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PacificBiosciences / pbbioconda

PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.
BSD 3-Clause Clear License
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gcpp:terminate called without an active exception #354

Closed yunshu1218 closed 3 years ago

yunshu1218 commented 4 years ago

Operating system CentOS Package name gcpp 2.0.0-v2.0.0 Conda environment What is the result of conda list? (Try to paste that between triple backticks.)

Name Version Build Channel

_libgcc_mutex 0.1 main defaults aragorn 1.2.38 h516909a_3 bioconda barrnap 0.9 3 bioconda bedtools 2.29.2 hc088bd4_0 bioconda blast 2.10.1 pl526he19e7b1_2 bioconda bzip2 1.0.8 h516909a_3 conda-forge c-ares 1.16.1 h516909a_3 conda-forge ca-certificates 2020.11.8 ha878542_0 conda-forge cairo 1.16.0 h3fc0475_1005 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge certifi 2020.11.8 py38h578d9bd_0 conda-forge cffi 1.14.0 py38he30daa8_1 defaults chardet 3.0.4 py38_1003 defaults conda 4.9.2 py38h578d9bd_0 conda-forge conda-package-handling 1.6.1 py38h7b6447c_0 defaults cryptography 2.9.2 py38h1ba5d50_0 defaults curl 7.71.1 he644dc0_8 conda-forge entrez-direct 13.9 pl526h375a9b1_0 bioconda expat 2.2.9 he1b5a44_2 conda-forge fontconfig 2.13.1 h7e3eb15_1002 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge freetype 2.10.4 h7ca028e_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge fribidi 1.0.10 h36c2ea0_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge gettext 0.19.8.1 h5e8e0c9_1 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge giflib 5.2.1 h36c2ea0_2 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge glib 2.66.1 h92f7085_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main graphite2 1.3.13 h58526e2_1001 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge graphviz 2.42.3 h0511662_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge harfbuzz 2.7.2 hee91db6_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge hmmer 3.3.1 he1b5a44_0 bioconda htslib 1.10.2 hd3b49d5_1 bioconda icu 67.1 he1b5a44_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge idna 2.9 py_1 defaults infernal 1.1.3 h516909a_0 bioconda jpeg 9d h36c2ea0_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge krb5 1.17.1 h173b8e3_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main ld_impl_linux-64 2.33.1 h53a641e_7 defaults libcurl 7.71.1 hcdd3856_8 conda-forge libdb 6.2.32 he1b5a44_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge libdeflate 1.6 h516909a_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge libedit 3.1.20181209 hc058e9b_0 defaults libev 4.33 h516909a_1 conda-forge libffi 3.3 he6710b0_1 defaults libgcc 7.2.0 h69d50b8_2 conda-forge libgcc-ng 9.1.0 hdf63c60_0 defaults libgd 2.2.5 h341251c_1008 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge libiconv 1.16 h516909a_0 conda-forge libidn11 1.34 h1cef754_0 conda-forge libnghttp2 1.41.0 h8cfc5f6_2 conda-forge libpng 1.6.37 h21135ba_2 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge libssh2 1.9.0 hab1572f_5 conda-forge libstdcxx-ng 9.1.0 hdf63c60_0 defaults libtiff 4.1.0 h4f3a223_6 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge libtool 2.4.6 h58526e2_1007 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge libuuid 2.32.1 h14c3975_1000 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge libwebp 1.1.0 h76fa15c_4 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge libwebp-base 1.1.0 h36c2ea0_3 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge libxcb 1.13 h14c3975_1002 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge libxml2 2.9.10 h68273f3_2 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge libxslt 1.1.33 h572872d_1 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge lz4-c 1.9.2 he1b5a44_3 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge minced 0.4.2 0 bioconda ncurses 6.2 he6710b0_1 defaults openjdk 11.0.1 h516909a_1016 conda-forge openssl 1.1.1h h516909a_0 conda-forge pango 1.42.4 h7062337_4 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge parallel 20200922 0 conda-forge pbgcpp 2.0.0 0 bioconda pbmm2 1.4.0 h56fc30b_0 bioconda pcre 8.44 he1b5a44_0 conda-forge perl 5.26.2 h36c2ea0_1008 conda-forge perl-aceperl 1.92 pl526_2 bioconda perl-algorithm-diff 1.1903 pl526_2 bioconda perl-algorithm-munkres 0.08 pl526_1 bioconda perl-apache-test 1.40 pl526_1 bioconda perl-app-cpanminus 1.7044 pl526_1 bioconda perl-appconfig 1.71 pl526_1 bioconda perl-archive-tar 2.32 pl526_0 bioconda perl-array-compare 3.0.1 pl526_1 bioconda perl-autoloader 5.74 pl526_2 bioconda perl-base 2.23 pl526_1 bioconda perl-bio-asn1-entrezgene 1.73 pl526_1 bioconda perl-bio-featureio 1.6.905 pl526_2 bioconda perl-bio-phylo 0.58 pl526_2 bioconda perl-bio-samtools 1.43 pl526h1341992_1 bioconda perl-bioperl 1.6.924 6 bioconda perl-bioperl-core 1.007002 pl526_2 bioconda perl-bioperl-run 1.007002 pl526_4 bioconda perl-business-isbn 3.004 pl526_0 bioconda perl-business-isbn-data 20140910.003 pl526_0 bioconda perl-cache-cache 1.08 pl526_0 bioconda perl-capture-tiny 0.48 pl526_0 bioconda perl-carp 1.38 pl526_3 bioconda perl-cgi 4.44 pl526h14c3975_1 bioconda perl-class-data-inheritable 0.08 pl526_1 bioconda perl-class-inspector 1.34 pl526_0 bioconda perl-class-load 0.25 pl526_0 bioconda perl-class-load-xs 0.10 pl526h6bb024c_2 bioconda perl-class-method-modifiers 2.12 pl526_0 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-constant 1.33 pl526_1 bioconda perl-convert-binary-c 0.78 pl526h6bb024c_3 bioconda perl-convert-binhex 1.125 pl526_1 bioconda perl-crypt-rc4 2.02 pl526_1 bioconda perl-data-dumper 2.173 pl526_0 bioconda perl-data-optlist 0.110 pl526_2 bioconda perl-data-stag 0.14 pl526_1 bioconda perl-date-format 2.30 pl526_2 bioconda perl-db-file 1.855 pl526h516909a_0 bioconda perl-dbd-sqlite 1.64 pl526h516909a_0 bioconda perl-dbi 1.642 pl526_0 bioconda perl-devel-globaldestruction 0.14 pl526_0 bioconda perl-devel-overloadinfo 0.005 pl526_0 bioconda perl-devel-stacktrace 2.04 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-digest-sha1 2.13 pl526h6bb024c_1 bioconda perl-dist-checkconflicts 0.11 pl526_2 bioconda perl-dynaloader 1.25 pl526_1 bioconda perl-email-date-format 1.005 pl526_2 bioconda perl-encode 2.88 pl526_1 bioconda perl-encode-locale 1.05 pl526_6 bioconda perl-error 0.17027 pl526_1 bioconda perl-eval-closure 0.14 pl526h6bb024c_4 bioconda perl-exception-class 1.44 pl526_0 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-slurp-tiny 0.004 pl526_1 bioconda perl-file-sort 1.01 pl526_2 bioconda perl-file-temp 0.2304 pl526_2 bioconda perl-file-which 1.23 pl526_0 bioconda perl-font-afm 1.20 pl526_2 bioconda perl-font-ttf 1.06 pl526_0 bioconda perl-gd 2.71 pl526he860b03_0 bioconda perl-getopt-long 2.50 pl526_1 bioconda perl-graph 0.9704 pl526_1 bioconda perl-graphviz 2.24 pl526h734ff71_0 bioconda perl-html-element-extended 1.18 pl526_1 bioconda perl-html-entities-numbered 0.04 pl526_1 bioconda perl-html-formatter 2.16 pl526_0 bioconda perl-html-parser 3.72 pl526h6bb024c_5 bioconda perl-html-tableextract 2.13 pl526_2 bioconda perl-html-tagset 3.20 pl526_3 bioconda perl-html-tidy 1.60 pl526_0 bioconda perl-html-tree 5.07 pl526_1 bioconda perl-html-treebuilder-xpath 0.14 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-image-info 1.38 pl526_1 bioconda perl-image-size 3.300 pl526_2 bioconda perl-io-compress 2.087 pl526he1b5a44_0 bioconda perl-io-html 1.001 pl526_2 bioconda perl-io-sessiondata 1.03 pl526_1 bioconda perl-io-socket-ssl 2.066 pl526_0 bioconda perl-io-string 1.08 pl526_3 bioconda perl-io-stringy 2.111 pl526_1 bioconda perl-io-tty 1.12 pl526_1 bioconda perl-io-zlib 1.10 pl526_2 bioconda perl-ipc-run 20180523.0 pl526_0 bioconda perl-ipc-sharelite 0.17 pl526h6bb024c_1 bioconda perl-jcode 2.07 pl526_2 bioconda perl-json 4.02 pl526_0 bioconda perl-json-xs 2.34 pl526h6bb024c_3 bioconda perl-lib 0.63 pl526_1 bioconda perl-libwww-perl 6.39 pl526_0 bioconda perl-libxml-perl 0.08 pl526_2 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-lwp-simple 6.15 pl526h470a237_4 bioconda perl-mailtools 2.21 pl526_0 bioconda perl-math-cdf 0.1 pl526h14c3975_5 bioconda perl-math-derivative 1.01 pl526_0 bioconda perl-math-random 0.72 pl526h14c3975_2 bioconda perl-math-spline 0.02 pl526_2 bioconda perl-mime-base64 3.15 pl526_1 bioconda perl-mime-lite 3.030 pl526_1 bioconda perl-mime-tools 5.508 pl526_1 bioconda perl-mime-types 2.17 pl526_0 bioconda perl-mldbm 2.05 pl526_1 bioconda perl-module-implementation 0.09 pl526_2 bioconda perl-module-runtime 0.016 pl526_1 bioconda perl-module-runtime-conflicts 0.003 pl526_0 bioconda perl-moo 2.003004 pl526_0 bioconda perl-moose 2.2011 pl526hf484d3e_1 bioconda perl-mozilla-ca 20180117 pl526_1 bioconda perl-mro-compat 0.13 pl526_0 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-ole-storage_lite 0.19 pl526_3 bioconda perl-package-deprecationmanager 0.17 pl526_0 bioconda perl-package-stash 0.38 pl526hf484d3e_1 bioconda perl-package-stash-xs 0.28 pl526hf484d3e_1 bioconda perl-params-util 1.07 pl526h6bb024c_4 bioconda perl-parent 0.236 pl526_1 bioconda perl-parse-recdescent 1.967015 pl526_0 bioconda perl-pathtools 3.75 pl526h14c3975_1 bioconda perl-pdf-api2 2.035 pl526_0 bioconda perl-pod-escapes 1.07 pl526_1 bioconda perl-pod-usage 1.69 pl526_1 bioconda perl-postscript 0.06 pl526_2 bioconda perl-role-tiny 2.000008 pl526_0 bioconda perl-scalar-list-utils 1.52 pl526h516909a_0 bioconda perl-set-scalar 1.29 pl526_2 bioconda perl-soap-lite 1.19 pl526_1 bioconda perl-socket 2.027 pl526_1 bioconda perl-sort-naturally 1.03 pl526_2 bioconda perl-spreadsheet-parseexcel 0.65 pl526_2 bioconda perl-spreadsheet-writeexcel 2.40 pl526_2 bioconda perl-statistics-descriptive 3.0702 pl526_0 bioconda perl-storable 3.15 pl526h14c3975_0 bioconda perl-sub-exporter 0.987 pl526_2 bioconda perl-sub-exporter-progressive 0.001013 pl526_0 bioconda perl-sub-identify 0.14 pl526h14c3975_0 bioconda perl-sub-install 0.928 pl526_2 bioconda perl-sub-name 0.21 pl526_1 bioconda perl-sub-quote 2.006003 pl526_1 bioconda perl-sub-uplevel 0.2800 pl526h14c3975_2 bioconda perl-svg 2.84 pl526_0 bioconda perl-svg-graph 0.02 pl526_3 bioconda perl-task-weaken 1.06 pl526_0 bioconda perl-template-toolkit 2.26 pl526_1 bioconda perl-test 1.26 pl526_1 bioconda perl-test-deep 1.128 pl526_1 bioconda perl-test-differences 0.67 pl526_0 bioconda perl-test-exception 0.43 pl526_2 bioconda perl-test-harness 3.42 pl526_0 bioconda perl-test-leaktrace 0.16 pl526h14c3975_2 bioconda perl-test-most 0.35 pl526_0 bioconda perl-test-requiresinternet 0.05 pl526_0 bioconda perl-test-warn 0.36 pl526_1 bioconda perl-text-diff 1.45 pl526_0 bioconda perl-threaded 5.26.0 0 bioconda perl-tie-ixhash 1.23 pl526_2 bioconda perl-time-hires 1.9760 pl526h14c3975_1 bioconda perl-time-local 1.28 pl526_1 bioconda perl-timedate 2.30 pl526_1 bioconda perl-tree-dag_node 1.31 pl526_0 bioconda perl-try-tiny 0.30 pl526_1 bioconda perl-type-tiny 1.004004 pl526_0 bioconda perl-types-serialiser 1.0 pl526_2 bioconda perl-unicode-map 0.112 pl526h6bb024c_3 bioconda perl-uri 1.76 pl526_0 bioconda perl-www-robotrules 6.02 pl526_3 bioconda perl-xml-dom 1.46 pl526_0 bioconda perl-xml-dom-xpath 0.14 pl526_1 bioconda perl-xml-filter-buffertext 1.01 pl526_2 bioconda perl-xml-libxml 2.0132 pl526h7ec2d77_1 bioconda perl-xml-libxslt 1.94 pl526_1 bioconda perl-xml-namespacesupport 1.12 pl526_0 bioconda perl-xml-parser 2.44_01 pl526ha1d75be_1002 conda-forge perl-xml-regexp 0.04 pl526_2 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-sax-writer 0.57 pl526_0 bioconda perl-xml-simple 2.25 pl526_1 bioconda perl-xml-twig 3.52 pl526_2 bioconda perl-xml-writer 0.625 pl526_2 bioconda perl-xml-xpath 1.44 pl526_0 bioconda perl-xml-xpathengine 0.14 pl526_2 bioconda perl-xsloader 0.24 pl526_0 bioconda perl-yaml 1.29 pl526_0 bioconda pip 20.0.2 py38_3 defaults pixman 0.38.0 h516909a_1003 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge prodigal 2.6.3 h516909a_2 bioconda prokka 1.13 2 bioconda pthread-stubs 0.4 h14c3975_1001 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge pycosat 0.6.3 py38h7b6447c_1 defaults pycparser 2.20 py_0 defaults pyopenssl 19.1.0 py38_0 defaults pysocks 1.7.1 py38_0 defaults python 3.8.3 hcff3b4d_0 defaults python_abi 3.8 1_cp38 conda-forge readline 8.0 h7b6447c_0 defaults requests 2.23.0 py38_0 defaults ruamel_yaml 0.15.87 py38h7b6447c_0 defaults setuptools 46.4.0 py38_0 defaults six 1.14.0 py38_0 defaults sqlite 3.31.1 h62c20be_1 defaults tbl2asn 25.7 0 bioconda tidyp 1.04 h516909a_2 bioconda tk 8.6.8 hbc83047_0 defaults tqdm 4.46.0 py_0 defaults urllib3 1.25.8 py38_0 defaults wheel 0.34.2 py38_0 defaults xorg-kbproto 1.0.7 h14c3975_1002 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge xorg-libice 1.0.10 h516909a_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge xorg-libsm 1.2.3 h84519dc_1000 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge xorg-libx11 1.6.12 h516909a_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge xorg-libxau 1.0.9 h14c3975_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge xorg-libxdmcp 1.1.3 h516909a_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge xorg-libxext 1.3.4 h516909a_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge xorg-libxpm 3.5.13 h516909a_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge xorg-libxrender 0.9.10 h516909a_1002 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge xorg-libxt 1.1.5 h516909a_1003 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge xorg-renderproto 0.11.1 h14c3975_1002 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge xorg-xextproto 7.3.0 h14c3975_1002 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge xorg-xproto 7.0.31 h14c3975_1007 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge xz 5.2.5 h7b6447c_0 defaults yaml 0.1.7 had09818_2 defaults zlib 1.2.11 h7b6447c_3 defaults zstd 1.4.5 h6597ccf_2 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge Describe the bug I am trying to polish a assembly of a staphylococcus epidermidis genome (about2.5M) with gcpp,and I see the error about terminate called without an active exception after running several hours, with output file 105Consensus.fasta.tmp

Error message terminate called without an active exception Aborted (core dumped)

To Reproduce

gcpp -j8 -r /pub/yuanjian/lsd/Biosoft/canu-2.1.1/output/105_1/105.contigs.fasta -o 105Variants.gff -o 105Consensus.fasta /pub/yuanjian/lsd/Biosoft/polishout/mapout/105.bam

Expected behavior I hope I can polish the assembly genome seccessfully! Thank you so much !

akiledal commented 3 years ago

I'm getting the same error message while polishing a Bacillus genome. However, it's working just fine for two other bacterial genomes (another Bacillus and a Rhodococcus) with identical pre-processing.

Operating system Fedora 31 Package name gcpp 2.0.0-v2.0.0 Conda environment

# packages in environment at /work/akiledal/isolate_genomes2/.snakemake/conda/c0f2acec:
#
# Name                    Version                   Build  Channel
pbgcpp                    2.0.0                         0    bioconda

End of the log file:

>|> 20210213 04:00:11.660 -|- INFO -|- AddResult -|- 0x7fc8ca7fc700|| -|- Processed 5742500/5748923 (99%) bases of contig 'contig_1'
>|> 20210213 04:00:11.717 -|- DEBUG -|- ConsensusForAlignments -|- 0x7fc8d36ef700|| -|- Coverage (all reads) in window "contig_1 [5744495, 5745005)": 90
>|> 20210213 04:00:12.235 -|- DEBUG -|- ConsensusForAlignments -|- 0x7fc8cbfff700|| -|- Coverage (all reads) in window "contig_1 [5744995, 5745505)": 91
>|> 20210213 04:00:12.427 -|- DEBUG -|- ConsensusForAlignments -|- 0x7fc8cb7fe700|| -|- Coverage (all reads) in window "contig_1 [5745495, 5746005)": 90
>|> 20210213 04:00:12.821 -|- DEBUG -|- ConsensusForAlignments -|- 0x7fc8d21ee700|| -|- Coverage (all reads) in window "contig_1 [5745995, 5746505)": 93
>|> 20210213 04:00:13.002 -|- DEBUG -|- ConsensusForAlignments -|- 0x7fc8d09eb700|| -|- Coverage (all reads) in window "contig_1 [5746495, 5747005)": 91
>|> 20210213 04:00:13.412 -|- DEBUG -|- ConsensusForAlignments -|- 0x7fc8caffd700|| -|- Coverage (all reads) in window "contig_1 [5746995, 5747505)": 92
>|> 20210213 04:00:14.273 -|- DEBUG -|- ConsensusForAlignments -|- 0x7fc8d19ed700|| -|- Coverage (all reads) in window "contig_1 [5747495, 5748005)": 94
>|> 20210213 04:00:14.985 -|- DEBUG -|- ConsensusForAlignments -|- 0x7fc8d11ec700|| -|- Coverage (all reads) in window "contig_1 [5747995, 5748505)": 92
>|> 20210213 04:00:15.130 -|- DEBUG -|- ConsensusForAlignments -|- 0x7fc8d36ef700|| -|- Coverage (all reads) in window "contig_1 [5748495, 5748923)": 96
>|> 20210213 04:00:15.539 -|- DEBUG -|- ConsensusForAlignments -|- 0x7fc8cbfff700|| -|- Coverage (all reads) in window "contig_3 [0, 505)": 95
>|> 20210213 04:00:16.163 -|- DEBUG -|- ConsensusForAlignments -|- 0x7fc8d21ee700|| -|- Coverage (all reads) in window "contig_3 [495, 1005)": 92
>|> 20210213 04:00:16.257 -|- DEBUG -|- ConsensusForAlignments -|- 0x7fc8cb7fe700|| -|- Coverage (all reads) in window "contig_3 [995, 1505)": 92
>|> 20210213 04:00:16.381 -|- DEBUG -|- ConsensusForAlignments -|- 0x7fc8d09eb700|| -|- Coverage (all reads) in window "contig_3 [1495, 2005)": 94
>|> 20210213 04:00:16.838 -|- INFO -|- AddResult -|- 0x7fc8ca7fc700|| -|- Processed 5748000/5748923 (99%) bases of contig 'contig_1'
>|> 20210213 04:00:16.937 -|- DEBUG -|- ConsensusForAlignments -|- 0x7fc8caffd700|| -|- Coverage (all reads) in window "contig_3 [1995, 2505)": 92
>|> 20210213 04:00:17.530 -|- INFO -|- MaybeFlushContig -|- 0x7fc8ca7fc700|| -|- Finished contig 'contig_1' with 5748923 expected bases
terminate called without an active exception
/usr/bin/bash: line 1: 766859 Aborted                 (core dumped) gcpp --log-level TRACE -j 8 -r data/assembly/C11_flye/C11_fixstart.fasta -o data/assembly/C11_flye/C11_polished.fasta data/assembly/C11_flye/C11_aligned.bam
elcortegano commented 3 years ago

I am also getting this error when polishing green alga genomes. The error appears after a call to "Calling variants for contig":

...
>|> 20210218 13:53:26.648 -|- INFO -|- AddResult -|- 0x7efc226e5700|| -|- Processed 51500/52007 (99%) bases of contig 'contig_133_1|arrow'
>|> 20210218 13:53:26.649 -|- INFO -|- AddResult -|- 0x7efc226e5700|| -|- Processed 52000/52007 (99%) bases of contig 'contig_133_1|arrow'
>|> 20210218 13:53:26.649 -|- INFO -|- MaybeFlushContig -|- 0x7efc226e5700|| -|- Finished contig 'contig_133_1|arrow' with 52007 expected bases
>|> 20210218 13:53:26.651 -|- INFO -|- MaybeFlushContig -|- 0x7efc226e5700|| -|- Calling variants for contig: contig_133_1|arrow
terminate called without an active exception
Aborted

It breaks for all our samples.

akiledal commented 3 years ago

pbgcpp 1.0.0-0 successfully polishes the same genome. @elcortegano, might be worth trying

pb-dseifert commented 3 years ago

If you're willing to boil down your data to a simple reproducing example and are willing to share it (which we obviously treat confidentially), we will have a look.

armintoepfer commented 3 years ago

You can upload data here https://portal.pacificbiosciences.com/ and send me the info to following mail: armin at pacb.com

elcortegano commented 3 years ago

Thank you all for the feedback. I am willing to submit files, so will prepare a zip shortly and submit it there (it should be smaller than 20GB in size) together with the commands used and the log generated.

Following @akiledal 's post, I was running now arrow from variantCaller 2.3.3, and seems to run well.

armintoepfer commented 3 years ago

We received your file and will report back with our findings.

pb-dseifert commented 3 years ago

With the help of @elcortegano we could finally fix the bug causing this. Version 2.0.2 includes the fixes. https://github.com/bioconda/bioconda-recipes/pull/27434