAGTGGCTTTTCTTTGCTGGAAAAG

How can I solve the problem?Hope you can help me. Thank you! wangchi