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quicksect has no attribute before_interval #14

Closed IanSudbery closed 5 years ago

IanSudbery commented 5 years ago

I see that the use of bx-python has been replaced with quicksect in IndexedGenome. However, this is causing gtf2table to raise a quicksect.IntervalTree has no attribute before_interval error. This is coming from the Quicksect class in IndexedGenome.

This is because the API to quicksect's IntervalTree is different to that of bx-python's. I think the equivalent to before_interval and after_interval are left and right. But because the documentation of both packages is a bit ropey, I can't be sure.

sebastian-luna-valero commented 5 years ago

bx-python has now been ported to Python 3 so we could switch back to it.

On the other hand, if you provide a reproducible example I would be happy to help.

CristinaAlexandru commented 5 years ago

We tried substituting left and right for before_interval and after_interval, but got the following error:

Traceback (most recent call last):
  File "/data/mb1cna/cgat/envs/sharc/bin/cgat", line 11, in <module>
    load_entry_point('CGAT', 'console_scripts', 'cgat')()
  File "/data/mb1cna/cgat/cgat-apps/CGAT/cgat.py", line 132, in main
    module.main(sys.argv)
  File "/data/mb1cna/cgat/cgat-apps/CGAT/tools/gtf2table.py", line 925, in main
    counter.update(gffs)
  File "GeneModelAnalysis.pyx", line 182, in CGAT.GeneModelAnalysis.Counter.update
  File "GeneModelAnalysis.pyx", line 3392, in CGAT.GeneModelAnalysis.ClassifierRNASeqSplicing.count
  File "GeneModelAnalysis.pyx", line 3099, in CGAT.GeneModelAnalysis.ClassifierRNASeqSplicing.classify_nonoverlap
  File "/data/mb1cna/cgat/cgat-apps/CGAT/IndexedGenome.py", line 145, in right
    max_dist=max_dist)]
  File "src/quicksect.pyx", line 95, in quicksect.IntervalTree.right (src/quicksect.c:3352)
  File "src/quicksect.pyx", line 400, in quicksect.IntervalNode.right (src/quicksect.c:7083)
IndexError: list index out of range

We think this is a bug in quicksect.

You can reproduce this with the following command:

cgat gtf2table            --counter=classifier-rnaseq-splicing            --reporter=transcripts            --gff-file=smallest_ref.gtf -I weird_transcript.gtf

where weird_transcript.gtf is:

chr22   StringTie       transcript      49989432        49989665        1000    -       .       gene_id "MSTRG.28419"; transcript_id "MSTRG.28419.1";
chr22   StringTie       exon    49989432        49989665        1000    -       .       gene_id "MSTRG.28419"; transcript_id "MSTRG.28419.1"; exon_number "1";

and smallest_ref.gtf is:

chr22   havana  exon    49994513        49996860        .       -       .       gene_id "ENSG00000188263"; gene_version "10"; transcript_id "ENST00000389983"; transcript_version "6"; exon_number "15"; gene_name "IL17REL"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000150242"; havana_gene_version "1"; transcript_name "IL17REL-001"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS33679"; havana_transcript "OTTHUMT00000317011"; havana_transcript_version "1"; exon_id "ENSE00001429024"; exon_version "1"; tag "basic"; transcript_support_level "2";
chr22   ensembl exon    49994513        49996860        .       -       .       gene_id "ENSG00000188263"; gene_version "10"; transcript_id "ENST00000341280"; transcript_version "5"; exon_number "13"; gene_name "IL17REL"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000150242"; havana_gene_version "1"; transcript_name "IL17REL-201"; transcript_source "ensembl"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS33679"; exon_id "ENSE00001429024"; exon_version "1"; tag "basic"; transcript_support_level "2";
sebastian-luna-valero commented 5 years ago

Thanks!

I am getting a different error:

Traceback (most recent call last):
  File "/ifs/devel/sebastian/cgat-developers-v0/conda-install/envs/cgat-f/bin/cgat", line 11, in <module>
    load_entry_point('CGAT', 'console_scripts', 'cgat')()
  File "/ifs/devel/sebastian/cgat-developers-v0/cgat-apps/CGAT/cgat.py", line 132, in main
    module.main(sys.argv)
  File "/ifs/devel/sebastian/cgat-developers-v0/cgat-apps/CGAT/tools/gtf2table.py", line 885, in main
    prefix=prefix))
  File "CGAT/GeneModelAnalysis.pyx", line 3056, in CGAT.GeneModelAnalysis.ClassifierRNASeqSplicing.__init__
  File "/ifs/devel/sebastian/cgat-developers-v0/cgat-apps/CGAT/GTF.py", line 119, in transcript_iterator
    for gff in gff_iterator:
  File "pysam/libctabix.pyx", line 1243, in pysam.libctabix.tabix_generic_iterator.__next__
  File "pysam/libctabix.pyx", line 100, in pysam.libctabix.Parser.__call__
  File "pysam/libctabix.pyx", line 196, in pysam.libctabix.asGTF.parse
  File "pysam/libctabixproxies.pyx", line 135, in pysam.libctabixproxies.TupleProxy.copy
  File "pysam/libctabixproxies.pyx", line 236, in pysam.libctabixproxies.TupleProxy.update
ValueError: parsing error: fewer than 9 fields in line: b'chr22   havana  exon    49994513        49996860        .       -       .       gene_id "ENSG00000188263"; gene_version "10"; transcript_id "ENST00000389983"; transcript_version "6"; exon_number "15"; gene_name "IL17REL"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000150242"; havana_gene_version "1"; transcript_name "IL17REL-001"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS33679"; havana_transcript "OTTHUMT00000317011"; havana_transcript_version "1"; exon_id "ENSE00001429024"; exon_version "1"; tag "basic"; transcript_support_level "2";'

Could you please paste the output of conda env export here so I can compare what's different between our environments?

IanSudbery commented 5 years ago

I think this is because github has converted the tabs to spaces in the GTF files.

sebastian-luna-valero commented 5 years ago

Thanks. Indeed, when I replaced spaces to tabs I managed to reproduce the error.

I have been playing with quicksect, following their examples: https://github.com/brentp/quicksect

The following does not fail:

from quicksect import IntervalNode, Interval, IntervalTree
tree3 = IntervalTree()
tree3.insert(Interval(22, 33, data='example1'))
tree3.right(Interval(44,55))
tree3.right(Interval(11,12))
tree3.left(Interval(44,55))
tree3.left(Interval(11,12))

The following fails and outputs the IndexError: list index out of range:

from quicksect import IntervalNode, Interval, IntervalTree
tree4 = IntervalTree()
tree4.insert(Interval(22, 33, data='example1'))
tree4.insert(Interval(22, 33, data='example2'))
tree4.right(Interval(44,55))
tree4.right(Interval(11,12))
tree4.left(Interval(44,55))
tree4.left(Interval(11,12))

Is it semantically correct to have two intervals with the same coordinates and different data?

That's what's happening with the data provided:

If that's correct, I think we should report to the developer.

Please let me know your thoughts.

Best regards, Sebastian

IanSudbery commented 5 years ago

Yes, these represent exons from two different transcripts that happen to have the same last exon. This was not a problem with bx-python, so perhaps we should go back to that. ALthough I seem to remember that bx had all sorts of dependency problems?

However, I do think this is a bug in quicksect and should be reported. I just worry that it might take a long time to get a response, and we kind of need things to work now-ish.

sebastian-luna-valero commented 5 years ago

xref: https://github.com/brentp/quicksect/issues/9

sebastian-luna-valero commented 5 years ago

Could you please update quicksect to version 0.2.0, pull https://github.com/cgat-developers/cgat-apps/pull/15 and let me know if it works?

CristinaAlexandru commented 5 years ago

Absolutely. Will update you if it works or not. Thanks a lot!

On 19 July 2018 at 17:35, Sebastian Luna-Valero notifications@github.com wrote:

Could you please update quicksect to version 0.2.0, pull #15 https://github.com/cgat-developers/cgat-apps/pull/15 and let me know if it works?

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/cgat-developers/cgat-apps/issues/14#issuecomment-406339001, or mute the thread https://github.com/notifications/unsubscribe-auth/Am9bhLqcHGnTu45Gze5MuWP5JDMr-goVks5uILVSgaJpZM4VQ08_ .

--

Cristina Alexandru-Crivac

Research Associate Bioinformatics Hub, Firth Court Department of Molecular Biology and Biotechnology (MBB), University of Sheffield, Western Bank, Sheffield S10 2TN England, UK. Tel. +44 (0)7703417022 c.alexandru@sheffield.ac.uk r01cna14@abdn.ac.uk

IanSudbery commented 5 years ago

When we try to update quicksect we get nothing.

If we force version 0.2 with

conda install quicksect=0.2 we get

PackageNotFound: Dependency Missing in current linux-64 channels:
   quicksect 0.2* => libgcc-ng >=4.9

libgcc-ng is listed as a dependency of quicksect=0.2 when quicksect=0.1 had libgcc. libgcc-ng is only available on the anaconda channel, which is not normally in the channels. libgcc-ng nor the anaconda channel are listed in any of your ymls that I can see.

conda install quicksect=0.2 -c conda-forge -c anaconda

wants to change the version of all sorts of things that make me nervous.

sebastian-luna-valero commented 5 years ago

Can you please copy and paste the output of conda env export

IanSudbery commented 5 years ago 
name: py3
channels:
- bioconda
- conda-forge
- defaults
dependencies:
- alignlib-lite=0.3=py36_0
- bioconductor-annotate=1.56.0=r3.4.1_0
- bioconductor-annotationdbi=1.40.0=r3.4.1_0
- bioconductor-annotationfilter=1.2.0=r3.4.1_0
- bioconductor-annotationforge=1.20.0=r3.4.1_0
- bioconductor-annotationhub=2.10.1=r3.4.1_0
- bioconductor-biobase=2.38.0=r3.4.1_0
- bioconductor-biocgenerics=0.24.0=r3.4.1_0
- bioconductor-biocinstaller=1.28.0=r3.4.1_0
- bioconductor-biocparallel=1.12.0=r3.4.1_0
- bioconductor-biomart=2.34.0=r3.4.1_0
- bioconductor-biostrings=2.46.0=r3.4.1_0
- bioconductor-biovizbase=1.26.0=r3.4.1_0
- bioconductor-bsgenome=1.46.0=r3.4.1_0
- bioconductor-bsgenome.hsapiens.ucsc.hg19=1.4.0=r3.4.1_2
- bioconductor-category=2.44.0=r3.4.1_0
- bioconductor-chipqc=1.14.0=r3.4.1_0
- bioconductor-chipseq=1.28.0=r3.4.1_0
- bioconductor-cummerbund=2.20.0=r3.4.1_0
- bioconductor-delayedarray=0.4.1=r3.4.1_0
- bioconductor-deseq=1.30.0=r3.4.1_0
- bioconductor-deseq2=1.18.1=r3.4.1_1
- bioconductor-dexseq=1.24.0=py36r3.4.1_1
- bioconductor-diffbind=2.6.6=r3.4.1_0
- bioconductor-dnacopy=1.52.0=r3.4.1_0
- bioconductor-edger=3.20.7=r3.4.1_0
- bioconductor-ensembldb=2.0.4=r3.4.1_0
- bioconductor-genefilter=1.60.0=r3.4.1_0
- bioconductor-geneplotter=1.56.0=r3.4.1_0
- bioconductor-genomeinfodb=1.14.0=r3.4.1_0
- bioconductor-genomeinfodbdata=1.0.0=r3.4.1_1
- bioconductor-genomicalignments=1.14.0=r3.4.1_0
- bioconductor-genomicfeatures=1.28.5=r3.4.1_0
- bioconductor-genomicranges=1.30.0=r3.4.1_0
- bioconductor-go.db=3.5.0=r3.4.1_1
- bioconductor-gostats=2.44.0=r3.4.1_0
- bioconductor-graph=1.56.0=r3.4.1_0
- bioconductor-gseabase=1.40.0=r3.4.1_0
- bioconductor-gviz=1.22.0=r3.4.1_0
- bioconductor-hilbertvis=1.36.0=r3.4.1_0
- bioconductor-hpar=1.20.0=r3.4.1_0
- bioconductor-ihw=1.6.0=r3.4.1_0
- bioconductor-impute=1.52.0=r3.4.1_0
- bioconductor-interactivedisplaybase=1.16.0=r3.4.1_0
- bioconductor-iranges=2.12.0=r3.4.1_0
- bioconductor-limma=3.34.6=r3.4.1_0
- bioconductor-lpsymphony=1.6.0=r3.4.1_0
- bioconductor-masigpro=1.50.0=0
- bioconductor-medips=1.30.0=r3.4.1_0
- bioconductor-metagenomeseq=1.20.0=r3.4.1_0
- bioconductor-multtest=2.34.0=r3.4.1_0
- bioconductor-preprocesscore=1.40.0=r3.4.1_0
- bioconductor-protgenerics=1.10.0=r3.4.1_0
- bioconductor-rbgl=1.54.0=r3.4.1_0
- bioconductor-rgraphviz=2.22.0=r3.4.1_0
- bioconductor-rhdf5=2.22.0=r3.4.1_0
- bioconductor-rsamtools=1.30.0=r3.4.1_0
- bioconductor-rtracklayer=1.38.0=r3.4.1_0
- bioconductor-s4vectors=0.16.0=r3.4.1_0
- bioconductor-shortread=1.36.0=r3.4.1_0
- bioconductor-siggenes=1.52.0=r3.4.1_0
- bioconductor-summarizedexperiment=1.8.0=r3.4.1_0
- bioconductor-systempiper=1.12.0=r3.4.1_0
- bioconductor-txdb.celegans.ucsc.ce6.ensgene=3.2.2=r3.4.1_1
- bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene=3.2.2=r3.4.1_2
- bioconductor-txdb.hsapiens.ucsc.hg18.knowngene=3.2.2=r3.4.1_1
- bioconductor-txdb.hsapiens.ucsc.hg19.knowngene=3.2.2=r3.4.1_1
- bioconductor-txdb.mmusculus.ucsc.mm10.knowngene=3.4.0=r3.4.1_1
- bioconductor-txdb.mmusculus.ucsc.mm9.knowngene=3.2.2=r3.4.1_1
- bioconductor-txdb.rnorvegicus.ucsc.rn4.ensgene=3.2.2=r3.4.1_1
- bioconductor-tximport=1.6.0=r3.4.1_0
- bioconductor-variantannotation=1.24.1=r3.4.1_0
- bioconductor-xvector=0.18.0=r3.4.1_0
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- biopython=1.70=np112py36_1
- bleach=1.4.2=py36_0
- cgat-report=0.8.0=py36_0
- gevent=1.1rc4=py36_0
- ggplot=0.6.8=py36_0
- htslib=1.7=0
- idr=2.0.3=py36_4
- intermine=1.09.09=py36_0
- multiqc=1.5a=py36_0
- mygene=3.0.0=py36_0
- mysql-connector-c=6.1.6=2
- openpyxl=2.4.0=py36_0
- picard=2.18.0=py36_0
- pybedtools=0.7.10=py36_2
- pybigwig=0.3.5=np112py36_0
- pysam=0.14.0=py36_htslib1.7_2
- quicksect=0.1.0=py36_0
- r-coloc=2.3_1=r3.4.1_0
- r-data.table=1.10.4=r3.4.1_0
- r-deconstructsigs=1.8.0=r3.4.1_0
- r-deoptimr=1.0_8=r3.4.1_0
- r-dynamictreecut=1.63_1=r3.4.1_0
- r-purrr=0.2.2=1
- r-qqman=0.1.4=r3.4.1_0
- r-samr=2.0=r3.4.1_0
- r-sleuth=0.29.0=r3.4.1_0
- r-wasabi=0.2=r3.4.1_0
- r-wgcna=1.61=r3.4.1_0
- ruffus=2.6.3=py36_0
- simplejson=3.8.1=py36_0
- typing=3.5.2.2=py36_0
- alabaster=0.7.10=py36_1
- asn1crypto=0.24.0=py36_0
- attrs=17.2.0=py36_0
- babel=2.5.3=py36_0
- backports=1.0=py36_1
- backports.functools_lru_cache=1.5=py36_0
- beautifulsoup4=4.6.0=py36_0
- blas=1.1=openblas
- bokeh=0.12.14=py36_0
- brewer2mpl=1.4.1=py36_2
- bzip2=1.0.6=1
- ca-certificates=2018.1.18=0
- cairo=1.14.10=0
- certifi=2018.1.18=py36_0
- cffi=1.11.5=py36_0
- chardet=3.0.4=py36_0
- click=6.7=py36_0
- colormath=3.0.0=py_2
- coverage=4.5.1=py36_0
- cryptography=2.1.4=py36_0
- curl=7.59.0=0
- cycler=0.10.0=py36_0
- cython=0.28.1=py36_0
- dbus=1.10.22=0
- decorator=4.2.1=py36_0
- docutils=0.14=py36_0
- entrypoints=0.2.3=py36_1
- et_xmlfile=1.0.1=py36_0
- expat=2.2.5=0
- fontconfig=2.12.6=0
- freetype=2.8.1=0
- future=0.16.0=py36_0
- gettext=0.19.8.1=0
- glib=2.55.0=0
- gmp=6.1.2=0
- graphite2=1.3.11=0
- graphviz=2.38.0=7
- greenlet=0.4.13=py36_0
- gsl=2.2.1=blas_openblas_3
- gst-plugins-base=1.8.0=0
- gstreamer=1.8.0=1
- harfbuzz=1.7.6=0
- html5lib=0.999999999=py36_0
- httplib2=0.10.3=py36_0
- hypothesis=3.50.2=py36_0
- icu=58.2=0
- idna=2.6=py36_1
- imagesize=1.0.0=py36_0
- ipykernel=4.8.2=py36_0
- ipython=6.2.1=py36_1
- ipython_genutils=0.2.0=py36_0
- ipywidgets=7.1.2=py36_0
- isodate=0.5.4=py36_0
- jdcal=1.3=py36_0
- jedi=0.11.1=py36_0
- jinja2=2.10=py36_0
- jpeg=9b=2
- jsonschema=2.6.0=py36_1
- jupyter=1.0.0=py36_0
- jupyter_client=5.2.3=py36_0
- jupyter_console=5.2.0=py36_0
- jupyter_core=4.4.0=py_0
- keepalive=0.5=py36_0
- kiwisolver=1.0.1=py36_1
- krb5=1.14.2=0
- libffi=3.2.1=3
- libiconv=1.15=0
- libpng=1.6.34=0
- libsodium=1.0.15=1
- libssh2=1.8.0=2
- libtiff=4.0.9=0
- libtool=2.4.6=0
- libuuid=1.0.3=1
- libxcb=1.13=0
- libxml2=2.9.8=0
- lzo=2.10=0
- lzstring=1.0.3=py36_0
- markdown=2.6.11=py_0
- markupsafe=1.0=py36_0
- matplotlib=2.2.2=py36_0
- matplotlib-venn=0.11.5=py36_0
- mistune=0.8=py36_0
- mmtf-python=1.0.7=py36_0
- mpc=1.0.3=4
- mpfr=3.1.5=0
- mpld3=0.3=py36_0
- msgpack-python=0.5.5=py36_0
- nbconvert=5.3.1=py36_0
- nbformat=4.4.0=py36_0
- ncurses=5.9=10
- networkx=2.0=py36_1
- nose=1.3.7=py36_2
- notebook=5.4.1=py36_0
- numpy=1.12.1=py36_blas_openblas_200
- olefile=0.45.1=py36_0
- openblas=0.2.19=2
- openssl=1.0.2n=0
- packaging=16.8=py36_0
- pandas=0.22.0=py36_0
- pandoc=2.1.3=0
- pandocfilters=1.4.1=py36_0
- pango=1.40.14=0
- paramiko=2.4.1=py36_0
- parso=0.1.1=py_0
- patsy=0.5.0=py36_0
- pcre=8.39=0
- pep8=1.7.1=py_0
- pexpect=4.4.0=py36_0
- pickleshare=0.7.4=py36_0
- pillow=5.0.0=py36_0
- pip=9.0.1=py36_1
- pixman=0.34.0=1
- pluggy=0.6.0=py_0
- prompt_toolkit=1.0.15=py36_0
- ptyprocess=0.5.2=py36_0
- py=1.5.2=py_0
- pyasn1=0.3.3=py36_0
- pycparser=2.18=py36_0
- pygments=2.2.0=py36_0
- pympler=0.5=py36_0
- pynacl=1.1.2=py36_0
- pyopenssl=17.5.0=py36_0
- pyparsing=2.2.0=py36_0
- pyqt=5.6.0=py36_4
- pysocks=1.6.8=py36_1
- pytest=3.4.2=py36_0
- python=3.6.4=0
- python-dateutil=2.6.1=py36_0
- python-drmaa=0.7.6=py36_0
- python-lzo=1.11=py36_0
- pytz=2017.3=py36_3
- pyyaml=3.12=py36_1
- pyzmq=17.0.0=py36_3
- qt=5.6.2=7
- qtconsole=4.3.1=py36_0
- r-acepack=1.4.1=r3.4.1_0
- r-amap=0.8_14=r3.4.1_0
- r-assertthat=0.2.0=r3.4.1_0
- r-backports=1.0.5=r3.4.1_0
- r-base=3.4.1=3
- r-base64enc=0.1_3=r3.4.1_0
- r-batchjobs=1.6=r3.4.1_0
- r-bbmisc=1.11=r3.4.1_0
- r-bh=1.66.0_1=r3.4.1_0
- r-bindr=0.1.1=r3.4.1_0
- r-bindrcpp=0.2=r3.4.1_0
- r-bit=1.1_12=r3.4.1_0
- r-bit64=0.9_5=r3.4.1_0
- r-bitops=1.0_6=r3.4.1_0
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- r-bma=3.18.7=r3.4.1_0
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- r-calibrate=1.7.2=r3.4.1_0
- r-catools=1.17.1=r3.4.1_0
- r-checkmate=1.8.2=r3.4.1_0
- r-cli=1.0.0=r3.4.1_0
- r-cluster=2.0.6=r3.4.1_0
- r-codetools=0.2_15=r3.4.1_0
- r-colorspace=1.3_2=r3.4.1_0
- r-crayon=1.3.4=r3.4.1_0
- r-crosstalk=1.0.0=r3.4.1_0
- r-curl=3.1=r3.4.1_0
- r-dbi=0.8=r3.4.1_0
- r-dichromat=2.0_0=r3.4.1_0
- r-digest=0.6.12=r3.4.1_0
- r-doparallel=1.0.11=r3.4.1_0
- r-dplyr=0.7.4=r3.4.1_0
- r-dt=0.4=r3.4.1_0
- r-evaluate=0.10.1=r3.4.1_0
- r-fail=1.3=r3.4.1_0
- r-fastcluster=1.1.24=r3.4.1_0
- r-fdrtool=1.2.15=r3.4.1_0
- r-fit.models=0.5_14=r3.4.1_0
- r-flashclust=1.01_2=r3.4.1_0
- r-foreach=1.4.4=r3.4.1_0
- r-foreign=0.8_67=r3.4.1_0
- r-formula=1.2_1=r3.4.1_0
- r-futile.logger=1.4.3=r3.4.1_0
- r-futile.options=1.0.0=r3.4.1_0
- r-gdata=2.18.0=r3.4.1_0
- r-getopt=1.20.0=r3.4.1_0
- r-ggplot2=2.2.1=r3.4.1_0
- r-ggrepel=0.7.0=r3.4.1_0
- r-glmnet=2.0_5=r3.4.1_0
- r-glue=1.2.0=r3.4.1_0
- r-gmd=0.3.3=r3.4.1_0
- r-gplots=3.0.1=r3.4.1_0
- r-gridbase=0.4_7=r3.4.1_0
- r-gridextra=2.3=r3.4.1_0
- r-gtable=0.2.0=r3.4.1_0
- r-gtools=3.5.0=r3.4.1_0
- r-hiddenmarkov=1.8_8=r3.4.1_0
- r-highr=0.6=r3.4.1_0
- r-hmisc=4.0_3=r3.4.1_0
- r-htmltable=1.9=r3.4.1_0
- r-htmltools=0.3.6=r3.4.1_0
- r-htmlwidgets=1.0=r3.4.1_0
- r-httpuv=1.3.6.2=r3.4.1_0
- r-httr=1.3.1=r3.4.1_0
- r-hwriter=1.3.2=r3.4.1_0
- r-inline=0.3.14=r3.4.1_0
- r-iterators=1.0.9=r3.4.1_0
- r-jsonlite=1.5=r3.4.1_0
- r-kernsmooth=2.23_15=r3.4.1_0
- r-knitr=1.20=r3.4.1_0
- r-labeling=0.3=r3.4.1_0
- r-lambda.r=1.2=r3.4.1_0
- r-lattice=0.20_34=r3.4.1_0
- r-latticeextra=0.6_28=r3.4.1_0
- r-lazyeval=0.2.1=r3.4.1_0
- r-leaps=3.0=r3.4.1_0
- r-locfit=1.5_9.1=r3.4.1_0
- r-magrittr=1.5=r3.4.1_0
- r-mapdata=2.2_6=r3.4.1_0
- r-maps=3.2.0=r3.4.1_0
- r-markdown=0.8=r3.4.1_1
- r-mass=7.3_48=r3.4.1_0
- r-matrix=1.2_12=r3.4.1_0
- r-matrixstats=0.52.2=r3.4.1_0
- r-mclust=5.4=r3.4.1_0
- r-memoise=1.1.0=r3.4.1_0
- r-mgcv=1.8_17=r3.4.1_0
- r-mime=0.5=r3.4.1_0
- r-munsell=0.4.3=r3.4.1_0
- r-mvtnorm=1.0_6=r3.4.1_0
- r-nlme=3.1_131=r3.4.1_0
- r-nnet=7.3_12=r3.4.1_0
- r-nozzle.r1=1.1_1=r3.4.1_0
- r-openssl=1.0.1=r3.4.1_0
- r-optparse=1.4.4=r3.4.1_0
- r-pcapp=1.9_61=r3.4.1_0
- r-permute=0.9_4=r3.4.1_1
- r-pheatmap=1.0.8=r3.4.1_0
- r-pillar=1.2.1=r3.4.1_0
- r-pkgconfig=2.0.1=r3.4.1_0
- r-plogr=0.1_1=r3.4.1_0
- r-plotrix=3.7=r3.4.1_0
- r-plyr=1.8.4=r3.4.1_0
- r-prettyunits=1.0.2=r3.4.1_0
- r-progress=1.1.2=r3.4.1_0
- r-r6=2.2.2=r3.4.1_0
- r-rcolorbrewer=1.1_2=r3.4.1_0
- r-rcpp=0.12.15=r3.4.1_0
- r-rcpparmadillo=0.7.800.2.0=r3.4.1_0
- r-rcurl=1.95_4.8=r3.4.1_0
- r-reshape=0.8.7=r3.4.1_0
- r-reshape2=1.4.3=r3.4.1_0
- r-rjson=0.2.15=r3.4.1_0
- r-rlang=0.2.0=r3.4.1_0
- r-rmarkdown=1.8=r3.4.1_0
- r-robust=0.4_18=r3.4.1_0
- r-robustbase=0.92_7=r3.4.1_0
- r-rpart=4.1_13=r3.4.1_0
- r-rprojroot=1.2=r3.4.1_0
- r-rrcov=1.4_3=r3.4.1_0
- r-rsqlite=2.0=r3.4.1_0
- r-scales=0.5.0=r3.4.1_0
- r-sendmailr=1.2_1=r3.4.1_0
- r-shiny=1.0.5=r3.4.1_0
- r-slam=0.1_40=r3.4.1_0
- r-snow=0.4_2=r3.4.1_0
- r-sourcetools=0.1.6=r3.4.1_0
- r-statmod=1.4.30=r3.4.1_0
- r-stringi=1.1.6=r3.4.1_0
- r-stringr=1.3.0=r3.4.1_0
- r-survival=2.40_1=r3.4.1_0
- r-tibble=1.4.2=r3.4.1_0
- r-tidyr=0.8.0=r3.4.1_0
- r-tidyselect=0.2.3=r3.4.1_0
- r-utf8=1.1.3=r3.4.1_0
- r-vegan=2.4_3=r3.4.1_0
- r-venn=1.2=r3.4.1_0
- r-venndiagram=1.6.18=r3.4.1_0
- r-viridis=0.4.0=r3.4.1_0
- r-viridislite=0.2.0=r3.4.1_0
- r-xml=3.98_1.6=r3.4.1_0
- r-xtable=1.8_2=r3.4.1_0
- r-yaml=2.1.14=r3.4.1_0
- rdflib=4.2.2=py36_0
- readline=7.0=0
- requests=2.18.4=py36_1
- rpy2=2.8.5=py36r3.4.1_0
- scikit-learn=0.19.1=py36_blas_openblas_200
- scipy=0.19.1=py36_blas_openblas_202
- seaborn=0.8.1=py36_0
- send2trash=1.5.0=py_0
- setuptools=39.0.1=py36_0
- simplegeneric=0.8.1=py36_0
- singledispatch=3.4.0.3=py36_0
- sip=4.18=py36_1
- six=1.11.0=py36_1
- snowballstemmer=1.2.1=py36_0
- sortedcontainers=1.5.9=py36_0
- sparqlwrapper=1.8.0=py36_0
- spectra=0.0.11=py_0
- sphinx=1.7.1=py36_0
- sphinxcontrib-websupport=1.0.1=py36_0
- sqlalchemy=1.2.5=py36_0
- sqlite=3.20.1=2
- statsmodels=0.8.0=py36_0
- terminado=0.8.1=py36_0
- testpath=0.3.1=py36_0
- time=1.7=0
- tk=8.6.7=0
- toposort=1.5=py36_0
- tornado=5.0.1=py36_1
- traitlets=4.3.2=py36_0
- urllib3=1.22=py36_0
- wcwidth=0.1.7=py36_0
- web.py=0.40.dev0=py36_0
- webencodings=0.5=py36_0
- wheel=0.30.0=py36_2
- widgetsnbextension=3.1.4=py36_0
- xorg-kbproto=1.0.7=1
- xorg-libice=1.0.9=2
- xorg-libsm=1.2.2=2
- xorg-libx11=1.6.5=0
- xorg-libxau=1.0.8=3
- xorg-libxdmcp=1.1.2=3
- xorg-libxext=1.3.3=2
- xorg-libxrender=0.9.10=0
- xorg-renderproto=0.11.1=1
- xorg-xextproto=7.3.0=1
- xorg-xproto=7.0.31=6
- xz=5.2.3=0
- yaml=0.1.7=0
- zeromq=4.2.3=2
- zlib=1.2.11=0
- bcrypt=3.1.3=py36_0
- cloog=0.18.0=0
- gcc=4.8.5=7
- isl=0.12.2=0
- libgcc=5.2.0=0
- libgfortran=3.0.0=1
- nomkl=1.0=0
- openjdk=8.0.121=1
- reportlab=3.4.0=py36_0
- util-linux=2.21=0
- wget=1.18=0
- zope=1.0=py36_0
- zope.interface=4.4.2=py36_0
- pip:
  - apipkg==1.4
  - backports.functools-lru-cache==1.5
  - cgat (/home/mb1ims/devel/cgat-apps)==0.4.0
  - cgatcore (/home/mb1ims/devel/cgat-core)==0.4.0
  - cgatpipelines (/home/mb1ims/devel/cgat-flow)==0.4.0
  - cgatreport==0.8.0
  - drmaa==0.7.6
  - et-xmlfile==1.0.1
  - execnet==1.5.0
  - ipython-genutils==0.2.0
  - jupyter-client==5.2.3
  - jupyter-console==5.2.0
  - jupyter-core==4.4.0
  - macs==1.4.1
  - macs2==2.1.1.20160309
  - prompt-toolkit==1.0.15
  - pytest-forked==0.2
  - pytest-xdist==1.22.2
sebastian-luna-valero commented 5 years ago

I agree with you, please don't run conda install quicksect=0.2 -c conda-forge -c anaconda

Do you get the following output:

$ conda search quicksect
Loading channels: done
# Name                  Version           Build  Channel             
quicksect                 0.1.0          py27_0  bioconda            
quicksect                 0.1.0  py27h470a237_1  bioconda            
quicksect                 0.1.0          py35_0  bioconda            
quicksect                 0.1.0  py35h470a237_1  bioconda            
quicksect                 0.1.0          py36_0  bioconda            
quicksect                 0.1.0  py36h470a237_1  bioconda            
quicksect                 0.2.0  py27h470a237_1  bioconda            
quicksect                 0.2.0  py35h470a237_1  bioconda            
quicksect                 0.2.0  py36h470a237_1  bioconda

Having this ~/.condarc:

$ cat ~/.condarc
channels:
  - bioconda
  - conda-forge
  - defaults
show_channel_urls: true

This is what I get for libgcc-ng:

$ conda search libgcc-ng
Loading channels: done
# Name                  Version           Build  Channel             
libgcc-ng                 5.4.0      hdf63c60_3  pkgs/main           
libgcc-ng                 7.2.0      h7cc24e2_2  pkgs/main           
libgcc-ng                 7.2.0      hcbc56d2_1  pkgs/main           
libgcc-ng                 7.2.0      hdf63c60_3  pkgs/main

Not sure how you ended up with libgcc=5.2.0=0 on your environment.

Can you also try conda update quicksect --no-deps?

You could also try: pip install quicksect, or go brute force with conda install quicksect=0.2.0 --force

IanSudbery commented 5 years ago 
$ conda search quicksect
Fetching package metadata .............
quicksect                    0.1.0                    py35_0  bioconda        
                             0.1.0                    py27_0  bioconda        
                          *  0.1.0                    py36_0  bioconda        
                             0.1.0            py36h470a237_1  bioconda        
                             0.1.0            py27h470a237_1  bioconda        
                             0.1.0            py35h470a237_1  bioconda        
                             0.2.0            py36h470a237_1  bioconda        
                             0.2.0            py35h470a237_1  bioconda        
                             0.2.0            py27h470a237_1  bioconda 
$ cat ~/.condarc
channels:
  - bioconda
  - conda-forge
  - defaults
show_channel_urls: true
$ conda search libgcc-ng
Fetching package metadata .............

(i.e. returns nothing)

sebastian-luna-valero commented 5 years ago

Please copy and paste conda info

CristinaAlexandru commented 5 years ago

$ conda info Current conda install:

               platform : linux-64
          conda version : 4.3.17
       conda is private : False
      conda-env version : 4.3.17
    conda-build version : 2.1.13
         python version : 3.5.3.final.0
       requests version : 2.13.0
       root environment : /usr/local/packages/apps/conda  (read only)
    default environment : /data/mb1cna/cgat/envs/sharc
       envs directories : /home/mb1cna/.conda/envs
                      /usr/local/packages/apps/conda/envs
          package cache : /usr/local/packages/apps/conda/pkgs
                      /home/mb1cna/.conda/pkgs
           channel URLs : https://conda.anaconda.org/bioconda/linux-64
                      https://conda.anaconda.org/bioconda/noarch
                      https://conda.anaconda.org/conda-forge/linux-64
                      https://conda.anaconda.org/conda-forge/noarch
                      https://conda.anaconda.org/default/linux-64
                      https://conda.anaconda.org/default/noarch
                      https://repo.continuum.io/pkgs/free/linux-64
                      https://repo.continuum.io/pkgs/free/noarch
                      https://repo.continuum.io/pkgs/r/linux-64
                      https://repo.continuum.io/pkgs/r/noarch
                      https://repo.continuum.io/pkgs/pro/linux-64
                      https://repo.continuum.io/pkgs/pro/noarch
            config file : /home/mb1cna/.condarc
           offline mode : False
             user-agent : conda/4.3.17 requests/2.13.0 CPython/3.5.3

Linux/3.10.0-862.6.3.el7.x86_64 CentOS Linux/7.5.1804 glibc/2.17 UID:GID : 173750:5300

On 20 July 2018 at 10:36, Sebastian Luna-Valero notifications@github.com wrote:

Please copy and paste conda info

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Research Associate Bioinformatics Hub, Firth Court Department of Molecular Biology and Biotechnology (MBB), University of Sheffield, Western Bank, Sheffield S10 2TN England, UK. Tel. +44 (0)7703417022 c.alexandru@sheffield.ac.uk r01cna14@abdn.ac.uk

sebastian-luna-valero commented 5 years ago

Apart from having a different conda version, I get slightly different result for the defaults channel

$ conda info

     active environment : cgat-f
    active env location : /ifs/devel/sebastian/cgat-developers-v0/conda-install/envs/cgat-f
            shell level : 2
       user config file : /ifs/home/sebastian/.condarc
 populated config files : /ifs/home/sebastian/.condarc
          conda version : 4.5.5
    conda-build version : not installed
         python version : 3.6.5.final.0
       base environment : /ifs/devel/sebastian/cgat-developers-v0/conda-install  (writable)
           channel URLs : https://conda.anaconda.org/bioconda/linux-64
                          https://conda.anaconda.org/bioconda/noarch
                          https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/free/linux-64
                          https://repo.anaconda.com/pkgs/free/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
                          https://repo.anaconda.com/pkgs/pro/linux-64
                          https://repo.anaconda.com/pkgs/pro/noarch
          package cache : /ifs/devel/sebastian/cgat-developers-v0/conda-install/pkgs
                          /ifs/home/sebastian/.conda/pkgs
       envs directories : /ifs/devel/sebastian/cgat-developers-v0/conda-install/envs
                          /ifs/home/sebastian/.conda/envs
               platform : linux-64
             user-agent : conda/4.5.5 requests/2.13.0 CPython/3.6.5 Linux/2.6.32-754.el6.x86_64 rhel/6.10 glibc/2.12
                UID:GID : 1362:1000
             netrc file : None
           offline mode : False

Can you please copy and paste cat ~/.condarc

CristinaAlexandru commented 5 years ago

$ cat ~/.condarc channels:

On 20 July 2018 at 11:12, Sebastian Luna-Valero notifications@github.com wrote:

Apart from having a different conda version, I get slightly different result for the defaults channel

$ conda info

 active environment : cgat-f
active env location : /ifs/devel/sebastian/cgat-developers-v0/conda-install/envs/cgat-f
        shell level : 2
   user config file : /ifs/home/sebastian/.condarc

populated config files : /ifs/home/sebastian/.condarc conda version : 4.5.5 conda-build version : not installed python version : 3.6.5.final.0 base environment : /ifs/devel/sebastian/cgat-developers-v0/conda-install (writable) channel URLs : https://conda.anaconda.org/bioconda/linux-64 https://conda.anaconda.org/bioconda/noarch https://conda.anaconda.org/conda-forge/linux-64 https://conda.anaconda.org/conda-forge/noarch https://repo.anaconda.com/pkgs/main/linux-64 https://repo.anaconda.com/pkgs/main/noarch https://repo.anaconda.com/pkgs/free/linux-64 https://repo.anaconda.com/pkgs/free/noarch https://repo.anaconda.com/pkgs/r/linux-64 https://repo.anaconda.com/pkgs/r/noarch https://repo.anaconda.com/pkgs/pro/linux-64 https://repo.anaconda.com/pkgs/pro/noarch package cache : /ifs/devel/sebastian/cgat-developers-v0/conda-install/pkgs /ifs/home/sebastian/.conda/pkgs envs directories : /ifs/devel/sebastian/cgat-developers-v0/conda-install/envs /ifs/home/sebastian/.conda/envs platform : linux-64 user-agent : conda/4.5.5 requests/2.13.0 CPython/3.6.5 Linux/2.6.32-754.el6.x86_64 rhel/6.10 glibc/2.12 UID:GID : 1362:1000 netrc file : None offline mode : False

Can you please copy and paste cat ~/.condarc

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--

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Research Associate Bioinformatics Hub, Firth Court Department of Molecular Biology and Biotechnology (MBB), University of Sheffield, Western Bank, Sheffield S10 2TN England, UK. Tel. +44 (0)7703417022 c.alexandru@sheffield.ac.uk r01cna14@abdn.ac.uk

sebastian-luna-valero commented 5 years ago

Can you please edit ~/.condarc so you have the following:

channels:
  - bioconda
  - conda-forge
  - defaults
show_channel_urls: true

After that, please copy and paste conda info and conda search libgcc-ng

CristinaAlexandru commented 5 years ago

After making the change, here it is:

$ conda info Current conda install:

               platform : linux-64
          conda version : 4.3.17
       conda is private : False
      conda-env version : 4.3.17
    conda-build version : 2.1.13
         python version : 3.5.3.final.0
       requests version : 2.13.0
       root environment : /usr/local/packages/apps/conda  (read only)
    default environment : /data/mb1cna/cgat/envs/sharc
       envs directories : /home/mb1cna/.conda/envs
                      /usr/local/packages/apps/conda/envs
          package cache : /usr/local/packages/apps/conda/pkgs
                      /home/mb1cna/.conda/pkgs
           channel URLs : https://conda.anaconda.org/bioconda/linux-64
                      https://conda.anaconda.org/bioconda/noarch
                      https://conda.anaconda.org/conda-forge/linux-64
                      https://conda.anaconda.org/conda-forge/noarch
                      https://repo.continuum.io/pkgs/free/linux-64
                      https://repo.continuum.io/pkgs/free/noarch
                      https://repo.continuum.io/pkgs/r/linux-64
                      https://repo.continuum.io/pkgs/r/noarch
                      https://repo.continuum.io/pkgs/pro/linux-64
                      https://repo.continuum.io/pkgs/pro/noarch
            config file : /home/mb1cna/.condarc
           offline mode : False
             user-agent : conda/4.3.17 requests/2.13.0 CPython/3.5.3

Linux/3.10.0-862.6.3.el7.x86_64 CentOS Linux/7.5.1804 glibc/2.17 UID:GID : 173750:5300

$ conda search libgcc-ng Fetching package metadata .............

Nothing else was returned.

On 20 July 2018 at 11:19, Sebastian Luna-Valero notifications@github.com wrote:

Can you please edit ~/.condarc so you have the following:

channels:

  • bioconda
  • conda-forge
  • defaults show_channel_urls: true

After that, please copy and paste conda info and conda search libgcc-ng

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/cgat-developers/cgat-apps/issues/14#issuecomment-406558015, or mute the thread https://github.com/notifications/unsubscribe-auth/Am9bhBObiTEcuNRLzz0Wl0Abe5vWCNl9ks5uIa6VgaJpZM4VQ08_ .

--

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Research Associate Bioinformatics Hub, Firth Court Department of Molecular Biology and Biotechnology (MBB), University of Sheffield, Western Bank, Sheffield S10 2TN England, UK. Tel. +44 (0)7703417022 c.alexandru@sheffield.ac.uk r01cna14@abdn.ac.uk

sebastian-luna-valero commented 5 years ago

I don't understand why you are missing the main channel:

                          https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch

That channel is where the libgcc-ng package is:

$ conda search libgcc-ng
Loading channels: done
# Name                  Version           Build  Channel             
libgcc-ng                 5.4.0      hdf63c60_3  pkgs/main           
libgcc-ng                 7.2.0      h7cc24e2_2  pkgs/main           
libgcc-ng                 7.2.0      hcbc56d2_1  pkgs/main           
libgcc-ng                 7.2.0      hdf63c60_3  pkgs/main

Let's be explicity. Please try replacing your ~/.condarc with:

channels:
  - https://conda.anaconda.org/bioconda
  - https://conda.anaconda.org/conda-forge
  - https://repo.anaconda.com/pkgs/main
  - https://repo.anaconda.com/pkgs/free
  - https://repo.anaconda.com/pkgs/r
  - https://repo.anaconda.com/pkgs/pro
show_channel_urls: true

After that, please copy and paste conda info and conda search libgcc-ng

CristinaAlexandru commented 5 years ago

Did that:

$ conda info Current conda install:

               platform : linux-64
          conda version : 4.3.17
       conda is private : False
      conda-env version : 4.3.17
    conda-build version : 2.1.13
         python version : 3.5.3.final.0
       requests version : 2.13.0
       root environment : /usr/local/packages/apps/conda  (read only)
    default environment : /data/mb1cna/cgat/envs/sharc
       envs directories : /home/mb1cna/.conda/envs
                      /usr/local/packages/apps/conda/envs
          package cache : /usr/local/packages/apps/conda/pkgs
                      /home/mb1cna/.conda/pkgs
           channel URLs : https://conda.anaconda.org/bioconda/linux-64
                      https://conda.anaconda.org/bioconda/noarch
                      https://conda.anaconda.org/conda-forge/linux-64
                      https://conda.anaconda.org/conda-forge/noarch
                      https://repo.anaconda.com/pkgs/main/linux-64
                      https://repo.anaconda.com/pkgs/main/noarch
                      https://repo.anaconda.com/pkgs/free/linux-64
                      https://repo.anaconda.com/pkgs/free/noarch
                      https://repo.anaconda.com/pkgs/r/linux-64
                      https://repo.anaconda.com/pkgs/r/noarch
                      https://repo.anaconda.com/pkgs/pro/linux-64
                      https://repo.anaconda.com/pkgs/pro/noarch
            config file : /home/mb1cna/.condarc
           offline mode : False
             user-agent : conda/4.3.17 requests/2.13.0 CPython/3.5.3

Linux/3.10.0-862.6.3.el7.x86_64 CentOS Linux/7.5.1804 glibc/2.17 UID:GID : 173750:5300

$ conda search libgcc-ng Fetching package metadata ............... libgcc-ng 5.4.0 hdf63c60_3 https://repo.anaconda.com/pkgs/main 7.2.0 hcbc56d2_1 https://repo.anaconda.com/pkgs/main 7.2.0 h7cc24e2_2 https://repo.anaconda.com/pkgs/main 7.2.0 hdf63c60_3 https://repo.anaconda.com/pkgs/main

On 20 July 2018 at 11:37, Sebastian Luna-Valero notifications@github.com wrote:

I don't understand why you are missing the main channel:

                      https://repo.anaconda.com/pkgs/main/linux-64
                      https://repo.anaconda.com/pkgs/main/noarch

That channel is where the libgcc-ng package is:

$ conda search libgcc-ng Loading channels: done

Name Version Build Channel

libgcc-ng 5.4.0 hdf63c60_3 pkgs/main libgcc-ng 7.2.0 h7cc24e2_2 pkgs/main libgcc-ng 7.2.0 hcbc56d2_1 pkgs/main libgcc-ng 7.2.0 hdf63c60_3 pkgs/main

Let's be explicity. Please try replacing your ~/.condarc with:

channels:

After that, please copy and paste conda info and conda search libgcc-ng

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/cgat-developers/cgat-apps/issues/14#issuecomment-406562519, or mute the thread https://github.com/notifications/unsubscribe-auth/Am9bhHrbpE_oRNieNU2aXFD6hQx_o9TDks5uIbMAgaJpZM4VQ08_ .

--

Cristina Alexandru-Crivac

Research Associate Bioinformatics Hub, Firth Court Department of Molecular Biology and Biotechnology (MBB), University of Sheffield, Western Bank, Sheffield S10 2TN England, UK. Tel. +44 (0)7703417022 c.alexandru@sheffield.ac.uk r01cna14@abdn.ac.uk

CristinaAlexandru commented 5 years ago

Then I tried:

$ conda search libgcc-ng Fetching package metadata ............... libgcc-ng 5.4.0 hdf63c60_3 https://repo.anaconda.com/pkgs/main 7.2.0 hcbc56d2_1 https://repo.anaconda.com/pkgs/main 7.2.0 h7cc24e2_2 https://repo.anaconda.com/pkgs/main 7.2.0 hdf63c60_3 https://repo.anaconda.com/pkgs/main (/data/mb1cna/cgat/envs/sharc) [mb1cna@sharc-node001 cgat]$ conda update quicksect Fetching package metadata ............... Solving package specifications: .

Package plan for installation in environment /data/mb1cna/cgat/envs/sharc:

The following NEW packages will be INSTALLED:

libgcc-ng: 7.2.0-hdf63c60_3      https://repo.anaconda.com/pkgs/main
sqlite:    3.20.1-2              conda-forge

The following packages will be UPDATED:

quicksect: 0.1.0-py36_0          bioconda

--> 0.2.0-py36h470a237_1 bioconda

The following packages will be DOWNGRADED due to dependency conflicts:

blas:      1.1-openblas          conda-forge

--> 1.0-openblas https://repo.anaconda.com/pkgs/main gsl: 2.2.1-blas_openblas_3 conda-forge [blas_openblas] --> 2.1-2 conda-forge

I am not sure if I should accept the downgraded packages. Perhaps a --no-deps will be better.

On 20 July 2018 at 11:44, Cristina N Alexandru c.alexandru@sheffield.ac.uk wrote:

Did that:

$ conda info Current conda install:

               platform : linux-64
          conda version : 4.3.17
       conda is private : False
      conda-env version : 4.3.17
    conda-build version : 2.1.13
         python version : 3.5.3.final.0
       requests version : 2.13.0
       root environment : /usr/local/packages/apps/conda  (read only)
    default environment : /data/mb1cna/cgat/envs/sharc
       envs directories : /home/mb1cna/.conda/envs
                      /usr/local/packages/apps/conda/envs
          package cache : /usr/local/packages/apps/conda/pkgs
                      /home/mb1cna/.conda/pkgs
           channel URLs : https://conda.anaconda.org/bioconda/linux-64
                      https://conda.anaconda.org/bioconda/noarch
                      https://conda.anaconda.org/conda-forge/linux-64
                      https://conda.anaconda.org/conda-forge/noarch
                      https://repo.anaconda.com/pkgs/main/linux-64
                      https://repo.anaconda.com/pkgs/main/noarch
                      https://repo.anaconda.com/pkgs/free/linux-64
                      https://repo.anaconda.com/pkgs/free/noarch
                      https://repo.anaconda.com/pkgs/r/linux-64
                      https://repo.anaconda.com/pkgs/r/noarch
                      https://repo.anaconda.com/pkgs/pro/linux-64
                      https://repo.anaconda.com/pkgs/pro/noarch
            config file : /home/mb1cna/.condarc
           offline mode : False
             user-agent : conda/4.3.17 requests/2.13.0 CPython/3.5.3

Linux/3.10.0-862.6.3.el7.x86_64 CentOS Linux/7.5.1804 glibc/2.17 UID:GID : 173750:5300

$ conda search libgcc-ng Fetching package metadata ............... libgcc-ng 5.4.0 hdf63c60_3 https://repo.anaconda.com/pkgs/main 7.2.0 hcbc56d2_1 https://repo.anaconda.com/pkgs/main 7.2.0 h7cc24e2_2 https://repo.anaconda.com/pkgs/main 7.2.0 hdf63c60_3 https://repo.anaconda.com/pkgs/main

On 20 July 2018 at 11:37, Sebastian Luna-Valero notifications@github.com wrote:

I don't understand why you are missing the main channel:

                      https://repo.anaconda.com/pkgs/main/linux-64
                      https://repo.anaconda.com/pkgs/main/noarch

That channel is where the libgcc-ng package is:

$ conda search libgcc-ng Loading channels: done

Name Version Build Channel

libgcc-ng 5.4.0 hdf63c60_3 pkgs/main libgcc-ng 7.2.0 h7cc24e2_2 pkgs/main libgcc-ng 7.2.0 hcbc56d2_1 pkgs/main libgcc-ng 7.2.0 hdf63c60_3 pkgs/main

Let's be explicity. Please try replacing your ~/.condarc with:

channels:

After that, please copy and paste conda info and conda search libgcc-ng

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/cgat-developers/cgat-apps/issues/14#issuecomment-406562519, or mute the thread https://github.com/notifications/unsubscribe-auth/Am9bhHrbpE_oRNieNU2aXFD6hQx_o9TDks5uIbMAgaJpZM4VQ08_ .

--

Cristina Alexandru-Crivac

Research Associate Bioinformatics Hub, Firth Court Department of Molecular Biology and Biotechnology (MBB), University of Sheffield, Western Bank, Sheffield S10 2TN England, UK. Tel. +44 (0)7703417022 c.alexandru@sheffield.ac.uk r01cna14@abdn.ac.uk

--

Cristina Alexandru-Crivac

Research Associate Bioinformatics Hub, Firth Court Department of Molecular Biology and Biotechnology (MBB), University of Sheffield, Western Bank, Sheffield S10 2TN England, UK. Tel. +44 (0)7703417022 c.alexandru@sheffield.ac.uk r01cna14@abdn.ac.uk

sebastian-luna-valero commented 5 years ago

It says will be DOWNGRADED due to dependency conflicts so it might be better to just say yes in this case. However, I would take a note of the versions being replaced just to make sure you can install them back if something else breaks.

CristinaAlexandru commented 5 years ago

I updated quicksect and made all the other modifications (#15 ) and that part of the pipeline works fine now. No more error related to index value.

Thank you so much for helping us with this issue.

sebastian-luna-valero commented 5 years ago

Great, thanks!

sebastian-luna-valero commented 5 years ago

Provided that we have got a reproducible example here, I would like to add a test to cover this issue.

Could you please confirm whether the expected output for the reproducible example above is this one:

$ cgat gtf2table            --counter=classifier-rnaseq-splicing            --reporter=transcripts            --gff-file=smallest_ref.gtf -I weird_transcript.gtf
# 2018-08-22 16:21:25,361 INFO output generated by gtf2table --counter=classifier-rnaseq-splicing --reporter=transcripts --gff-file=smallest_ref.gtf -I weird_transcript.gtf \
#                              job started at Wed Aug 22 16:21:25 2018 on cgath1.anat.ox.ac.uk -- bc8194f6-81a8-4dee-9084-ef1a3170e01f \
#                              pid: 35935, system: Linux 2.6.32-754.el6.x86_64 #1 SMP Thu May 24 18:18:25 EDT 2018 x86_64
# 2018-08-22 16:21:25,361 INFO add_gtf_source                          : False \
#                              bam_files                               : None \
#                              bigwig_file                             : None \
#                              counters                                : ['classifier-rnaseq-splicing'] \
#                              filename_format                         : None \
#                              filename_gff                            : ['smallest_ref.gtf'] \
#                              genome_file                             : None \
#                              gff_features                            : [] \
#                              gff_sources                             : [] \
#                              library_type                            : fr-unstranded \
#                              log_config_filename                     : None \
#                              loglevel                                : 1 \
#                              minimum_mapping_quality                 : 0 \
#                              multi_mapping                           : all \
#                              output_filename_pattern                 : %s \
#                              output_force                            : False \
#                              prefixes                                : [] \
#                              proximal_distance                       : 10000 \
#                              quality_file                            : None \
#                              random_seed                             : None \
#                              reporter                                : transcripts \
#                              sample_probability                      : 1.0 \
#                              sections                                : [] \
#                              short_help                              : None \
#                              stderr                                  : <_io.TextIOWrapper name='<stderr>' mode='w' encoding='UTF-8'> \
#                              stdin                                   : <_io.TextIOWrapper name='weird_transcript.gtf' mode='r' encoding='utf-8'> \
#                              stdlog                                  : <_io.TextIOWrapper name='<stdout>' mode='w' encoding='UTF-8'> \
#                              stdout                                  : <_io.TextIOWrapper name='<stdout>' mode='w' encoding='UTF-8'> \
#                              timeit_file                             : None \
#                              timeit_header                           : None \
#                              timeit_name                             : all \
#                              tracing                                 : None \
#                              use_barcodes                            : False \
#                              with_values                             : True
# 2018-08-22 16:21:25,361 INFO counters will use the default section (exons)
# 2018-08-22 16:21:25,361 INFO loading data from smallest_ref.gtf
# 2018-08-22 16:21:25,362 INFO loaded data from smallest_ref.gtf
transcript_id   noverlap_transcripts    noverlap_genes  match_transcript_id match_gene_id   source  class   sense
MSTRG.28419.1   0   0   ENST00000341280 ENSG00000188263 ensembl flank3  s
# 2018-08-22 16:21:25,362 INFO input=1, output=1
# 2018-08-22 16:21:25,362 INFO <CGAT.GeneModelAnalysis.ClassifierRNASeqSplicing object at 0x7f1139d2c208>   
# 2018-08-22 16:21:25,362 INFO job finished in 0 seconds at Wed Aug 22 16:21:25 2018 --  1.43  2.91  0.00  0.00 -- bc8194f6-81a8-4dee-9084-ef1a3170e01f

Best regards, Sebastian

CristinaAlexandru commented 5 years ago

Yes, the expected output should look exactly like that for this given example.

On 22 August 2018 at 16:24, Sebastian Luna-Valero notifications@github.com wrote:

Provided that we have got a reproducible example here, I would like to add a test to cover this issue.

Could you please confirm whether the expected output for the reproducible example above is this one:

$ cgat gtf2table --counter=classifier-rnaseq-splicing --reporter=transcripts --gff-file=smallest_ref.gtf -I weird_transcript.gtf

2018-08-22 16:21:25,361 INFO output generated by gtf2table --counter=classifier-rnaseq-splicing --reporter=transcripts --gff-file=smallest_ref.gtf -I weird_transcript.gtf \

job started at Wed Aug 22 16:21:25 2018 on cgath1.anat.ox.ac.uk -- bc8194f6-81a8-4dee-9084-ef1a3170e01f \

pid: 35935, system: Linux 2.6.32-754.el6.x86_64 #1 SMP Thu May 24 18:18:25 EDT 2018 x86_64

2018-08-22 16:21:25,361 INFO add_gtf_source : False \

bam_files : None \

bigwig_file : None \

counters : ['classifier-rnaseq-splicing'] \

filename_format : None \

filename_gff : ['smallest_ref.gtf'] \

genome_file : None \

gff_features : [] \

gff_sources : [] \

library_type : fr-unstranded \

log_config_filename : None \

loglevel : 1 \

minimum_mapping_quality : 0 \

multi_mapping : all \

output_filename_pattern : %s \

output_force : False \

prefixes : [] \

proximal_distance : 10000 \

quality_file : None \

random_seed : None \

reporter : transcripts \

sample_probability : 1.0 \

sections : [] \

short_help : None \

stderr : <_io.TextIOWrapper name='' mode='w' encoding='UTF-8'> \

stdin : <_io.TextIOWrapper name='weird_transcript.gtf' mode='r' encoding='utf-8'> \

stdlog : <_io.TextIOWrapper name='' mode='w' encoding='UTF-8'> \

stdout : <_io.TextIOWrapper name='' mode='w' encoding='UTF-8'> \

timeit_file : None \

timeit_header : None \

timeit_name : all \

tracing : None \

use_barcodes : False \

with_values : True

2018-08-22 16:21:25,361 INFO counters will use the default section (exons)

2018-08-22 16:21:25,361 INFO loading data from smallest_ref.gtf

2018-08-22 16:21:25,362 INFO loaded data from smallest_ref.gtf

transcript_id noverlap_transcripts noverlap_genes match_transcript_id match_gene_id source class sense MSTRG.28419.1 0 0 ENST00000341280 ENSG00000188263 ensembl flank3 s

2018-08-22 16:21:25,362 INFO input=1, output=1

2018-08-22 16:21:25,362 INFO <CGAT.GeneModelAnalysis.ClassifierRNASeqSplicing object at 0x7f1139d2c208>

2018-08-22 16:21:25,362 INFO job finished in 0 seconds at Wed Aug 22 16:21:25 2018 -- 1.43 2.91 0.00 0.00 -- bc8194f6-81a8-4dee-9084-ef1a3170e01f

Best regards, Sebastian

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Research Associate Bioinformatics Hub, Firth Court Department of Molecular Biology and Biotechnology (MBB), University of Sheffield, Western Bank, Sheffield S10 2TN England, UK. Tel. +44 (0)7703417022 c.alexandru@sheffield.ac.uk r01cna14@abdn.ac.uk

sebastian-luna-valero commented 5 years ago

Thanks for confirming. Regression test added in https://github.com/cgat-developers/cgat-apps/pull/19