Closed huyuem closed 5 years ago
Magdoll
commented
5 years ago Hi @huyuem ,
Can you please upgrade to Cupcake v8.6 and SQANTI2 v4.1 and let me know if error persists? I've made some GFF changes and this could be the issue. Apologies. -Liz
arjeffries
commented
5 years ago Hi Liz, Unfortunately I get the same error both on CentOS (upgraded SQANTI2) and a clean install on Ubuntu 18.04. Versions are below. R (&libraries) were installed via conda after the SQANTI2 and cDNA_cupcake install instructions.
SQANTI2 v4.1 cDNA_cupcake v8.7 R 3.5.1 openssl 1.0.2t gffread 0.11.4 ucsc-gtftogenepred 366 minimap2 2.17
Thanks for any help you can give. Hopefully its just a dependency I'm missing. bw, Aaron
Error message:
**** Performing Classification of Isoforms....
Number of classified isoforms: 54584
Traceback (most recent call last):
File "/home/ubuntu/SQANTI2/sqanti_qc2.py", line 1793, in
Magdoll
commented
5 years ago Hi, For those following this issue I am unable to reproduce the error.... -Liz
defendant602
commented
5 years ago It's because of the different gffread versions. Try to install the newest version of gffread and add to your PATH. Do not use gffread embedded in cufflinks.
Magdoll
commented
5 years ago Closing unless otherwise noted.
Hi Elizabeth,
I am running sqanti_qc2.py on version 4.0, use your example data to test and my commands are like this: python sqanti_qc2.py -t 6 touse.rep.fasta gencode.v31.annotation.gtf hg38.genome.fa --cage_peak hg38.cage_peak_phase1and2combined_coord.bed
In my STDERR, I get this Error :
R scripting front-end version 3.4.4 (2018-03-15) Cleaning up isoform IDs... Cleaned up isoform fasta file written to: /home/hcd_lab/software/SQANTI2-master/example/touse.rep.renamed.fasta [M::mm_idx_gen::42.9061.75] collected minimizers [M::mm_idx_gen::54.0572.60] sorted minimizers [M::main::54.0572.60] loaded/built the index for 25 target sequence(s) [M::mm_mapopt_update::56.5132.53] mid_occ = 763 [M::mm_idx_stat] kmer size: 15; skip: 5; is_hpc: 0; #seq: 25 [M::mm_idx_stat::57.9332.49] distinct minimizers: 167178949 (35.44% are singletons); average occurrences: 6.015; average spacing: 3.071 [M::worker_pipeline::65.1642.88] mapped 4730 sequences [M::main] Version: 2.17-r954-dirty [M::main] CMD: minimap2 -ax splice --secondary=no -C5 -uf -t 6 /media/huyueming/disk1/data/hg38/hg38.genome.fa /home/hcd_lab/software/SQANTI2-master/example/touse.rep.renamed.fasta [M::main] Real time: 65.291 sec; CPU: 187.598 sec; Peak RSS: 18.696 GB output written to /home/hcd_lab/software/SQANTI2-master/example/touse.rep.renamed_corrected.fasta Parsing Isoforms.... Running SQANTI... Parsing provided files.... Reading genome fasta /media/huyueming/disk1/data/hg38/hg38.genome.fa.... Aligning reads with Minimap2... Predicting ORF sequences... Parsing Reference Transcriptome.... Splice Junction Coverage files not provided. Reading CAGE Peak data. Performing Classification of Isoforms.... Number of classified isoforms: 4730 Traceback (most recent call last): File "/home/hcd_lab/software/SQANTI2-master/sqanti_qc2.py", line 1762, in
main()
File "/home/hcd_lab/software/SQANTI2-master/sqanti_qc2.py", line 1758, in main
run(args)
File "/home/hcd_lab/software/SQANTI2-master/sqanti_qc2.py", line 1405, in run
write_collapsed_GFF_with_CDS(isoforms_info, corrGTF, corrGTF+'.cds.gff')
File "/home/hcd_lab/software/SQANTI2-master/sqanti_qc2.py", line 399, in write_collapsed_GFF_with_CDS
for r in reader:
File "/home/hcd_lab/software/anaconda2/lib/python2.7/site-packages/cupcake-8.5-py2.7-linux-x86_64.egg/cupcake/io/GFF.py", line 393, in next
return self.read()
File "/home/hcd_lab/software/anaconda2/lib/python2.7/site-packages/cupcake-8.5-py2.7-linux-x86_64.egg/cupcake/io/GFF.py", line 550, in read
assert raw[2] == 'transcript'
AssertionError