alexpan00
commented
7 months ago Hi,
This bug should be fixed with the last commit, could you do git pull and try to run SQANTI again?
Alejandro
Closed dawangran closed 7 months ago
alexpan00
commented
7 months ago Hi,
This bug should be fixed with the last commit, could you do git pull and try to run SQANTI again?
Alejandro
Is there an existing issue for this?
Have you loaded the SQANTI3.env conda environment?
Problem description
hello， An error occurred when I was running qc. How can I solve it.
Code sample
python sqanti3_qc.py merge.novel.transcript_models.gtf /media/AnalysisTempDisk2/Wangxue/project/15.cyclone_paper/00.data/ref/zebrafish/genes.gtf /media/AnalysisTempDisk2/Wangxue/project/15.cyclone_paper/00.data/ref/zebrafish/genome.fasta --report pdf -d sqanti_report
Error
Rscript (R) version 4.3.1 (2023-06-16) Write arguments to /media/AnalysisTempDisk2/Wangxue/project/tools/SQANTI3/sqanti_report/merge.novel.transcript_models.params.txt... Running SQANTI3... Parsing provided files.... Reading genome fasta /media/AnalysisTempDisk2/Wangxue/project/15.cyclone_paper/00.data/ref/zebrafish/genome.fasta.... Skipping aligning of sequences because GTF file was provided.
Indels will be not calculated since you ran SQANTI3 without alignment step (SQANTI3 with gtf format as transcriptome input). Predicting ORF sequences... Parsing Reference Transcriptome.... Parsing Isoforms.... Splice Junction Coverage files not provided. TSS ratio will not be calculated since SR information was not provided **** Performing Classification of Isoforms.... Traceback (most recent call last): File "/media/AnalysisTempDisk2/Wangxue/project/tools/SQANTI3/sqanti3_qc.py", line 2546, in
main()
File "/media/AnalysisTempDisk2/Wangxue/project/tools/SQANTI3/sqanti3_qc.py", line 2529, in main
run(args)
File "/media/AnalysisTempDisk2/Wangxue/project/tools/SQANTI3/sqanti3_qc.py", line 1874, in run
isoforms_info, ratio_TSS_dict = isoformClassification(args, isoforms_by_chr, refs_1exon_by_chr, refs_exons_by_chr, junctions_by_chr, junctions_by_gene, start_ends_by_gene, genome_dict, indelsJunc, orfDict, corrGTF)
File "/media/AnalysisTempDisk2/Wangxue/project/tools/SQANTI3/sqanti3_qc.py", line 1614, in isoformClassification
isoform_hit = associationOverlapping(isoform_hit, rec, junctions_by_chr)
File "/media/AnalysisTempDisk2/Wangxue/project/tools/SQANTI3/sqanti3_qc.py", line 1346, in associationOverlapping
if da_pairs[j][0] <= trec.txStart <= trec.txEnd <= da_pairs[j][1]:
IndexError: list index out of range
Anything else?
No response