DEXSeq - dexseq_count.py issue
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@marijadurdevic-15182
Last seen 6.7 years ago

Hi all,

I wanted to use dexseq_count for quantification, but I got strange error:

Fatal error: Exit code 1 ()
Traceback (most recent call last):
  File "dexseq_count.py", line 102, in 
    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 gtf file is prepared with dexseq. Any idea what colud be wrong?

Thanks in advance,

Marija
dexseq dexseq_count genomicfeatures • 3.6k views
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1
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Hi Marija. One quick question, are you using python 3.4 or above?

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Hi Alejandro,

It's Python 3.6.4. I installed DEXSeq over conda. Could that be the problem?

Thanks,

Marija

 

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I am not sure yet. Sorry for the multiple questions, but would you mind posting the first 100 lines of your gtf file? 

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Sure & thanks for your help :)

Seqname Source Feature Start End Score Strand Frame Attributes
AERX01071043.1 dexseq_prepare_annotation.py aggregate_gene 8384 9414 . - . gene_id "MSTRG.1"
AERX01071043.1 dexseq_prepare_annotation.py exonic_part 8384 9414 . - . gene_id "MSTRG.1"; transcripts "MSTRG.1.1"; exonic_part_number "001"
AERX01071043.1 dexseq_prepare_annotation.py aggregate_gene 9773 14866 . - . gene_id "MSTRG.13"
AERX01071043.1 dexseq_prepare_annotation.py exonic_part 9773 10155 . - . gene_id "MSTRG.13"; transcripts "MSTRG.13.1"; exonic_part_number "001"
AERX01071043.1 dexseq_prepare_annotation.py exonic_part 10310 10354 . - . gene_id "MSTRG.13"; transcripts "MSTRG.13.1"; exonic_part_number "002"
AERX01071043.1 dexseq_prepare_annotation.py exonic_part 10568 10678 . - . gene_id "MSTRG.13"; transcripts "MSTRG.13.1"; exonic_part_number "003"
AERX01071043.1 dexseq_prepare_annotation.py exonic_part 10767 10918 . - . gene_id "MSTRG.13"; transcripts "MSTRG.13.1"; exonic_part_number "004"
AERX01071043.1 dexseq_prepare_annotation.py exonic_part 11019 11303 . - . gene_id "MSTRG.13"; transcripts "MSTRG.13.1"; exonic_part_number "005"
AERX01071043.1 dexseq_prepare_annotation.py exonic_part 11386 11655 . - . gene_id "MSTRG.13"; transcripts "MSTRG.13.1"; exonic_part_number "006"
AERX01071043.1 dexseq_prepare_annotation.py exonic_part 11770 11902 . - . gene_id "MSTRG.13"; transcripts "MSTRG.13.1"; exonic_part_number "007"
AERX01071043.1 dexseq_prepare_annotation.py exonic_part 12041 12189 . - . gene_id "MSTRG.13"; transcripts "MSTRG.13.1"; exonic_part_number "008"
AERX01071043.1 dexseq_prepare_annotation.py exonic_part 14552 14594 . - . gene_id "MSTRG.13"; transcripts "MSTRG.13.1"; exonic_part_number "009"
AERX01071043.1 dexseq_prepare_annotation.py exonic_part 14844 14866 . - . gene_id "MSTRG.13"; transcripts "MSTRG.13.1"; exonic_part_number "010"
AERX01071043.1 dexseq_prepare_annotation.py aggregate_gene 16324 18991 . + . gene_id "MSTRG.5"
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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?

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Sure! That's my original gtf file and this is file after DEXSeq prepare.

 

Thanks,

Marija

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Sorry, I still can't reproduce the error message. How are you invoking the dexseq_count.py script?

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Yes, I am using dexseq_count.py: 
dexseq_count.py -f bam -p yes -s reverse -a 10 -r pos my_gtf_file.gtf data.bam output
Thanks for your help. Best, Marija
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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

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a.brooks • 0
@abrooks-15596
Last seen 6.6 years ago

Hi

Did you fix this problem?
I have exactly the same error, but only when I run the script through Galaxy. Running through command line seems to work.

Thanks

Tony
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I have been unable to solve this issue because I can't reproduce the error. But this might be a good start! Are you running the same versions of python and HTSeq through the command line and through Galaxy?

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Hi Tony,

Since you can run it through command line (but not in Galaxy), it would help now to know your environment (python version, htseq version, pysam version, at least).

Thanks

Christophe

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hazards • 0
@hazards-11550
Last seen 6.6 years ago

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
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I am working with hazards who posted above, and wanted to provide some details.

We have tested with two of the quay dexseq images.

1.24.0--py36r3.4.1_1

1.24.0--py27r3.4.1_1

Both seemed to work with the annotation script.

3.6 failed on the count script. 2.7 count appears to be working with the output from 3.6 annotation.

 

I created a dockerfile which inherited from each of them with  the folloiwng lines.


from quay.io/biocontainers/bioconductor-dexseq:VERSION

RUN PATH=/usr/local/lib/R/library/DEXSeq/python_scripts:$PATH

RUN pip install HTSeq\

     numpy \

     pysam

both seem to have the same pip packeges installed...


certifi==2017.11.5

HTSeq==0.9.1

numpy==1.14.2

pysam==0.14.1

 

 

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