search

GoekeLab / xpore

Identification of differential RNA modifications from nanopore direct RNA sequencing
https://xpore.readthedocs.io/
MIT License
137 stars 23 forks source link

DataPrep error and empty output files #222

Open cent0134 opened 4 months ago

cent0134 commented 4 months ago

Hello I kept receiving error messages and empty output files (data_idex data.json、data.log、data.readcount eventalign.index）。 After I finish running xpore dataprep --eventalign reads-ref.eventalign.txt --gtf_or_gff NL4-3.gtf --transcript_fasta NL4-3.fa --out_dir dataprep --genome_，an error warning appeared，This is the complete error repot；

xpore dataprep --eventalign reads-ref.eventalign.txt --gtf_or_gff NL4-3.gtf --transcript_fasta NL4-3.fa --out_dir dataprep --genome /home/dell/miniconda3/envs/xpore/lib/python3.12/site-packages/xpore/scripts/dataprep.py:72: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy chunk_split['line_length'] = np.array(lines)

These are my ref fasta, gtf ，and eventalign file。

gtf；AF003887 GenBank transcript 790 2292 . + . transcript_id "gag_t01"; gene_id "gag" AF003887 GenBank exon 790 2292 . + . transcript_id "gag_t01"; gene_id "gag"; AF003887 GenBank CDS 790 2292 . + 0 transcript_id "gag_t01"; gene_id "gag"; AF003887 GenBank transcript 2358 5096 . + . transcript_id "pol_t01"; gene_id "pol" AF003887 GenBank exon 2358 5096 . + . transcript_id "pol_t01"; gene_id "pol"; AF003887 GenBank CDS 2358 5096 . + 0 transcript_id "pol_t01"; gene_id "pol"; AF003887 GenBank transcript 5041 5619 . + . transcript_id "vif_t01"; gene_id "vif" AF003887 GenBank exon 5041 5619 . + . transcript_id "vif_t01"; gene_id "vif"; AF003887 GenBank CDS 5041 5619 . + 0 transcript_id "vif_t01"; gene_id "vif"; AF003887 GenBank transcript 5559 5849 . + . transcript_id "vpr_t01"; gene_id "vpr" AF003887 GenBank exon 5559 5849 . + . transcript_id "vpr_t01"; gene_id "vpr"; AF003887 GenBank CDS 5559 5849 . + 0 transcript_id "vpr_t01"; gene_id "vpr"; AF003887 GenBank transcript 5830 8489 . + . transcript_id "tat_t01"; gene_id "tat" AF003887 GenBank exon 5830 6044 . + . transcript_id "tat_t01"; gene_id "tat"; AF003887 GenBank exon 8399 8489 . + . transcript_id "tat_t01"; gene_id "tat"; AF003887 GenBank CDS 5830 6044 . + 0 transcript_id "tat_t01"; gene_id "tat"; AF003887 GenBank CDS 8399 8489 . + 1 transcript_id "tat_t01"; gene_id "tat"; AF003887 GenBank transcript 5969 8673 . + . transcript_id "rev_t01"; gene_id "rev" AF003887 GenBank exon 5969 6044 . + . transcript_id "rev_t01"; gene_id "rev"; AF003887 GenBank exon 8399 8673 . + . transcript_id "rev_t01"; gene_id "rev"; AF003887 GenBank CDS 5969 6044 . + 0 transcript_id "rev_t01"; gene_id "rev"; AF003887 GenBank CDS 8399 8673 . + 2 transcript_id "rev_t01"; gene_id "rev"; AF003887 GenBank transcript 6224 8815 . + . transcript_id "env_t01"; gene_id "env" AF003887 GenBank exon 6224 8815 . + . transcript_id "env_t01"; gene_id "env"; AF003887 GenBank CDS 6224 8815 . + 0 transcript_id "env_t01"; gene_id "env"; AF003887 GenBank transcript 8817 9437 . + . transcript_id "nef_t01"; gene_id "nef" AF003887 GenBank exon 8817 9437 . + . transcript_id "nef_t01"; gene_id "nef"; AF003887 GenBank CDS 8817 9437 . + 0 transcript_id "nef_t01"; gene_id "nef";

ref fasta；

AF003887 TGGAAGGGCTAATTTGGTCCCAAAAAAGACAAGAGATCCTTGATCTGTGG ATCTACCACACACAAGGCTACTTCCCTGATTGGCAGAACTACACACCAGG GCCAGGGATCAGATATCCACTGACCTTTGGATGGTGCTTCAAGTTAGTAC CAGTTGAACCAGAGCAAGTAGAAGAGGCCAAATAAGGAGAGAAGAACAGC TTGTTACACCCTATGAGCCAGCATGGGATGGAGGACCCGGAGGGAGAAGT ATTAGTGTGGAAGTTTGACAGCCTCCTAGCATTTCGTCACATGGCCCGAG AGCTGCATCCGGAGTACTACAAAGACTGCTGACATCGAGCTTTCTACAAG GGACTTTCCGCTGGGGACTTTCCAGGGAGGTGTGGCCTGGGCGGGACTGG GGAGTGGCGAGCCCTCAGATGCTACATATAAGCAGCTGCTTTTTGCCTGT ACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTA ACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTCA AAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTC AGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCAGTGGCGCCCGAACAGG GACTTGAAAGCGAAAGTAAAGCCAGAGGAGATCTCTCGACGCAGGACTCG GCTTGCTGAAGCGCGCACGGCAAGAGGCGAGGGGCGGCGACTGGTGAGTA CGCCAAAAATTTTGACTAGCGGAGGCTAGAAGGAGAGAGATGGGTGCGAG AGCGTCAGTATTAAGCGGGGGAGAATTAGATAGATGGGAAAAAATTCGGC TAAGGCCAGGGGGAAAGAAAAAATATAAATTAAAACATATAGTATGGGCA AGCAGGGAGCTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATC AGAAGGCTGTAGACAAATACTGGGACAGCTACAACCAGCCCTCCAGACAG GATCAGAAGAACTTAGATCATTACATAATACAGTAGCAGTCCTCTATTGT GTGCATCAAAGGATAGAGGTAAAAGACACCAAGGAAGCTTTAGAGAAAAT AGAGGAAGAGCAAAACAAAAGTAAGAAAACAGCACAGCAAGCAGCAGCTG ACACAGGAAACAGCAACAAGGTCAGCCAAAATTACCCTATAGTGCAGAAC ATCCAGGGGCAAATGGTACATCAGGCCATATCACCTAGAACTTTAAATGC ATGGGTAAAAGTAGTAGAAGAGAAGGCTTTTAGCCCAGAAGTAATACCCA TGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATG CTAAACACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGAGAC CATCAATGAGGAAGCTGCAGAATGGGATAGATTGCATCCAGTGCAGGCAG GGCCTGTCGCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCA GGAACTACTAGTACCCTTCAGGAACAAATAGGATGGATGACAAATAATCC ACCTATCCCAGTAGGAGAAATCTATAAAAGATGGATAATCCTGGGATTAA ATAAAATAGTAAGGATGTATAGCCCTGCCAGCATTCTGGACATAAGACAA GGACCAAAGGAACCCTTTAGAGATTATGTAGACCGGTTCTATAAAACTCT AAGAGCCGAGCAAGCTTCACAGGAGGTAAAAAATTGGATGACAGAAACCT TGTTGGTCCAAAATTCGAACCCAGATTGTAAGACTATTTTAAAAGCATTG GGACCAGCAGCTACACTAGAAGAAATGATGACAGCATGTCAGGGAGTGGG AGGACCCAGCCATAAAGCAAGAGTTTTGGCTGAAGCAATGAGCCAAGCAA CAAATGCAGCTACCATAATGATGCAGAGAGGCAATTTTAGGAATCAAAGA AAGATTGTTAAATGTTTTAATTGTGGCAAAGAAGGGCACATAGCCAGGAA TTGCAGGGCTCCTAGGAAAAAGGGCTGTTGGAAATGTGGAAAGGAAGGAC ACCAAATGAAAGATTGTACTGAGAGACAGGCTAATTTTTTAGGGAAGATC TGGCCTTCCTACAAGGGAAGGCCAGGGAATTTTCTTCAGAGCAGACCAGA GCCAACAGCCCCACCAGAAGAGAGCTTCAGGTTTGGGGAGGAGACAACAA CTCCCTCTCAGAAGCAGGAGCCGATAGACAAGGAACTGTATCCTTTAGCT TCCCTCAGATCACTCTTTGGCAACGACCCCTCGTCAAAGTAAAGATAGGG GGGCAACTAAAGGAAGCTCTATTAGATACAGGAGCAGATGATACAGTATT AGAAGAAATGAATTTGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAA TTGGAGGTTTTATCAAAGTAAGACAGTATGATCAGGTACTTGTAGAAATC TGTGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACACCCGTCAA CATAATTGGAAGAAATCTGTTGACTCAGATTGGTTGCACTTTAAATTTTC CCATTAGTCCTATTGAAACTGTACCAGTAAAATTAAAGCCAGGAATGGAT GGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAGGCATT AGTAGAAATTTGTACAGAAATGGAAAAAGAAGGGAAAATTTCAAAAATTG GGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGAC AGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAAC TCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAA AAAAGAAAAAATCAGTAACAGTATTGGATGTGGGTGATGCATATTTTTCA GTTCCCTTAGATAAAGACTTCAGAAAGTATACTGCATTTACCATACCTAG TACAAACAATGAGACACCAGGGATTAGGTATCAGTACAATGTGCTTCCAC AGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAGAATC TTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACAT GGATGATTTGTATGTAGGATCTGACTTAGAGATAGGGCAGCATAGAACAA AAATAGAGGAACTGAGGCAACATCTGTTGAGATGGGGATTTACCACACCA GACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACT CCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGACA GCTGGACTGTCAATGACATACAGAAGTTAGTGGGAAAATTAAATTGGGCA AGTCAGATCTACGCAGGGATTAAAGTAAAGCAATTATGTAAACTCCTCAG GGGAGCCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAGC TAGAACTGGCAGAAAACAGGGAGATTTTAAAAGAACCAGTACATGGAGTG TATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCA GGGCCAATGGACATATCAAATTTATCAAGAGCCATATAAAAATCTGAAAA CAGGAAAATATGCAAGAATGAGGGGTGCCCACACTAATGATGTTAAACAA TTAACAGAGGCAGTGCAAAAAATAGCCACAGAAAGCATAGTAATATGGAG AAAGATTCCTAAATTTAAACTACCCATACAAAGAGAAACATGGGAAACAT GGTGGATAGAGTATTGGCAAGCAACCTGGATTCCTGAGTGGGAGTATGTC AATACCCCTCCCTTAGTAAAATTATGGTACCAGTTAGAGAAAGAACCCAT AGTAGGAGCAGAAACTTTCTATGTAGATGGGGCAGCTAACAGAGAAACTA AATTAGGAAAAGCAGGATATGTTACTGACAGAGGAAGACAAAAAGTTGTC TCCCTAAGTGACACAACAAATCAGAAAACTGAGTTACAAGCAATTCATCT AGCTTTGCAGGATTCGGGCTTAGAAGTAAACATAGTAACAGACTCACAAT ATGCATTAGGAATCATTCAAGCACAACCAGATAAAAGTGAATCAGAGTTA GTCAGTCAAATAATAGAGCAGTTAATAAAAAAGGAAAAGGTCTACCTGGC ATGGGTACCAGCACACAAAGGAATTGGAGGAAATGAACAAGTAGATAAAT TAGTCAGTGCTGGAATCAGGAAAGTACTATTTTTAGATGGAATAGATAAG GCCCAAGAAGAACATGAGAAATATCACAGTAATTGGAGAGCAATGGCTGG TGATTTTAACCTGCCACCTGTAGTAGCAAAAGAAATAGTAGCCTGCTGTG ATAAATGTCAGCTAAAAGGAGAAGCCATGCATGGACAAGTAGACTGTAGT CCAGGAATATGGCAACTAGATTGTACACATTTAGAAGGAAAAGTTATCCT GGTAGCAGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTCATTCCAG CAGAGACAGGGCAGGAAACAGCATACTTTCTCTTAAAATTAGCAGGAAGA TGGCCAGTAAAAACAATACATACAGATAATGGCAGCAATTTCACCAGTAC TACAGTTAAGGCTGCTTGTTGGTGGGCAGGGATCAAGCAGGAATTTGGCA TTCCCTACAATCCCCAAAGTCAAGGAGTAGTAGAATCTATGAATAAAGAA TTAAAGAAAATTATAGGACAGGTAAGAGATCAGGCTGAACATCTTAAGAC AGCAGTCCAAATGGCAGTATTCATCCACAATTTTAAGAGAAAAGGGGGGA TTGGGGGGTACAGTGCAGGGGAAAGAATAGTAGACATAATAGCAACAGAC ATACAAACTAAAGAATTACAAAAACACATTACAAAGATTCAAAATTTTCG GGTTTATTACAGGGACAGCAGAGATCCACTTTGGAAAGGACCAGCAAAGC TTCTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACATA AAAGTAGTGCCAAGAAGAAAAGCAAAGATCATTAGGGATTATGGAAAACA GATGGCAGGTGAAGATTGTGTGGCAAGTAGACAGGATGAGGATTAGAACA TGGAAAAGTTTAGTAAAGCACCATATGTATGTTTCAGGGAAAGCCAAGAA ATGGTTTTATAGACATCACTATGAAAGCACTCATCCTAGAATAAGTTCAG AAGTGCACATCCCACTAGGAGATGCTAATTTGGTAATAACAACATATTGG GGTCTGCATTCAGGAGAAAGAGACTGGCATTTGGGCCAGGGAGTCTCCAT AGAATGGAGGAAAAAGAGATATAGCACACAAGTAGACCCTGGCCTAGCAG ACCAACTAATTCATCTGTATTATTTTGATTGTTTTTCAGAATCTGCTATA AGAAATGCCATATTAGGACATAGAGTTAGTCCTAGTTGTGAATATCAAGC AGGACATAACAAGGTAGGATCTCTACAATACTTGGCACTAGTTGCATTAG TAGCACCAAAAAAGATAAAGCCACCTTTGCCTAGTGTTACGAAACTGACA GAGGATAGATGGAACAAGCCCCAGAAGACCAAGGGCCACAGAGGGAGCCA TACAATGAATGGACACTAGAGCTTTTAGAGGAGCTTAAGAGTGAAGCTGT TAGACATTTTCCTAGGTTATGGCTCCATAGCTTAGGACAACATATCTATG AAACTTATGGGGATACTTGGGCAGGAGTGGAAGCCATAATAAGAATTCTG CAACAACTGCTGTTTATTCATTTCAGAATTGGGTGTCGACATAGCAGAAT AGGCATAATTCGACAGAGGAGAGCAAGAAATGGAGCCAGTAGATCCTAGC CTAGAGCCCTGGAAGCATCCAGGAAGTCAGCCTAAAACTGCTTGTACCAA TTGCTATTGTAAATATTGTTGCCTTCATTGCCAAGTTTGTTTCACAAGAA AAGGCTTAGGCATCTCCTATGGCAGGAAGAAGCGGAGACAGCGACGAAGA GCTCCTCAAGACAGTCAGACTCATCAAGTTTCTCTATCAAAGCAGTAAGT AGTACATGTAATGCAACCTTTAGAAATATTAGCAATAGTAGCATTAGTAG TAGCAGCAATAATAGCAATAGTTGTGTGGACCATAGTATTTATAGAATAT AGGAAAATATTAAGACAAAGAAAGATAGACAGGTTAATTGATAGAATAAG AGAAAGAGCAGAAGACAGTGGCAATGAAAGCGAAGGGGACCAGGAAGAAT TATCAGCACTTGTGGAGATGGGGCATCACGCTCCTTGGAATGTTGATGAT CTGTAGTGTTGCAGAACAATGGTGGGTCACAGTCTATTATGGGGTACCTG TGTGGAAAGAAGCAACCACCACTCTATTTTGTGCATCAGATGCTAAGGCA TATGATACAGAGGTGCATAATGTTTGGGCCACACATGCCTGTGTACCCAC AGACCCCAACCCACAAGAAGTAGTATTGAGAAATGTGACAGAAAATTTTA ACATGTGGAAAAATAACATGGTAGAACAGATGCATGAGGATATAATCAGT TTATGGGATCAAAGTCTAAAGCCATGTGTAAAATTAACCCCACTCTGTGT TACTCTAAATTGCACTGATAACTTAAAAAATGCTACTGTAAATAATGCTA ATAATACCAATAATAGTAGCTGGGAAAAGATGGAGAAAGGAGAAATAAAA AACTGCTCTTTCAATATCACCACTAGCATAAGAGATAAGGTGCAGAAAGA ATATGCACTTTTTTATAAACTTGATGTAGTACCAATAGATAATGCTAATA ATAGTAATGCTACTAACTATACCAGCTATAGATTGATAAGTTGTAACACC TCAGTCATTACACAGGCCTGTCCAAAGGTATCCTTTGAGCCAATTCCTAT ACATTATTGTGCCCCGGCTGGTTTTGCGATTCTAAAGTGTAATGATAAGA AGTTCAATGGAACAGGACCATGTACAAATGTCAGTACGGTACAATGTACA CATGGAATTAGGCCAGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCT AGCAGAAGAGGAGGTAGTAATTAGATCTGAAAATTTCACGAACAATGCTA AAACCATAATAGTACAGCTGAATGAAACTGTAGTAATTAATTGTACAAGA CCCAACAACAATACAAGGAAAAGTATACCTATAGGACCAGGGAGAGCATT TTATACAACAGGAGACATAATAGGAGATATAAGACAAGCTCATTGTAACG TTAGTAGAGCAAAATGGAATAACACTTTAGTAAAGATAGTTGAAAAATTA AAAGAACAATTTGGGCATAATAAAACAATAGTCTTCAATCACTCCTCAGG AGGGGACCTAGAAATTGTAACACACAGTTTTATTTGTGGAGGGGAATTCT TCTACTGTAATACATCACAATTGTTTACTTGGAATAGTACTTGGAATAAT ACTAGAGAGTCAGATAACAATACAGAAGAGATCATACTCCCATGCAGAAT AAAACAAATTATAAACATGTGGCAGAAAGTAGGAAAGGCAATGTATGCCC CTCCCATCAGAGGACAAATTAGATGTTTATCAAATATTACAGGGCTGCTA TTAACAAGAGATGGTGGTGATACCCCGAACGGGACCGAGGTCTTCAGACC TGGAGGAGGAGATATGAGGGACAATTGGAGAAGTGAATTATACAAATATA AAGTAGTAAAAATTGAACCATTAGGAGTAGCACCCACCAAGGCAAAGAGA AGAGTGGTGCAGAGAGAAAAAAGAGCAGTGGGAACAATAGGAGCTATGTT CCTTGGGTTCTTGGGAGCAGCGGGAAGCACTATGGGCGCAGCGTCAATGA CGCTGACGGTACAGGCCAGACTATTATTGTCTGGTATAGTGCAACAGCAG AACAATTTGCTGAGGGCTATTGAGGCGCAACAGCATCTGTTGCAACTCAC AGTCTGGGGCATCAAGCAGCTCCAGGCAAGAGTCCTGGCTGTGGAAAGAT ACCTAAAGGATCAACAGCTCCTAGGGATTTGGGGTTGCTCTGGAAAACTC ATTTGCACCACTGCTGTGCCTTGGAATGCTAGTTGGAGTAATAAATCTCT GAATGAAATTTGGAATAACATGACCTGGATGGAATGGGAAAGAGAAATTA ACAATTACACAGACCTAATATACACCCTAATTGAAGAATCGCAGAACCAG CAAGAAAAGAATGAACAAGAATTATTGGAATTAGATAAATGGGCAAGTTT GTGGAATTGGTTTGACATAACAAATTGGCTGTGGTATATAAAAATATTCA TAATGATAGTAGGAGGCTTGGTAGGCTTAAGAATAGTCTTTACTGTACTT TCTATAGTAAATAGAGTTAGGAAGGGATACTCACCATTATCGTTTCAGAC CCGCCTCCCAACCCCGAGGGGACCCGACAGGCCCGAAGGAATCGCAGAAG AAGGTGGAGAGCGAGACAGAGACAGATCCGAGCGCTTAGTGGATGGATTC TTAGCAATTATCTGGGTCGACCTGCGGAGCCTGTGCCTCTTCAGCTACCA CCGATTGAGAGACTTACTCTTGATTGTAGCGAGGATTGTGGAACTTCTGG GACGCAGGGGGTGGGAAGTCCTCAAATATTGGTGGAATCTCCTGCAGTAT TGGAGTCAGGAACTAAAGAATAGTGCTGTTAGCTTGCTCAATGCCACAGC TATAGCAGTAGCTGAGGGGACAGATAGGGTTATAGAAGTATTACAAAGAG CTTGTAGAGCTATCCTCCACATACCTACAAGAATAAGACAGGGCTTAGAA AGGGCTTTGCTATAAGATGGGTGGCAAGTGGTCCAAAAGTAGTATAGTTG GATGGCCTACTGTAAGGGAAAGAATGAGACGAGCTGAGCCAGCAGCAGAT GGGGTGGGAGCAGTATCTCGAGACCTGGAAAAACATGGAGCAATCACAAG TAGCAATACAGCAGCTACTAATGCTGATTGTGCCTGGCTAGAAGCACAAG AGGAGGAAGAGGTGGGTTTTCCAGTCACACCTCAGGTACCTTTAAGACCA ATGACTTACAAGGCAGCTGTAGATCTTAGCCACTTTTTAAAAGAAAAGGG GGGACTGGAAGGGCTAATTCACTCCCAAAGAAGACAAGATATCCTTGATC TGTGGATCTACCACACACAAGGCTACTTCCCTGATTGGCAGAACTACACA CCAGGGCCAGGGGTCAGATATCCACTGACCTTTGGATGGTGCTACAAGCT AGTACCAGTTGAGCCAGATAAGGTAGAAGAGGCCAATAAAGGAGAGAACA CCAGCTTGTTACACCCTGTGAGCCTGCATGGAATGGATGACCCTGAGAGA GAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACGTGGC CCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCT ACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGG ACTGGGGAGTGGCGAGCCCTCAGATGCTGCATATAAGCAGCTGCTTTTTG CCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCT

eventalign file； contig position reference_kmer read_index strand event_index event_level_mean event_stdv event_length model_kmer model_mean model_stdv standardized_level AF003887 1 GGAAG 0 t 1389 100.39 2.906 0.00564 GGAAG 115.76 5.56 -2.37 AF003887 1 GGAAG 0 t 1390 120.60 7.913 0.02191 GGAAG 115.76 5.56 0.75 AF003887 2 GAAGG 0 t 1391 110.99 6.816 0.00266 GAAGG 105.26 4.06 1.21 AF003887 3 AAGGG 0 t 1392 116.69 7.518 0.02324 AAGGG 113.12 7.84 0.39 AF003887 4 AGGGC 0 t 1393 111.36 5.661 0.01195 AGGGC 116.40 4.05 -1.07 AF003887 5 GGGCT 0 t 1394 105.70 3.247 0.00432 GGGCT 113.28 5.31 -1.23 AF003887 6 GGCTA 0 t 1395 113.84 4.058 0.00830 GGCTA 110.69 3.55 0.76 AF003887 7 GCTAA 0 t 1396 88.25 2.053 0.00498 GCTAA 84.40 2.63 1.26 AF003887 7 GCTAA 0 t 1397 84.09 1.143 0.00299 GCTAA 84.40 2.63 -0.10 AF003887 8 CTAAT 0 t 1398 95.87 4.933 0.00730 CTAAT 96.70 3.04 -0.23 AF003887 8 CTAAT 0 t 1399 104.79 1.832 0.00365 CTAAT 96.70 3.04 2.28

Can you please help me solve this problem? Thank you very much。

yuukiiwa commented 4 months ago

Hi @cent0134,

The warning is normal. You can try running xpore without the --genome, --gtf_or_gff, and --transcript_fasta flags:

xpore dataprep --eventalign reads-ref.eventalign.txt --out_dir dataprep

Thanks!

Best wishes, Yuk Kei

cent0134 commented 4 months ago

HI, @yuukiiwa ,Thank you for taking the time to answer my question, but the key issue is that the file I output is empty. Or do you mean that the problem of outputting empty files can also be solved by removing these flags? Looking forward to your reply again.