search

dieterich-lab / DCC

DCC uses output from the STAR read mapper to systematically detect back-splice junctions in next-generation sequencing data. DCC applies a series of filters and integrates data across replicate sets to arrive at a precise list of circRNA candidates.
https://dieterichlab.org/software/
GNU General Public License v3.0
36 stars 20 forks source link

DCC gtf annotation file issue #105

Open alessio134298 opened 9 months ago

alessio134298 commented 9 months ago

Hi @tjakobi! i can't understand what i'm doing wrong here. It seems that my GTF files are OK but i have this error. How can i fix it?

DCC @samplesheet -mt1 @mate1 -mt2 @mate2 -D -R /home/alessio/Downloads/repeats.gtf -an /home/alessio/Downloads/Genes_and_genepred.gtf -a /home/alessio/data/CircRNA_exercise/genome110/Homo_sapiens.GRCh38.dna.primary_assembly.fa -B @bam_list -N

Output folder ./ already exists, reusing Temporary folder _tmp_DCC/ already exists, reusing DCC 0.5.0 started 12 CPU cores available, using 2 WARNING: non-stranded data, the strand of circRNAs guessed from the strand of host genes started circRNA detection from file /home/alessio/data/CircRNA_exercise/STAR_output/SRR15242806.Chimeric.out.junction started circRNA detection from file /home/alessio/data/CircRNA_exercise/STAR_output/SRR15242805.Chimeric.out.junction => locating circRNAs (unstranded mode) [/home/alessio/data/CircRNA_exercise/STAR_output/SRR15242806.Chimeric.out.junction] => locating circRNAs (unstranded mode) [/home/alessio/data/CircRNA_exercise/STAR_output/SRR15242805.Chimeric.out.junction] => sorting circRNAs (unstranded mode) [/home/alessio/data/CircRNA_exercise/STAR_output/SRR15242805.Chimeric.out.junction] finished circRNA detection from file /home/alessio/data/CircRNA_exercise/STAR_output/SRR15242805.Chimeric.out.junction started circRNA detection from file /home/alessio/data/CircRNA_exercise/STAR_output/SRR15242810.Chimeric.out.junction => locating circRNAs (unstranded mode) [/home/alessio/data/CircRNA_exercise/STAR_output/SRR15242810.Chimeric.out.junction] => sorting circRNAs (unstranded mode) [/home/alessio/data/CircRNA_exercise/STAR_output/SRR15242806.Chimeric.out.junction] finished circRNA detection from file /home/alessio/data/CircRNA_exercise/STAR_output/SRR15242806.Chimeric.out.junction started circRNA detection from file /home/alessio/data/CircRNA_exercise/STAR_output/SRR15242811.Chimeric.out.junction => locating circRNAs (unstranded mode) [/home/alessio/data/CircRNA_exercise/STAR_output/SRR15242811.Chimeric.out.junction] => sorting circRNAs (unstranded mode) [/home/alessio/data/CircRNA_exercise/STAR_output/SRR15242810.Chimeric.out.junction] finished circRNA detection from file /home/alessio/data/CircRNA_exercise/STAR_output/SRR15242810.Chimeric.out.junction started circRNA detection from file /home/alessio/data/CircRNA_exercise/STAR_output/SRR15242815.Chimeric.out.junction => locating circRNAs (unstranded mode) [/home/alessio/data/CircRNA_exercise/STAR_output/SRR15242815.Chimeric.out.junction] => sorting circRNAs (unstranded mode) [/home/alessio/data/CircRNA_exercise/STAR_output/SRR15242811.Chimeric.out.junction] finished circRNA detection from file /home/alessio/data/CircRNA_exercise/STAR_output/SRR15242811.Chimeric.out.junction started circRNA detection from file /home/alessio/data/CircRNA_exercise/STAR_output/SRR15242816.Chimeric.out.junction => locating circRNAs (unstranded mode) [/home/alessio/data/CircRNA_exercise/STAR_output/SRR15242816.Chimeric.out.junction] => sorting circRNAs (unstranded mode) [/home/alessio/data/CircRNA_exercise/STAR_output/SRR15242815.Chimeric.out.junction] finished circRNA detection from file /home/alessio/data/CircRNA_exercise/STAR_output/SRR15242815.Chimeric.out.junction => sorting circRNAs (unstranded mode) [/home/alessio/data/CircRNA_exercise/STAR_output/SRR15242816.Chimeric.out.junction] finished circRNA detection from file /home/alessio/data/CircRNA_exercise/STAR_output/SRR15242816.Chimeric.out.junction Combining individual circRNA read counts This is line: >1 dna:chromosome chromosome:GRCh38:1:1:248956422:1 REF

Traceback (most recent call last): File "/home/alessio/.local/bin/DCC", line 33, in sys.exit(load_entry_point('DCC==0.5.0', 'console_scripts', 'DCC')()) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/alessio/.local/lib/python3.11/site-packages/DCC-0.5.0-py3.11.egg/DCC/main.py", line 320, in main File "/home/alessio/.local/lib/python3.11/site-packages/DCC-0.5.0-py3.11.egg/DCC/circAnnotate.py", line 26, in selectGeneGtf File "/home/alessio/.local/lib/python3.11/site-packages/HTSeq-2.0.4-py3.11-linux-x86_64.egg/HTSeq/features.py", line 139, in iter (seqname, source, feature, start, end, score, strand, frame, attributeStr) = line.split("\t", 8) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ValueError: not enough values to unpack (expected 9, got 1)