I believe I have the same issue.
I see no one has posted any solutions. Any one had a similar issue?
I am attempting to run a DEXseq python script to count reads from a STAR alignment to the human genome. I am trying to a “docker” procedure to setup the environment and execute the program.
docker pull quay.io/biocontainers/bioconductor-dexseq:1.24.0--py36r3.4.1_1
Here is the docker result:
docker run -it -v ~/Meissner-Tsao-April2018:/data musc/dexseq dexseq_count.py data/Homo_sapiens.GRCh38.92_DEXSeq.gff data/STAR_aligned_5021_S20_L005Aligned.sortedByCoord.out.bam data/STAR_aligned_5021_S20_L005_STAR_dexseq_count_fpsr.txt -f bam -p yes -s no -r pos
Traceback (most recent call last):
File "/usr/local/bin/dexseq_count.py", line 98, in <module>
features[f.iv] += f
File "python3/src/HTSeq/_HTSeq.pyx", line 451, in HTSeq._HTSeq.ChromVector.__iadd__
File "python3/src/HTSeq/_HTSeq.pyx", line 466, in HTSeq._HTSeq.ChromVector.apply
File "python3/src/HTSeq/_HTSeq.pyx", line 449, in HTSeq._HTSeq.ChromVector.__iadd__.addval
TypeError: unhashable type: 'GenomicFeature'
The GFF was prepared ash show here
docker run -it -v ~/Meissner-Tsao-April2018:/data musc/dexseq dexseq_prepare_annotation.pydata/Homo_sapiens.GRCh38.92.gtf data/Homo_sapiens.GRCh38.92_DEXSeq.gff
The python version in the docker is
docker run -it -v ~/Meissner-Tsao-April2018:/data musc/dexseq python -V
Python 3.6.4
Hi Marija. One quick question, are you using python 3.4 or above?
Hi Alejandro,
It's Python 3.6.4. I installed DEXSeq over conda. Could that be the problem?
Thanks,
Marija
I am not sure yet. Sorry for the multiple questions, but would you mind posting the first 100 lines of your gtf file?
Sure & thanks for your help :)
I'm still not sure what is going on. Would you mind giving me access to the original gtf file to check what is going on?
Sure! That's my original gtf file and this is file after DEXSeq prepare.
Thanks,
Marija
Sorry, I still can't reproduce the error message. How are you invoking the dexseq_count.py script?
Not sure if still relevant. I had the same error when running in Python3.6 environment but was okay when using Python2.7 environment. Muxin