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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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Lima terminate called without an active exception #463

Closed zmz1988 closed 1 year ago

zmz1988 commented 2 years ago

Operating system Linux on HPC

Package name lima 2.4.0, conda environment was newly updated

Conda environment What is the result of conda list? 

(base) [user@608-4 Analysis]$ conda list

Name Version Build Channel

_libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 1_gnu conda-forge _r-mutex 1.0.1 anacondar_1 conda-forge abseil-cpp 20210324.1 h9c3ff4c_0 conda-forge alabaster 0.7.12 pypi_0 pypi appdirs 1.4.4 pypi_0 pypi argcomplete 1.12.3 pyhd8ed1ab_2 conda-forge argh 0.26.2 pyh9f0ad1d_1002 conda-forge arrow-cpp 4.0.0 py38h8e6f228_3_cpu conda-forge asciitree 0.3.3 pypi_0 pypi attrs 20.3.0 pypi_0 pypi augustus 3.4.0 pl526h0faeac2_0 bioconda aws-c-cal 0.5.10 h3622835_0 conda-forge aws-c-common 0.5.11 h7f98852_0 conda-forge aws-c-event-stream 0.2.7 hd2d8ebb_9 conda-forge aws-c-io 0.10.2 he6d800f_1 conda-forge aws-checksums 0.1.11 hc0e0e8b_6 conda-forge aws-sdk-cpp 1.8.186 h9ad65fb_2 conda-forge babel 2.9.1 pypi_0 pypi bamtools 2.5.1 h9a82719_9 bioconda bcftools 1.10.2 h4f4756c_3 bioconda bedtools 2.30.0 h7d7f7ad_2 bioconda binutils_impl_linux-64 2.36.1 h193b22a_2 conda-forge binutils_linux-64 2.36 hf3e587d_33 conda-forge biopython 1.76 pypi_0 pypi blasr 5.3.5 0 bioconda blast 2.11.0 pl526he19e7b1_0 bioconda blessed 1.18.0 pypi_0 pypi bokeh 2.3.0 pypi_0 pypi boost-cpp 1.70.0 h7b93d67_3 conda-forge bowtie2 2.4.3 py38h72fc82f_0 bioconda brotli 1.0.9 h7f98852_6 conda-forge brotli-bin 1.0.9 h7f98852_6 conda-forge brotlipy 0.7.0 py38h497a2fe_1003 conda-forge busco 5.1.3 pyhdfd78af_0 bioconda bwa 0.7.17 h5bf99c6_8 bioconda bwidget 1.9.14 ha770c72_1 conda-forge bzip2 1.0.8 h7f98852_4 conda-forge c-ares 1.18.1 h7f98852_0 conda-forge ca-certificates 2021.10.8 ha878542_0 conda-forge cached-property 1.5.2 hd8ed1ab_1 conda-forge cached_property 1.5.2 pyha770c72_1 conda-forge cairo 1.16.0 h9f066cc_1006 conda-forge cd-hit 4.8.1 h2e03b76_5 bioconda cdbtools 0.99 h9a82719_6 bioconda certifi 2021.10.8 py38h578d9bd_1 conda-forge cffi 1.15.0 py38h3931269_0 conda-forge charset-normalizer 2.0.8 pyhd8ed1ab_0 conda-forge click 8.0.3 py38h578d9bd_1 conda-forge cloudpickle 2.0.0 pyhd8ed1ab_0 conda-forge cmake 3.19.6 h973ab73_0
colorama 0.4.4 pyh9f0ad1d_0 conda-forge coloredlogs 15.0.1 py38h578d9bd_2 conda-forge colormath 3.0.0 pypi_0 pypi commonmark 0.9.1 py_0 conda-forge conda 4.11.0 py38h578d9bd_0 conda-forge conda-package-handling 1.7.3 py38h497a2fe_1 conda-forge cooler 0.8.11 pypi_0 pypi coreutils 8.31 h516909a_0 conda-forge cryptography 36.0.0 py38h3e25421_0 conda-forge curl 7.76.1 h979ede3_1 conda-forge cycler 0.11.0 pyhd8ed1ab_0 conda-forge cython 0.29.24 pypi_0 pypi cytoolz 0.10.1 pypi_0 pypi dask 2021.11.2 pyhd8ed1ab_0 conda-forge dask-core 2021.11.2 pyhd8ed1ab_0 conda-forge datrie 0.8.2 pypi_0 pypi deeptools 3.5.1 pypi_0 pypi deeptoolsintervals 0.1.9 pypi_0 pypi dendropy 4.5.2 pyh3252c3a_0 bioconda deprecated 1.2.13 pyh6c4a22f_0 conda-forge diamond 2.0.8 h56fc30b_0 bioconda dill 0.3.4 pyhd8ed1ab_0 conda-forge distlib 0.3.1 pypi_0 pypi distributed 2021.11.2 py38h578d9bd_0 conda-forge docutils 0.17b1 pypi_0 pypi entrez-direct 16.2 he881be0_0 bioconda expat 2.4.1 h9c3ff4c_0 conda-forge falcon-kit 1.8.1 pypi_0 pypi falcon-phase 1.2.0 pypi_0 pypi falcon-unzip 1.3.7 pypi_0 pypi fastme 2.1.6.1 h779adbc_0 bioconda fastqc 0.11.9 hdfd78af_1 bioconda fasttree 2.1.10 h779adbc_5 bioconda filelock 3.0.12 pypi_0 pypi flye 2.9 py38h69e0bdc_0 bioconda font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge font-ttf-inconsolata 3.000 h77eed37_0 conda-forge font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge font-ttf-ubuntu 0.83 hab24e00_0 conda-forge fontconfig 2.13.1 hba837de_1005 conda-forge fonts-conda-ecosystem 1 0 conda-forge fonts-conda-forge 1 0 conda-forge fonttools 4.28.2 py38h497a2fe_0 conda-forge freetype 2.10.4 h0708190_1 conda-forge fribidi 1.0.10 h36c2ea0_0 conda-forge fsspec 2021.11.1 pyhd8ed1ab_0 conda-forge future 0.18.2 py38h578d9bd_4 conda-forge gatk4 4.2.0.0 hdfd78af_1 bioconda gawk 5.1.0 h7f98852_0 conda-forge gcc_impl_linux-64 7.5.0 habd7529_19 conda-forge gcc_linux-64 7.5.0 h47867f9_33 conda-forge genometools-genometools 1.6.1 py38h23571c4_2 bioconda gettext 0.19.8.1 h73d1719_1008 conda-forge gfaffix 0.1.2.1 h779adbc_0 bioconda gffutils 0.10.1 pyh864c0ab_1 bioconda gflags 2.2.2 he1b5a44_1004 conda-forge gfortran_impl_linux-64 7.5.0 h56cb351_19 conda-forge gfortran_linux-64 7.5.0 h78c8a43_33 conda-forge gitdb 4.0.5 pypi_0 pypi gitpython 3.1.14 pypi_0 pypi glib 2.68.4 h9c3ff4c_1 conda-forge glib-tools 2.68.4 h9c3ff4c_1 conda-forge glog 0.5.0 h48cff8f_0 conda-forge gmp 6.1.2 hf484d3e_1000 conda-forge gnutls 3.5.19 h2a4e5f8_1 conda-forge google-auth 1.27.1 pypi_0 pypi google-auth-oauthlib 0.4.3 pypi_0 pypi gpustat 1.0.0b1 pypi_0 pypi graphite2 1.3.13 h58526e2_1001 conda-forge grpc-cpp 1.37.1 h2519f57_2 conda-forge gsl 2.6 he838d99_2 conda-forge gxx_impl_linux-64 7.5.0 hd0bb8aa_19 conda-forge gxx_linux-64 7.5.0 h555fc39_33 conda-forge h5py 3.4.0 pypi_0 pypi harfbuzz 2.7.2 ha5b49bf_1 conda-forge hdf5 1.10.6 nompi_h7c3c948_1111 conda-forge heapdict 1.0.1 py_0 conda-forge hmmer 3.1b2 3 bioconda htslib 1.10.2 hd3b49d5_1 bioconda humanfriendly 10.0 py38h578d9bd_1 conda-forge icu 67.1 he1b5a44_0 conda-forge idna 3.1 pyhd3deb0d_0 conda-forge imagesize 1.2.0 pypi_0 pypi importlib-metadata 4.8.2 py38h578d9bd_0 conda-forge importlib_metadata 4.8.2 hd8ed1ab_0 conda-forge interlap 0.2.7 pyh9f0ad1d_0 conda-forge intervaltree 3.0.2 py_0 conda-forge iqtree 2.1.4_beta hdcc8f71_0 bioconda isoseq3 3.4.0 0 bioconda jemalloc 5.2.1 h9c3ff4c_6 conda-forge jinja2 2.11.3 pypi_0 pypi joblib 1.0.1 pypi_0 pypi joypy 0.2.4 pypi_0 pypi jpeg 9d h36c2ea0_0 conda-forge jsonschema 3.2.0 pypi_0 pypi k8 0.2.5 h9a82719_1 bioconda kaleido 0.2.0 pypi_0 pypi kaleido-core 0.2.1 h3644ca4_0 conda-forge kernel-headers_linux-64 2.6.32 he073ed8_15 conda-forge kiwisolver 1.3.2 py38h1fd1430_1 conda-forge krb5 1.17.2 h926e7f8_0 conda-forge lcms2 2.12 hddcbb42_0 conda-forge ld_impl_linux-64 2.36.1 hea4e1c9_2 conda-forge libblas 3.9.0 8_openblas conda-forge libbrotlicommon 1.0.9 h7f98852_6 conda-forge libbrotlidec 1.0.9 h7f98852_6 conda-forge libbrotlienc 1.0.9 h7f98852_6 conda-forge libcblas 3.9.0 8_openblas conda-forge libcurl 7.76.1 hc4aaa36_1 conda-forge libdeflate 1.6 h516909a_0 conda-forge libedit 3.1.20191231 he28a2e2_2 conda-forge libev 4.33 h516909a_1 conda-forge libevent 2.1.10 h9b69904_4 conda-forge libffi 3.4.2 h7f98852_5 conda-forge libgcc 7.2.0 h69d50b8_2 conda-forge libgcc-devel_linux-64 7.5.0 hda03d7c_19 conda-forge libgcc-ng 11.1.0 hc902ee8_8 conda-forge libgfortran-ng 7.5.0 h14aa051_19 conda-forge libgfortran4 7.5.0 h14aa051_19 conda-forge libglib 2.68.4 h174f98d_1 conda-forge libgomp 11.1.0 hc902ee8_8 conda-forge libiconv 1.16 h516909a_0 conda-forge libidn2 2.3.2 h7f98852_0 conda-forge libjemalloc 5.2.1 h9c3ff4c_6 conda-forge liblapack 3.9.0 8_openblas conda-forge libnghttp2 1.43.0 h812cca2_1 conda-forge libopenblas 0.3.12 pthreads_hb3c22a3_1 conda-forge libpng 1.6.37 h21135ba_2 conda-forge libprotobuf 3.16.0 h780b84a_0 conda-forge libssh2 1.10.0 ha56f1ee_2 conda-forge libstdcxx-devel_linux-64 7.5.0 hb016644_19 conda-forge libstdcxx-ng 11.2.0 he4da1e4_11 conda-forge libthrift 0.14.1 he6d91bd_2 conda-forge libtiff 4.2.0 hbd63e13_2 conda-forge libunistring 0.9.10 h7f98852_0 conda-forge libutf8proc 2.6.1 h7f98852_0 conda-forge libuuid 2.32.1 h7f98852_1000 conda-forge libuv 1.42.0 h7f98852_0 conda-forge libwebp-base 1.2.1 h7f98852_0 conda-forge libxcb 1.13 h7f98852_1004 conda-forge libxml2 2.9.10 h68273f3_2 conda-forge liftoff 1.6.1 pyhdfd78af_0 bioconda lima 2.4.0 h9ee0642_1 bioconda llvm-openmp 8.0.1 hc9558a2_0 conda-forge locket 0.2.0 py_2 conda-forge lp_solve 5.5.2.5 h14c3975_1001 conda-forge ltr_retriever 2.9.0 hdfd78af_1 bioconda lz4-c 1.9.3 h9c3ff4c_1 conda-forge lzstring 1.0.4 pypi_0 pypi mafft 7.490 h779adbc_0 bioconda make 4.3 hd18ef5c_1 conda-forge mappy 2.17 pypi_0 pypi markdown 3.3.6 pyhd8ed1ab_0 conda-forge markupsafe 1.1.1 pypi_0 pypi mathjax 2.7.7 0 conda-forge matplotlib-base 3.5.0 py38hf4fb855_0 conda-forge mcl 14.137 pl5262h779adbc_6 bioconda medaka 1.3.4 pypi_0 pypi metaeuk 5.34c21f2 h95f258a_0 bioconda metis 5.1.0 h58526e2_1006 conda-forge miniasm 0.3_r179 h5bf99c6_2 bioconda minimap2 2.22 h5bf99c6_0 bioconda mmseqs2 13.45111 h95f258a_1 bioconda mpfr 4.0.2 he80fd80_0 conda-forge mpi 1.0 openmpi conda-forge mreps 2.6.01 h779adbc_1 bioconda msgpack-python 1.0.3 py38h1fd1430_0 conda-forge multiprocess 0.70.12.2 py38h497a2fe_1 conda-forge multiqc 1.11 pyhdfd78af_0 bioconda mummer 3.23 pl5262h1b792b2_12 bioconda mummer4 4.0.0rc1 pl5262h1b792b2_1 bioconda munkres 1.1.4 pyh9f0ad1d_0 conda-forge muscle 3.8.1551 h7d875b9_6 bioconda mysql-connector-c 6.1.11 h6eb9d5d_1007 conda-forge nanocomp 1.13.1 pypi_0 pypi nanofilt 2.8.0 pypi_0 pypi nanoget 1.15.0 pypi_0 pypi nanolyse 1.2.0 pypi_0 pypi nanomath 1.2.1 pyhdfd78af_0 bioconda nanopack 1.1.0 pypi_0 pypi nanoplot 1.34.1 pypi_0 pypi nanoqc 0.9.4 pypi_0 pypi nanostat 1.5.0 pypi_0 pypi ncurses 6.2 h58526e2_4 conda-forge necat 0.0.1_update20200803 h2e03b76_1 bioconda nettle 3.3 0 conda-forge networkx 2.6.3 pyhd8ed1ab_1 conda-forge nextflow 21.04.0 h4a94de4_0 bioconda nim-falcon 3.0.2 h18d090a_1 bioconda nodejs 6.13.1 0 conda-forge nose 1.3.7 pypi_0 pypi nseg 1.0.1 h779adbc_1 bioconda nspr 4.32 h9c3ff4c_1 conda-forge nss 3.69 hb5efdd6_1 conda-forge numpy 1.18.5 pypi_0 pypi numpydoc 1.1.0 pypi_0 pypi oauthlib 3.1.0 pypi_0 pypi odgi 0.6.2 py38h8e3bb3f_0 bioconda olefile 0.46 pyh9f0ad1d_1 conda-forge ont-pyguppy-client-lib 6.0.1 pypi_0 pypi openblas 0.3.12 pthreads_h43bd3aa_1 conda-forge opencv-python 4.5.1.48 pypi_0 pypi openjdk 8.0.302 h7f98852_0 conda-forge openjpeg 2.4.0 hb52868f_1 conda-forge openmp 8.0.1 0 conda-forge openmpi 4.0.5 ha4a8674_4 conda-forge openssl 1.1.1l h7f98852_0 conda-forge orc 1.6.7 h89a63ab_2 conda-forge orthofinder 2.5.4 hdfd78af_0 bioconda packaging 21.3 pyhd8ed1ab_0 conda-forge pairix 0.3.7 py38h390ddb8_3 bioconda pairtools 0.3.0 py38h81e7a2c_5 bioconda pandas 1.2.3 pypi_0 pypi pango 1.42.4 h69149e4_5 conda-forge parallel 20211022 ha770c72_0 conda-forge parasail-python 1.2.4 py38h8e3bb3f_1 bioconda parquet-cpp 1.5.1 2 conda-forge partd 1.2.0 pyhd8ed1ab_0 conda-forge pauvre 0.2 pypi_0 pypi pb-assembly 0.0.8 hdfd78af_1 bioconda pb-dazzler 0.0.1 h779adbc_1 bioconda pb-falcon 2.2.4 py38h1bd3507_1 bioconda pb-falcon-phase 0.1.0 h8e334b0_1 bioconda pbccs 6.0.0 h9ee0642_2 bioconda pbgcpp 2.0.2 h9ee0642_1 bioconda pbgzip 2016.08.04 h36cd882_2 bioconda pbmm2 1.4.0 h56fc30b_0 bioconda pcre 8.45 h9c3ff4c_0 conda-forge pcre2 10.35 h032f7d1_2 conda-forge perl 5.26.2 h36c2ea0_1008 conda-forge perl-apache-test 1.40 pl526_1 bioconda perl-app-cpanminus 1.7044 pl526_1 bioconda perl-archive-tar 2.32 pl526_0 bioconda perl-base 2.23 pl526_1 bioconda perl-carp 1.38 pl526_3 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-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-cpan-meta 2.150010 pl526_0 bioconda perl-cpan-meta-requirements 2.140 pl526_0 bioconda perl-cpan-meta-yaml 0.018 pl526_0 bioconda perl-data-dumper 2.173 pl526_0 bioconda perl-data-optlist 0.110 pl526_2 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-size 0.83 pl526h14c3975_0 bioconda perl-devel-stacktrace 2.04 pl526_0 bioconda perl-dist-checkconflicts 0.11 pl526_2 bioconda perl-encode 2.88 pl526_1 bioconda perl-env 1.04 pl526_1 bioconda perl-eval-closure 0.14 pl526h6bb024c_4 bioconda perl-exporter 5.72 pl526_1 bioconda perl-exporter-tiny 1.002001 pl526_0 bioconda perl-extutils-cbuilder 0.280230 pl526_1 bioconda perl-extutils-makemaker 7.36 pl526_1 bioconda perl-extutils-manifest 1.72 pl526_0 bioconda perl-extutils-parsexs 3.35 pl526_0 bioconda perl-file-path 2.16 pl526_0 bioconda perl-file-temp 0.2304 pl526_2 bioconda perl-file-which 1.23 pl526_0 bioconda perl-getopt-long 2.50 pl526_1 bioconda perl-io-compress 2.087 pl526he1b5a44_0 bioconda perl-io-zlib 1.10 pl526_2 bioconda perl-ipc-cmd 1.02 pl526_0 bioconda perl-json 4.02 pl526_0 bioconda perl-json-pp 4.04 pl526_0 bioconda perl-json-xs 2.34 pl526h6bb024c_3 bioconda perl-list-moreutils 0.428 pl526_1 bioconda perl-list-moreutils-xs 0.428 pl526_0 bioconda perl-locale-maketext-simple 0.21 pl526_2 bioconda perl-module-build 0.4224 pl526_3 bioconda perl-module-corelist 5.20190524 pl526_0 bioconda perl-module-implementation 0.09 pl526_2 bioconda perl-module-load 0.32 pl526_1 bioconda perl-module-load-conditional 0.68 pl526_2 bioconda perl-module-metadata 1.000036 pl526_0 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-mro-compat 0.13 pl526_0 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-parallel-forkmanager 2.02 pl526_0 bioconda perl-params-check 0.38 pl526_1 bioconda perl-params-util 1.07 pl526h6bb024c_4 bioconda perl-parent 0.236 pl526_1 bioconda perl-pathtools 3.75 pl526h14c3975_1 bioconda perl-perl-ostype 1.010 pl526_1 bioconda perl-role-tiny 2.000008 pl526_0 bioconda perl-scalar-list-utils 1.52 pl526h516909a_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-test-simple 1.302164 pl526_0 bioconda perl-text-abbrev 1.02 pl526_0 bioconda perl-text-parsewords 3.30 pl526_0 bioconda perl-text-soundex 3.05 pl526_1000 conda-forge perl-try-tiny 0.30 pl526_1 bioconda perl-types-serialiser 1.0 pl526_2 bioconda perl-vcftools-vcf 0.1.16 pl526_2 bioconda 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Describe the bug Run of Lima terminates immediately. I got some lima outputs but they only only have one line in the file...

`$ ls -llt`
-rw-r--r-- 1 user       662 Jan 14 07:52 Sample.fl.lima.report
-rw-r--r-- 1 user       692 Jan 14 07:52 Sample.fl.lima.summary
-rw-r--r-- 1 user       125 Jan 14 07:52 Sample.fl.json
-rw-r--r-- 1 user        69 Jan 14 07:52 Sample.fl.lima.counts
-rw-r--r-- 1 user     1114 Jan 14 07:52 Sample.fl.consensusreadset.xml
-rw-r--r-- 1 user         0 Jan 14 07:52 Sample.fl.lima.clips

`$ less Sample.fl.lima.report`

ZMW     IdxFirst        IdxCombined     IdxSecondCandidate      IdxFirstAlt     IdxSecondAlt    ScoreFirst      ScoreCombined   ScoreSecondCandidate    ScoreFirstAlt   ScoreSecondAlt  ScoreCombinedFirst      ScoreCombinedSecond     ScoresFirst     ScoresCombined  ScoresSecondCandidate   ScoresFirstAlt  ScoresSecondAlt ReadLengths     IdxsCombined    ClipsFirst
      ClipsCombined   ClipsSecondCandidate    ClipsFirstAlt   ClipsSecondAlt  ScoreLead
       SignalIncrease  NumPasses       NumAdapters     NumBadAdapters  NumBadAdapterRatio
      NumScoredAdapters       NumBarcodedRegions      NumBarcodedRegionsPassed        PassedFilters   IdxFirstNamed   IdxCombinedNamed        IdxSecondCandidateNamed IdxFirstAltNamed        IdxSecondAltNamed       IdxLowest       IdxHighest      IdxLowestNamed  IdxHighestNamed

I tried deleting --isoseq, and the error is the same.

I also attach my primer.fasta file here, in case it's the problem. `>Clontech_5p AAGCAGTGGTATCAACGCAGAGTACATGGGG

SMART_CDS_Primer_II_A_3p AAGCAGTGGTATCAACGCAGAGTACT`

The input .ccs.bam file is generated by ccs command, with 89% sequence passed the filters.

Error message

(base) [user@608-4 Analysis]$ lima Sample.ccs.bam primer.fasta Sample.fl.bam --isoseq
terminate called without an active exception
Aborted
armintoepfer commented 2 years ago

Can you provide a minimal test example for me to reproduce? Instructions for uploading are on the main pbbioconda page. Thank you

zmz1988 commented 2 years ago

Thanks for replying me, @armintoepfer. I'm having problem to extract e.g. the first 1000 reads from the .ccs.bam file. Seems like something in the bam file is changed if I use samtools view sample.ccs.bam | head -n 1000 | samtools -S -b > test.ccs.bam. I used lima to run on the test.ccs.bam file, it complains that lima can't recognise the read type.

I tried the same samtools command on the subheads.bam file before ccs analysis, and ccs can't recognise the test.subreads.bam either. Could you please give me some hints how to generate a small file for me to share? Thanks!

armintoepfer commented 2 years ago

Include the header :)

samtools view -h sample.ccs.bam | head -n 1000 | samtools -bS > test.ccs.bam
zmz1988 commented 2 years ago

thanks! File is shared :)

zmz1988 commented 2 years ago

Hello @armintoepfer, may I ask whether you could give me some advice on this issue? :) I still have problem in running lima with our isoseq data. Thanks a lot in advance!

armintoepfer commented 2 years ago

I haven't had time yet to look at it. If this is blocking you, please reach out to PacBio's official tech support.

zmz1988 commented 2 years ago

Ok, thanks for letting me know!