pb-cdunn
commented
4 years ago It looks like you are running an old version. Please post your conda env, conda list.
Closed NicMAlexandre closed 4 years ago
pb-cdunn
commented
4 years ago It looks like you are running an old version. Please post your conda env, conda list.
NicMAlexandre
commented
4 years ago # Name Version Build Channel
_libgcc_mutex 0.1 main
_r-mutex 1.0.0 anacondar_1
adapterremoval 2.3.1 hf3e9acd_0 bioconda
angsd 0.931 ha52163a_0 bioconda
arrow 0.13.1 py27_0
asn1crypto 1.2.0 py27_0
avro-python2 1.9.0 py_0 bioconda
backports 1.0 py_2
backports.functools_lru_cache 1.5 py_2
backports_abc 0.5 py27_0
bam2fastq 1.1.0 0 yuxiang
bam2fastx 1.3.0 h4ef8376_6 bioconda
bbmap 38.45 h14c3975_0 bioconda
beagle 5.1_24Aug19.3e8 0 bioconda
bedtools 2.29.0 h6ed99ea_1 bioconda
binutils_impl_linux-64 2.28.1 had2808c_3
binutils_linux-64 7.2.0 had2808c_27
blas 1.0 mkl
blasr 5.3.2 hac9d22c_4 bioconda
blasr_libcpp 5.3.1 hac9d22c_3 bioconda
blast 2.9.0 pl526h979a64d_3 bioconda
bwa 0.7.17 hed695b0_6 bioconda
bwidget 1.9.11 1
bzip2 1.0.8 h7b6447c_0
ca-certificates 2019.10.16 0
cairo 1.14.12 h8948797_3
certifi 2019.9.11 py27_0
cffi 1.13.1 py27h2e261b9_0
chardet 3.0.4 py27_1003
circos 0.69.8 0 bioconda
cryptography 2.8 py27h1ba5d50_0
curl 7.65.3 hbc83047_0
cycler 0.10.0 py27_0
cyrus-sasl 2.1.26 h82bf5a1_4
cython 0.29.13 py27he6710b0_0
dbus 1.13.12 h746ee38_0
decorator 4.4.1 py_0
emboss 6.6.0 h6debe1e_0 bioconda
entrez-direct 11.0 pl526_0 bioconda
enum34 1.1.6 py27_1
expat 2.2.6 he6710b0_0
falcon-kit 1.2.6 pypi_0 pypi
falcon-phase 1.0.0 pypi_0 pypi
falcon-unzip 1.1.7 pypi_0 pypi
font-ttf-dejavu-sans-mono 2.37 h6964260_0
font-ttf-inconsolata 2.001 hcb22688_0
font-ttf-source-code-pro 2.030 h7457263_0
font-ttf-ubuntu 0.83 h8b1ccd4_0
fontconfig 2.13.0 h9420a91_0
fonts-anaconda 1 h8fa9717_0
freetype 2.9.1 h8a8886c_1
fribidi 1.0.5 h7b6447c_0
functools32 3.2.3.2 py27_1
future 0.17.1 py27_0
futures 3.3.0 py27_0
gcc_impl_linux-64 7.2.0 habb00fd_3
gcc_linux-64 7.2.0 h550dcbe_27
gcta 1.26.0 0 biobuilds
gctb 2.0 1 genomedk
genomicconsensus 2.3.3 py27_0 bioconda
gfortran_impl_linux-64 7.2.0 hdf63c60_3
gfortran_linux-64 7.2.0 h550dcbe_27
giflib 5.1.4 h14c3975_1
glib 2.56.2 hd408876_0
glimmerhmm 3.0.4 pl526hf484d3e_3 bioconda
gmp 6.1.2 h6c8ec71_1
gnuplot 5.0.3 4 bioconda
graphite2 1.3.13 h23475e2_0
gsl 2.4 h14c3975_4
gst-plugins-base 1.14.0 hbbd80ab_1
gstreamer 1.14.0 hb453b48_1
gxx_impl_linux-64 7.2.0 hdf63c60_3
gxx_linux-64 7.2.0 h550dcbe_27
h5py 2.8.0 py27h989c5e5_3
harfbuzz 1.8.8 hffaf4a1_0
hdf5 1.10.2 hba1933b_1
htslib 1.9 h47928c2_5 bioconda
icu 58.2 h9c2bf20_1
idna 2.8 py27_0
impute2 2.3.2 1 bioconda
intel-openmp 2019.4 243
ipaddress 1.0.23 py_0
iso8601 0.1.12 py27_1
jellyfish 2.2.10 h6bb024c_1 bioconda
jemalloc 5.0.1 hf484d3e_1
joblib 0.13.2 py27_0
jpeg 9b h024ee3a_2
kiwisolver 1.1.0 py27he6710b0_0
krb5 1.16.1 h173b8e3_7
libcurl 7.65.3 h20c2e04_0
libdb 6.1.26 he6710b0_0
libdeflate 1.0 h14c3975_1 bioconda
libedit 3.1.20181209 hc058e9b_0
libffi 3.2.1 hd88cf55_4
libgcc 7.2.0 h69d50b8_2
libgcc-ng 9.1.0 hdf63c60_0
libgd 2.2.5 hceca4fd_3
libgfortran 3.0.0 1 https://repo.anaconda.com/pkgs/free
libgfortran-ng 7.3.0 hdf63c60_0
libntlm 1.5 h7b6447c_0
libpng 1.6.37 hbc83047_0
libssh2 1.8.2 h1ba5d50_0
libstdcxx-ng 9.1.0 hdf63c60_0
libtiff 4.0.10 h2733197_2
libuuid 1.0.3 h1bed415_2
libwebp 1.0.1 h8e7db2f_0
libxcb 1.13 h1bed415_1
libxml2 2.9.9 hea5a465_1
linecache2 1.0.0 py27_0
make 4.2.1 h1bed415_1
matplotlib 2.2.2 py27hb69df0a_2
miniasm 0.3_r179 ha92aebf_0 bioconda
minimap 0.2 0 bioconda
minimap2 2.17 h8b12597_1 bioconda
mkl 2019.4 243
mkl-service 2.3.0 py27he904b0f_0
mkl_fft 1.0.14 py27ha843d7b_0
mkl_random 1.1.0 py27hd6b4f25_0
mummer 3.23 pl526_8 bioconda
mummer4 4.0.0beta2 pl526hf484d3e_4 bioconda
ncurses 6.1 he6710b0_1
networkx 2.2 py27_1
nim-falcon 0.0.1 h2f8a211_0 bioconda
numpy 1.16.5 py27h7e9f1db_0
numpy-base 1.16.5 py27hde5b4d6_0
openblas 0.2.19 0 https://repo.anaconda.com/pkgs/free
openjdk 8.0.152 h46b5887_1
openssl 1.1.1d h7b6447c_3
pandoc 2.2.3.2 0
pango 1.42.4 h049681c_0
pb-assembly 0.0.4 py27_6 bioconda
pb-dazzler 0.0.1 h516909a_0 bioconda
pb-falcon 0.2.6 py27hc0aa232_3 bioconda
pbalign 0.3.2 py27_0 bioconda
pbbam 0.19.0 h6678c95_1 bioconda
pbcommand 1.1.1 py27_2 bioconda
pbcopper 0.4.2 h02d93b8_0 bioconda
pbcore 1.7.1 py27_0 bioconda
pbmm2 0.12.0 ha87ae23_0 bioconda
pcre 8.43 he6710b0_0
pear 0.9.6 h98de208_5 bioconda
perl 5.26.2 h14c3975_0
perl-app-cpanminus 1.7044 pl526_1 bioconda
perl-archive-tar 2.32 pl526_0 bioconda
perl-autoloader 5.74 pl526_2 bioconda
perl-base 2.23 pl526_1 bioconda
perl-business-isbn 3.004 pl526_0 bioconda
perl-business-isbn-data 20140910.003 pl526_0 bioconda
perl-carp 1.38 pl526_3 bioconda
perl-clone 0.42 pl526h516909a_0 bioconda
perl-common-sense 3.74 pl526_2 bioconda
perl-compress-raw-bzip2 2.087 pl526he1b5a44_0 bioconda
perl-compress-raw-zlib 2.087 pl526hc9558a2_0 bioconda
perl-config-general 2.63 pl526_0 bioconda
perl-constant 1.33 pl526_1 bioconda
perl-data-dumper 2.173 pl526_0 bioconda
perl-digest-hmac 1.03 pl526_3 bioconda
perl-digest-md5 2.55 pl526_0 bioconda
perl-digest-perl-md5 1.9 pl526_1 bioconda
perl-dynaloader 1.25 pl526_1 bioconda
perl-encode 2.88 pl526_1 bioconda
perl-encode-locale 1.05 pl526_6 bioconda
perl-exporter 5.72 pl526_1 bioconda
perl-exporter-tiny 1.002001 pl526_0 bioconda
perl-extutils-makemaker 7.36 pl526_1 bioconda
perl-file-listing 6.04 pl526_1 bioconda
perl-file-path 2.16 pl526_0 bioconda
perl-file-temp 0.2304 pl526_2 bioconda
perl-font-ttf 1.06 pl526_0 bioconda
perl-gd 2.71 pl526he860b03_0 bioconda
perl-html-parser 3.72 pl526h6bb024c_5 bioconda
perl-html-tagset 3.20 pl526_3 bioconda
perl-html-tree 5.07 pl526_1 bioconda
perl-http-cookies 6.04 pl526_0 bioconda
perl-http-daemon 6.01 pl526_1 bioconda
perl-http-date 6.02 pl526_3 bioconda
perl-http-message 6.18 pl526_0 bioconda
perl-http-negotiate 6.01 pl526_3 bioconda
perl-io-compress 2.087 pl526he1b5a44_0 bioconda
perl-io-html 1.001 pl526_2 bioconda
perl-io-socket-ssl 2.066 pl526_0 bioconda
perl-io-string 1.08 pl526_3 bioconda
perl-io-zlib 1.10 pl526_2 bioconda
perl-json 4.02 pl526_0 bioconda
perl-json-xs 2.34 pl526h6bb024c_3 bioconda
perl-libwww-perl 6.39 pl526_0 bioconda
perl-list-moreutils 0.428 pl526_1 bioconda
perl-list-moreutils-xs 0.428 pl526_0 bioconda
perl-lwp-mediatypes 6.04 pl526_0 bioconda
perl-lwp-protocol-https 6.07 pl526_4 bioconda
perl-math-bezier 0.01 pl526_1 bioconda
perl-math-round 0.07 pl526_1 bioconda
perl-math-vecstat 0.08 pl526_1 bioconda
perl-mime-base64 3.15 pl526_1 bioconda
perl-module-implementation 0.09 pl526_2 bioconda
perl-module-runtime 0.016 pl526_1 bioconda
perl-mozilla-ca 20180117 pl526_1 bioconda
perl-net-http 6.19 pl526_0 bioconda
perl-net-ssleay 1.88 pl526h90d6eec_0 bioconda
perl-ntlm 1.09 pl526_4 bioconda
perl-number-format 1.75 pl526_3 bioconda
perl-params-validate 1.29 pl526h14c3975_1 bioconda
perl-parent 0.236 pl526_1 bioconda
perl-pathtools 3.75 pl526h14c3975_1 bioconda
perl-readonly 2.05 pl526_0 bioconda
perl-regexp-common 2017060201 pl526_0 bioconda
perl-scalar-list-utils 1.52 pl526h516909a_0 bioconda
perl-set-intspan 1.19 pl526_1 bioconda
perl-socket 2.027 pl526_1 bioconda
perl-statistics-basic 1.6611 pl526_2 bioconda
perl-storable 3.15 pl526h14c3975_0 bioconda
perl-svg 2.84 pl526_0 bioconda
perl-test-requiresinternet 0.05 pl526_0 bioconda
perl-text-format 0.59 pl526_2 bioconda
perl-time-hires 1.9760 pl526h14c3975_1 bioconda
perl-time-local 1.28 pl526_1 bioconda
perl-try-tiny 0.30 pl526_1 bioconda
perl-types-serialiser 1.0 pl526_2 bioconda
perl-uri 1.76 pl526_0 bioconda
perl-www-robotrules 6.02 pl526_3 bioconda
perl-xml-namespacesupport 1.12 pl526_0 bioconda
perl-xml-parser 2.44 pl526h4e0c4b3_7 bioconda
perl-xml-sax 1.02 pl526_0 bioconda
perl-xml-sax-base 1.09 pl526_0 bioconda
perl-xml-sax-expat 0.51 pl526_3 bioconda
perl-xml-simple 2.25 pl526_1 bioconda
perl-xsloader 0.24 pl526_0 bioconda
picard 2.21.1 0 bioconda
pilon 1.23 0 bioconda
pip 19.3.1 py27_0
pixman 0.38.0 h7b6447c_0
plink 1.90b4 1 bioconda
pycparser 2.19 py27_0
pyfaidx 0.5.5.2 py_1 bioconda
pyopenssl 19.0.0 py27_0
pyparsing 2.4.2 py_0
pyqt 5.6.0 py27h22d08a2_6
pysam 0.15.3 py27hda2845c_1 bioconda
pysocks 1.7.1 py27_0
python 2.7.17 h9bab390_0
python-consensuscore 1.1.1 py27h02d93b8_2 bioconda
python-consensuscore2 3.4.1 py27_0 bioconda
python-dateutil 2.8.0 py27_0
python-edlib 1.2.3.post1 py27h470a237_0 bioconda
python-intervaltree 3.0.2 py_0 bioconda
python-msgpack 0.5.6 py27h470a237_0 bioconda
python-sortedcontainers 2.1.0 py_0 bioconda
pytz 2019.3 py_0
qt 5.6.3 h8bf5577_3
qualimap 2.2.2a 1 bioconda
quast 5.0.2 py27pl526ha92aebf_0 bioconda
r-askpass 1.0 r36h14c3975_0
r-assertthat 0.2.1 r36h6115d3f_0
r-backports 1.1.4 r36h96ca727_0
r-base 3.6.1 h9bb98a2_1
r-base64enc 0.1_3 r36h96ca727_4
r-bh 1.69.0_1 r36h6115d3f_0
r-bit 1.1_14 r36h96ca727_0 r
r-bit64 0.9_7 r36h96ca727_0 r
r-bitops 1.0_6 r36h96ca727_4
r-blob 1.1.1 r36h6115d3f_0 r
r-catools 1.17.1.2 r36h29659fb_0 r
r-cellranger 1.1.0 r36h6115d3f_0 r
r-cli 1.1.0 r36h6115d3f_0
r-clipr 0.6.0 r36h6115d3f_0
r-config 0.3 r36h6115d3f_0
r-crayon 1.3.4 r36h6115d3f_0
r-curl 3.3 r36h96ca727_0 r
r-dbi 1.0.0 r36h6115d3f_0
r-dbplyr 1.4.0 r36h6115d3f_0
r-digest 0.6.18 r36h96ca727_0 r
r-dplyr 0.8.0.1 r36h29659fb_0 r
r-ellipsis 0.1.0 r36h96ca727_0
r-evaluate 0.13 r36h6115d3f_0 r
r-fansi 0.4.0 r36h96ca727_0
r-forcats 0.4.0 r36h6115d3f_0
r-forge 0.2.0 r36h6115d3f_0
r-generics 0.0.2 r36h6115d3f_0
r-glue 1.3.1 r36h96ca727_0
r-haven 2.1.0 r36h29659fb_0 r
r-highr 0.8 r36h6115d3f_0
r-hms 0.4.2 r36h6115d3f_0
r-htmltools 0.3.6 r36h29659fb_0 r
r-htmlwidgets 1.3 r36h6115d3f_0
r-httpuv 1.5.1 r36h29659fb_0
r-httr 1.4.0 r36h6115d3f_0
r-jsonlite 1.6 r36h96ca727_0 r
r-knitr 1.22 r36h6115d3f_0
r-later 0.8.0 r36h29659fb_0
r-magrittr 1.5 r36h6115d3f_4
r-markdown 0.9 r36h96ca727_0
r-mime 0.6 r36h96ca727_0 r
r-miniui 0.1.1.1 r36h6115d3f_0
r-mongolite 2.0.1 r36h96ca727_0 r
r-odbc 1.1.5 r36hf484d3e_0 r
r-openssl 1.3 r36h96ca727_0 r
r-packrat 0.5.0 r36h6115d3f_0 r
r-pillar 1.3.1 r36h6115d3f_0
r-pkgconfig 2.0.2 r36h6115d3f_0 r
r-pki 0.1_5.1 r36h96ca727_1
r-plogr 0.2.0 r36h6115d3f_0 r
r-prettyunits 1.0.2 r36h6115d3f_0
r-profvis 0.3.5 r36h96ca727_0 r
r-progress 1.2.0 r36h6115d3f_0
r-promises 1.0.1 r36h29659fb_0
r-purrr 0.3.2 r36h96ca727_0
r-r2d3 0.2.3 r36h6115d3f_0 r
r-r6 2.4.0 r36h6115d3f_0
r-rappdirs 0.3.1 r36h96ca727_0 r
r-rcpp 1.0.1 r36h29659fb_0
r-rcurl 1.95_4.12 r36h96ca727_0
r-readr 1.3.1 r36h29659fb_0
r-readxl 1.3.1 r36h29659fb_0
r-rematch 1.0.1 r36h6115d3f_0
r-rjava 0.9_11 r36h96ca727_0
r-rjdbc 0.2_7.1 r36h6115d3f_0
r-rjsonio 1.3_1.1 r36h29659fb_0
r-rlang 0.3.4 r36h96ca727_0
r-rmarkdown 1.12 r36h6115d3f_0
r-rprojroot 1.3_2 r36h6115d3f_0
r-rsconnect 0.8.13 r36h6115d3f_0 r
r-rstudioapi 0.10 r36h6115d3f_0
r-shiny 1.3.2 r36h6115d3f_0 r
r-sourcetools 0.1.7 r36h29659fb_0 r
r-sparklyr 1.0.0 r36h6115d3f_0
r-stringi 1.4.3 r36h29659fb_0
r-stringr 1.4.0 r36h6115d3f_0
r-sys 3.2 r36h96ca727_0
r-tibble 2.1.1 r36h96ca727_0
r-tidyr 0.8.3 r36h29659fb_0
r-tidyselect 0.2.5 r36h29659fb_0
r-tinytex 0.12 r36h6115d3f_0
r-utf8 1.1.4 r36h96ca727_0
r-withr 2.1.2 r36h6115d3f_0 r
r-xfun 0.6 r36h6115d3f_0
r-xml2 1.2.0 r36h29659fb_0 r
r-xtable 1.8_4 r36h6115d3f_0
r-yaml 2.2.0 r36h96ca727_0
racon 1.3.2 he860b03_1 bioconda
readline 7.0 h7b6447c_5
requests 2.22.0 py27_0
rstudio 1.1.456 h6bb024c_1 r
samtools 1.9 h8571acd_11 bioconda
setuptools 41.6.0 py27_0
simplejson 3.16.0 py27h14c3975_0
singledispatch 3.4.0.3 py27_0
sip 4.18.1 py27hf484d3e_2
six 1.12.0 py27_0
sqlite 3.30.1 h7b6447c_0
subprocess32 3.5.4 py27h7b6447c_0
tk 8.6.8 hbc83047_0
tktable 2.10 h14c3975_0
tornado 5.1.1 py27h7b6447c_0
traceback2 1.4.0 py27_0
unittest2 1.1.0 py27_0
unixodbc 2.3.7 h14c3975_0
urllib3 1.24.2 py27_0
wheel 0.33.6 py27_0
xz 5.2.4 h14c3975_4
zlib 1.2.11 h7b6447c_3
zstd 1.3.7 h0b5b093_0 python 2.7.17
We support only python3.7 in Bioconda.
Hello,
I commented on a previous post referenced here, but did not receive a response: https://github.com/PacificBiosciences/pbbioconda/issues/21
I have a similar error to the post above, but the ref.fa file looks fine as do the bam files. Additionally I have no contigs of length zero in the fasta files.
When I take a look at all the stderr files in quiver-run and quiver-chunks, it looks like over 300 completed, which has been the case each time I run. So it seems to be working and then stopping after processing roughly 300 files. The files also seem to be different each time with around 11,000 remaining.
ls /global/scratch/nalexandre/spikedace/4-polish/quiver-chunks//run.sh.done /global/scratch/nalexandre/spikedace/4-polish/quiver-chunks//*.bash.stderr | wc -l 670
ls /global/scratch/nalexandre/spikedace/4-polish/quiver-chunks/*/run.sh.done | wc -l 335
ls /run.sh
000163F_002/run.sh 000195F_003/run.sh 000198F_001/run.sh 000211F_001/run.sh 000628F/run.sh 001764F/run.sh There are no run.sh.done files in quiver-run.