FileNotFoundError: [Errno 2] No such file or directory: '/data/work/temp2/sqan/refAnnotation_./output.genePred'

[handesome]

Hi！Thank you for develop the package!!when I run the code sqanti3_qc.py /data/work/temp/gtf__talon.gtf /data/work/gencode.v46.primary_assembly.basic.annotation.gtf /data/work/GRCh38.primary_assembly.genome.fa \ --polyA_motif_list /opt/SQANTI3/data/polyA_motifs/mouse_and_human.polyA_motif.txt \ --coverage /data/work/pass2/pass2SJ.out.tab\ --force_id_ignore \ --skipORF \ --report pdf \ --dir /data/work/sqanti \ --output ./output,the error says **** Parsing Reference Transcriptome.... mustOpen: Can't open /data/work/temp2/sqan/refAnnotation_./output.genePred to write: No such file or directory Traceback (most recent call last): File "/opt/SQANTI3/sqanti3_qc.py", line 2627, in <module> main() File "/opt/SQANTI3/sqanti3_qc.py", line 2610, in main run(args) File "/opt/SQANTI3/sqanti3_qc.py", line 1896, in run refs_1exon_by_chr, refs_exons_by_chr, junctions_by_chr, junctions_by_gene, start_ends_by_gene = reference_parser(args, list(genome_dict.keys())) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/opt/SQANTI3/sqanti3_qc.py", line 676, in reference_parser for r in genePredReader(referenceFiles): ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/opt/SQANTI3/sqanti3_qc.py", line 124, in __init__ self.f = open(filename) ^^^^^^^^^^^^^^ FileNotFoundError: [Errno 2] No such file or directory: '/data/work/temp2/sqan/refAnnotation_./output.genePred'
so could anyone help me out?Thanks!!!!

[lkondratova]

This discussion is similar to #343:
#343 (comment)