Comments (12)
I got the same mistake, and I want to know why.
from sqanti2.
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
from sqanti2.
Hi Liz,
I installed the latest version of Cupcake using
git clone https://github.com/Magdoll/cDNA_Cupcake.git
cd cDNA_Cupcake/
python setup.py build
python setup.py install --user
but I get the error,
<open file '<stderr>', mode 'w' at 0x2b2c214f81e0> Cupcake version must be 8.6 or higher! Got 8.1 instead.
Am I doing something wrong?
Best Regards,
Priyanka
from sqanti2.
Hi @psur9757 ,
You need to update Cupcake first to v8.6 or above. This is intended to let you know that!
-Liz
from sqanti2.
Hi @Magdoll
I did update Cupcake. I re-installed Cupcake a few hours ago. I did git clone
when that version gave me the error:
<open file '<stderr>', mode 'w' at 0x2b2c214f81e0> Cupcake version must be 8.6 or higher! Got 8.1 instead.
I downloaded https://github.com/Magdoll/cDNA_Cupcake/archive/v8.7.0.tar.gz
and tried again but I got the same error.
from sqanti2.
Hi @Magdoll
Cupcake works fine for me now. The test runs successfully and everything. But I still get error with SQANTI2.
The python and Conda versions are good.
% conda -V
conda 4.7.12
% python -V
Python 3.7.4
cDNA_Cupcake test command runs successfully. I have version 9.0.1 installed correctly.
collapse_isoforms_by_sam.py --input cDNA_Cupcake/cupcake/test_data/hq_isoforms.fastq --fq -s cDNA_Cupcake/cupcake/test_data/hq_isoforms.fastq.sorted.sam --dun-merge-5-shorter -o test
I have SQANTI2 version 4.1 correctly and the cDNA_Cupcake is version 9.0.1 but I still get error.
% python SQANTI2-4.1/sqanti_qc2.py
File "SQANTI2-4.1/sqanti_qc2.py", line 68
print sys.stderr, "Cupcake version must be 8.6 or higher! Got {0} instead.".format(cupcake.__version__)
^
SyntaxError: invalid syntax
This computer has no other version of either software installed so this cannot be leftover from previous attempt. Any help to get SQANTI2 running will be much appreciated, we have a deadline end of the month to meet.
from sqanti2.
Hi @psur9757 ,
Apologies on the SQANTI2 part - I did not check in the Python 3.7 version of SQANTI2 until just now. PLease head to SQANTI2 and check out the latest version (5.0.0).
Let me know if you encounter more issues and I will try to respond promptly so you can meet your deadline.
--Liz
from sqanti2.
Hi @Magdoll
I updated to the latest version and here is the last few lines of the stderr file. Let me know what to modify to fix this.
Cleaning up isoform IDs...
Cleaned up isoform fasta file written to: /scratch/BLRseq/BLR/results/annotation/structural/BLR560/sqanti5/hq.collapsed.rep.renamed.fasta
output written to
**** Parsing Isoforms....
Traceback (most recent call last):
File "/scratch/BLRseq/bin/SQANTI2/sqanti_qc2.py", line 1794, in <module>
main()
File "/scratch/BLRseq/bin/SQANTI2/sqanti_qc2.py", line 1790, in main
run(args)
File "/scratch/BLRseq/bin/SQANTI2/sqanti_qc2.py", line 1437, in run
write_collapsed_GFF_with_CDS(isoforms_info, corrGTF, corrGTF+'.cds.gff')
File "/scratch/BLRseq/bin/SQANTI2/sqanti_qc2.py", line 400, in write_collapsed_GFF_with_CDS
for r in reader:
File "/home/psur9757/.local/lib/python3.7/site-packages/cupcake-9.0.1-py3.7-linux-x86_64.egg/cupcake/io/GFF.py", line 395, in __next__
return self.read()
File "/home/psur9757/.local/lib/python3.7/site-packages/cupcake-9.0.1-py3.7-linux-x86_64.egg/cupcake/io/GFF.py", line 552, in read
assert raw[2] == 'transcript'
AssertionError
PBS script
#!/bin/bash
#PBS -P BLRseq
#PBS -N sqanti
#PBS -l select=1:ncpus=8:mem=64GB
#PBS -l walltime=20:00:00
#PBS -e /scratch/BLRseq/BLR/results/annotation/structural/BLR560/sqanti5/sqanti.err
#PBS -o /scratch/BLRseq/BLR/results/annotation/structural/BLR560/sqanti5/sqanti.out
wdir=/scratch/BLRseq/BLR
outdir=$wdir/results/annotation/structural/BLR560/sqanti5
ref=$wdir/results/annotation/structural/BLR560/ref.fa
isoforms=$wdir/data/BLR560/isoseq/SMRT/cluster/hq_isoforms.fasta
ann=$wdir/results/annotation/structural/BLR560/.old/isoseq/braker/augustus.ab_initio.gff3
sqanti=/scratch/BLRseq/bin/SQANTI2
cupcake=/scratch/BLRseq/bin/cDNA_Cupcake
module load python/3.7.2
module load cufflinks/2.2.1
module load ucsc-userapps/348
module load R/3.6.0
module load minimap2/2.3
module load samtools/1.9
export PYTHONPATH=$PYTHONPATH:$cupcake/sequence/
minimap2 -ax splice -uf $ref $isoforms > $outdir/aln.sam
samtools sort -O sam -o $outdir/aln.sorted.sam -@ 8 $outdir/aln.sam
gffread -E -O -T $ann -o $outdir/augustus.ab_initio.gtf
python3.7 $cupcake/cupcake/tofu/collapse_isoforms_by_sam.py --input $isoforms -s $outdir/aln.sorted.sam -o $outdir/hq --dun-merge-5-shorter
python3.7 $sqanti/sqanti_qc2.py -t 8 --aligner_choice minimap2 --output BLR560 --dir $outdir $outdir/hq.collapsed.rep.fa $outdir/augustus.ab_initio.gtf $ref
from sqanti2.
Hi @Magdoll
I am experiencing the same issue with SQANTI2 with complete new installation of SQANTI and Cupcake.
Traceback (most recent call last):
File "/home/userA/bin/SQANTI2/sqanti_qc2.py", line 2198, in <module>
main()
File "/home/userA/bin/SQANTI2/sqanti_qc2.py", line 2191, in main
run(args)
File "/home/userA/bin/SQANTI2/sqanti_qc2.py", line 1676, in run
write_collapsed_GFF_with_CDS(isoforms_info, corrGTF, corrGTF+'.cds.gff')
File "/home/userA/bin/SQANTI2/sqanti_qc2.py", line 422, in write_collapsed_GFF_with_CDS
for r in reader:
File "/home/userA/anaconda31/envs/anaCogent3/lib/python3.7/site-packages/cupcake-11.0.0-py3.7-linux-x86_64.egg/cupcake/io/GFF.py", line 408, in __next__
return self.read()
File "/home/userA/anaconda31/envs/anaCogent3/lib/python3.7/site-packages/cupcake-11.0.0-py3.7-linux-x86_64.egg/cupcake/io/GFF.py", line 579, in read
assert raw[2] == 'transcript'
AssertionError
raw[2] can be "exon" too. It seems it fails to assert raw[2]=="exon" entries.
Any idea how I can fix this issue?
Thanks!
from sqanti2.
@AminMahpour ,
This error is most seen when your reference annotation or input GTF format is unexpected. Can you post the first few entries from your annotation GTF and input GTF (if your input is GTF)
--Liz
from sqanti2.
Thanks Liz. My input is a fastq file (minimap2 aligner). Genomic annotation GTF is from Gencode v32.
I am attaching a few entries from the SQANTI2-corrected GTF file. As can be seen, "Transcript" lines are missing. When I manually fix the GTF file to add the missing lines, SQUANTI works fine.
Thanks!
Amin
chr1 GRCh38 exon 167121 168165 . - . transcript_id "PB.1.1"; gene_id "PB.1.1"; gene_name "PB.1.1";
chr1 GRCh38 exon 169049 169264 . - . transcript_id "PB.1.1"; gene_id "PB.1.1"; gene_name "PB.1.1";
chr1 GRCh38 exon 172557 172688 . - . transcript_id "PB.1.1"; gene_id "PB.1.1"; gene_name "PB.1.1";
chr1 GRCh38 exon 173753 173862 . - . transcript_id "PB.1.1"; gene_id "PB.1.1"; gene_name "PB.1.1";
chr1 GRCh38 exon 181037 181128 . - . transcript_id "PB.1.1"; gene_id "PB.1.1"; gene_name "PB.1.1";
chr1 GRCh38 exon 184877 185350 . - . transcript_id "PB.2.1"; gene_id "PB.2.1"; gene_name "PB.2.1";
chr1 GRCh38 exon 185491 185559 . - . transcript_id "PB.2.1"; gene_id "PB.2.1"; gene_name "PB.2.1";
chr1 GRCh38 exon 186317 186469 . - . transcript_id "PB.2.1"; gene_id "PB.2.1"; gene_name "PB.2.1";
chr1 GRCh38 exon 187129 187287 . - . transcript_id "PB.2.1"; gene_id "PB.2.1"; gene_name "PB.2.1";
chr1 GRCh38 exon 187380 187577 . - . transcript_id "PB.2.1"; gene_id "PB.2.1"; gene_name "PB.2.1";
chr1 GRCh38 exon 187755 187890 . - . transcript_id "PB.2.1"; gene_id "PB.2.1"; gene_name "PB.2.1";
chr1 GRCh38 exon 188130 188266 . - . transcript_id "PB.2.1"; gene_id "PB.2.1"; gene_name "PB.2.1";
chr1 GRCh38 exon 188439 188584 . - . transcript_id "PB.2.1"; gene_id "PB.2.1"; gene_name "PB.2.1";
chr1 GRCh38 exon 188791 188889 . - . transcript_id "PB.2.1"; gene_id "PB.2.1"; gene_name "PB.2.1";
chr1 GRCh38 exon 195263 195416 . - . transcript_id "PB.2.1"; gene_id "PB.2.1"; gene_name "PB.2.1";
chr1 GRCh38 exon 199837 199885 . - . transcript_id "PB.2.1"; gene_id "PB.2.1"; gene_name "PB.2.1";
chr1 GRCh38 exon 184924 185350 . - . transcript_id "PB.2.2"; gene_id "PB.2.2"; gene_name "PB.2.2";
chr1 GRCh38 exon 185491 185559 . - . transcript_id "PB.2.2"; gene_id "PB.2.2"; gene_name "PB.2.2";
chr1 GRCh38 exon 186317 186469 . - . transcript_id "PB.2.2"; gene_id "PB.2.2"; gene_name "PB.2.2";
chr1 GRCh38 exon 187129 187287 . - . transcript_id "PB.2.2"; gene_id "PB.2.2"; gene_name "PB.2.2";
chr1 GRCh38 exon 187376 187577 . - . transcript_id "PB.2.2"; gene_id "PB.2.2"; gene_name "PB.2.2";
chr1 GRCh38 exon 187755 187890 . - . transcript_id "PB.2.2"; gene_id "PB.2.2"; gene_name "PB.2.2";
chr1 GRCh38 exon 188130 188266 . - . transcript_id "PB.2.2"; gene_id "PB.2.2"; gene_name "PB.2.2";
chr1 GRCh38 exon 188439 188584 . - . transcript_id "PB.2.2"; gene_id "PB.2.2"; gene_name "PB.2.2";
chr1 GRCh38 exon 188791 188902 . - . transcript_id "PB.2.2"; gene_id "PB.2.2"; gene_name "PB.2.2";
chr1 GRCh38 exon 195263 195416 . - . transcript_id "PB.2.2"; gene_id "PB.2.2"; gene_name "PB.2.2";
chr1 GRCh38 exon 199837 199862 . - . transcript_id "PB.2.2"; gene_id "PB.2.2"; gene_name "PB.2.2";
chr1 GRCh38 exon 629640 629774 . + . transcript_id "PB.7657.24"; gene_id "PB.7657.24"; gene_name "PB.7657.24";
from sqanti2.
I am getting similar error with example file:
sqanti_qc2.py example/test_mini.fasta gencode.v28.annotation.gtf hg38.fa
Error i get:
Number of classified isoforms: 11
Traceback (most recent call last):
File "/home/SQANTI2/sqanti_qc2.py", line 2198, in
main()
File "/home/SQANTI2/sqanti_qc2.py", line 2191, in main
run(args)
File "/home/SQANTI2/sqanti_qc2.py", line 1676, in run
write_collapsed_GFF_with_CDS(isoforms_info, corrGTF, corrGTF+'.cds.gff')
File "/home/spthapa/software/SQUANTI2/SQANTI2/sqanti_qc2.py", line 422, in write_collapsed_GFF_with_CDS
for r in reader:
File "/home/.conda/envs/anaCogent5.2/lib/python3.6/site-packages/cupcake-12.0.0-py3.6-linux-x86_64.egg/cupcake/io/GFF.py", line 408, in next
return self.read()
File "/home/.conda/envs/anaCogent5.2/lib/python3.6/site-packages/cupcake-12.0.0-py3.6-linux-x86_64.egg/cupcake/io/GFF.py", line 579, in read
assert raw[2] == 'transcript'
AssertionError
Any help would be great.
Thanks
from sqanti2.
Related Issues (20)
- input isoforms.fasta for chain_samples.py HOT 4
- isoform map to scaffold which without reference gene HOT 1
- Assertion Error HOT 7
- gene_id annotation HOT 2
- Possible error from input gff files instead of fasta/fastq/gtf files HOT 10
- Tamma Collapse for 5' cap selected samples HOT 1
- sqanti2_qc.py fails with assertion error HOT 6
- Isoform class transcript distribution versus rarefaction curve HOT 1
- How to utilize sqanti2 classification result for genome optimizaion? HOT 1
- python 3.7 bx-python error HOT 1
- About adapting SQANTI2 to process transcripts from nanopore cDNA sequencing HOT 2
- Problem running with cage_peak HOT 2
- _corrected.gtf file without transcript line HOT 4
- FileNotFoundError: missing refAnnotation_***.genePred file? HOT 3
- Error with sqanti_qc2.py command HOT 4
- sqanti_filter.py HOT 4
- issue with python=3.7
- Gene_IDs in GTFs HOT 3
- Recurring perl errors - gmst.pl HOT 7
- error using GFF or converted GTF HOT 1
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from sqanti2.