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FusionSimulatorToolkit / FusionSimulatorToolkit.github.io

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The input file were PE FASTQ files, but the final output file is .fa file. #1

Open bioPG opened 1 year ago

bioPG commented 1 year ago

code: time /data2/dev_projects/dujun/miniconda3/bin/conda run -n fusion_simulation \ align_and_estimate_abundance.pl \ --transcripts combined.transcripts.fasta \ --est_method RSEM \ --aln_method bowtie \ --prep_reference \ --seqType fq \ --thread_count 8 \ --left test_1.fastq \ --right test_2.fastq \ --output_dir RSEM_outdir && \ echo done at date >> 03.quantify_transcripts.sh.sign

output: sim_reads.fa

brianjohnhaas commented 1 year ago

that command and that output file look entirely unrelated to me. sorry!

On Tue, Aug 8, 2023 at 7:40 AM jundu @.***> wrote:

code: time /data2/dev_projects/dujun/miniconda3/bin/conda run -n fusion_simulation align_and_estimate_abundance.pl --transcripts combined.transcripts.fasta --est_method RSEM --aln_method bowtie --prep_reference --seqType fq --thread_count 8 --left test_1.fastq --right test_2.fastq --output_dir RSEM_outdir && echo done at date >> 03.quantify_transcripts.sh.sign

output: sim_reads.fa

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you are subscribed to this thread.Message ID: @.***>

--

Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas

bioPG commented 1 year ago

Sorry, I was too hasty earlier and failed to provide enough information. Here is all of my scripts and related supporting files information.

supporting files

gencode.v19.annotation.gff3

$ head gencode.v19.annotation.gff3
chr1    HAVANA  gene    203274619       203278730       .       +       .       ID=BTG2|ENSG00000159388.5;Name=BTG2
chr1    HAVANA  mRNA    203274664       203278730       .       +       .       ID=BTG2|ENST00000290551.4;Parent=BTG2|ENSG00000159388.5;Name=BTG2
chr1    HAVANA  five_prime_UTR  203274664       203274734       .       +       .       ID=BTG2|ENST00000290551.4.utr5p1;Parent=BTG2|ENST00000290551.4
chr1    HAVANA  exon    203274664       203274876       .       +       .       ID=BTG2|ENST00000290551.4.exon1;Parent=BTG2|ENST00000290551.4
chr1    HAVANA  CDS     203274735       203274876       .       +       .       ID=cds.BTG2|ENST00000290551.4;Parent=BTG2|ENST00000290551.4
chr1    HAVANA  exon    203276232       203278730       .       +       .       ID=BTG2|ENST00000290551.4.exon2;Parent=BTG2|ENST00000290551.4
chr1    HAVANA  CDS     203276232       203276566       .       +       .       ID=cds.BTG2|ENST00000290551.4;Parent=BTG2|ENST00000290551.4
chr1    HAVANA  three_prime_UTR 203276567       203278730       .       +       .       ID=BTG2|ENST00000290551.4.utr3p1;Parent=BTG2|ENST00000290551.4
chr1    HAVANA  mRNA    203274619       203278697       .       +       .       ID=BTG2|ENST00000475157.1;Parent=BTG2|ENSG00000159388.5;Name=BTG2
chr1    HAVANA  five_prime_UTR  203274619       203274734       .       +       .       ID=BTG2|ENST00000475157.1.utr5p1;Parent=BTG2|ENST00000475157.1

GRCh37.p13.genome.primary.fa

$ grep '>' GRCh37.p13.genome.primary.fa | head 
>chr1 1
>chr2 2
>chr3 3
>chr4 4
>chr5 5
>chr6 6
>chr7 7
>chr8 8
>chr9 9
>chr10 10

ref_annot.cdna.fa

>ENST00000438210.1 ENSG00000228477.1 RP3-342P20.2 
GCCGAAGCTGCGGAGCTTGCTGAGGCAAGGCCGAGGATAAGGAGTGGATGCCTGTCACCA
AGCTGGGCCGCTTGGTGAAGGACATGAAGATCAAGTCCCTGCAGGAGATCTATCTCTTCT
CTCTGCCCATTAAGGGATCTGAGATCATTGACTTTTTCCTGGGGGCCTCTCTCAAGGATG
AGGTTTTGAAGATTATGCCAGTGCAGAAGCAGACCCGTGCCGGCCAGCGCACCAGGTTCA
AGGCGTTTGTTGCTATCGGAGACTACAATGGCCATGTCGGTCTGGGTGTTAAGTGCTCCA
AGGAGGTGGCCACCGCCATCCGTGGGGCCATCATCCTGGCCAAGCTCTCCATTGTCCCCG
TGCGCAGAGGCTACTGGGGGAACAAGATCAGCAAGCCCCACACCGTCCCTTGCAAGGTGA
CAGGCCGCTGCGGCTCTGTGCTGGTGCGTCTCATCCCTGCACCCAGGAGCACTGGCATCG
TCTCCACACCTGTGCCCAAGAAGCTGCTCATGATGGCTGGTATCGATGACTGCTACACCT

Conda environment

$ conda list
# packages in environment at /data2/dev_projects/dujun/miniconda3/envs/fusion_simulation:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
_openmp_mutex             4.5                       2_gnu    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
_r-mutex                  1.0.1               anacondar_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
alsa-lib                  1.2.9                hd590300_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
binutils_impl_linux-64    2.40                 hf600244_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
bioconductor-biobase      2.60.0            r43ha9d7317_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
bioconductor-biocgenerics 0.46.0            r43hdfd78af_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
bioconductor-ebseq        1.40.0            r43hdfd78af_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
bowtie                    1.3.1            py38h70e88c0_6    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
bwidget                   1.9.14               ha770c72_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
bzip2                     1.0.8                h7f98852_4    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
c-ares                    1.19.1               hd590300_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
ca-certificates           2023.7.22            hbcca054_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
cairo                     1.16.0            hbbf8b49_1016    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
collectl                  4.0.4                         1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
curl                      8.2.1                hca28451_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
expat                     2.5.0                hcb278e6_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
fastool                   0.1.4                he4a0461_8    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
font-ttf-dejavu-sans-mono 2.37                 hab24e00_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
font-ttf-inconsolata      3.000                h77eed37_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
font-ttf-source-code-pro  2.038                h77eed37_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
font-ttf-ubuntu           0.83                 hab24e00_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
fontconfig                2.14.2               h14ed4e7_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
fonts-conda-ecosystem     1                             0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
fonts-conda-forge         1                             0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
freetype                  2.12.1               hca18f0e_1    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
gcc_impl_linux-64         13.1.0               hc4be1a9_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
gettext                   0.21.1               h27087fc_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
gfortran_impl_linux-64    13.1.0               hd511a9b_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
giflib                    5.2.1                h0b41bf4_3    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
graphite2                 1.3.13            h58526e2_1001    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
gsl                       2.7                  he838d99_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
gxx_impl_linux-64         13.1.0               hc4be1a9_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
harfbuzz                  7.3.0                hdb3a94d_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
htslib                    1.17                 h81da01d_2    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
icu                       72.1                 hcb278e6_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
java-jdk                  7.0.91                        1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
jellyfish                 2.2.10               h6bb024c_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
jemalloc                  4.5.0                         0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
kernel-headers_linux-64   2.6.32              he073ed8_16    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
keyutils                  1.6.1                h166bdaf_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
krb5                      1.21.1               h659d440_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
lcms2                     2.15                 haa2dc70_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
ld_impl_linux-64          2.40                 h41732ed_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
lerc                      4.0.0                h27087fc_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libblas                   3.9.0           17_linux64_openblas    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libcblas                  3.9.0           17_linux64_openblas    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libcups                   2.3.3                h4637d8d_4    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libcurl                   8.2.1                hca28451_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libdb                     6.2.32               h9c3ff4c_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libdeflate                1.18                 h0b41bf4_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libedit                   3.1.20191231         he28a2e2_2    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libev                     4.33                 h516909a_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libexpat                  2.5.0                hcb278e6_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libffi                    3.4.2                h7f98852_5    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libgcc                    7.2.0                h69d50b8_2    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libgcc-devel_linux-64     13.1.0               he3cc6c4_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libgcc-ng                 13.1.0               he5830b7_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libgfortran-ng            13.1.0               h69a702a_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libgfortran5              13.1.0               h15d22d2_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libglib                   2.76.4               hebfc3b9_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libgomp                   13.1.0               he5830b7_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libhwloc                  2.9.2           nocuda_h7313eea_1008    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libiconv                  1.17                 h166bdaf_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libjpeg-turbo             2.1.5.1              h0b41bf4_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
liblapack                 3.9.0           17_linux64_openblas    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libnghttp2                1.52.0               h61bc06f_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libnsl                    2.0.0                h7f98852_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libopenblas               0.3.23          pthreads_h80387f5_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libpng                    1.6.39               h753d276_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libsanitizer              13.1.0               hfd8a6a1_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libsqlite                 3.42.0               h2797004_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libssh2                   1.11.0               h0841786_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libstdcxx-devel_linux-64  13.1.0               he3cc6c4_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libstdcxx-ng              13.1.0               hfd8a6a1_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libtiff                   4.5.1                h8b53f26_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libuuid                   2.38.1               h0b41bf4_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libwebp-base              1.3.1                hd590300_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libxcb                    1.15                 h0b41bf4_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libxml2                   2.11.4               h0d562d8_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libzlib                   1.2.13               hd590300_5    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
make                      4.3                  hd18ef5c_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
mysql-connector-c         6.1.6                         2    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
ncurses                   6.4                  hcb278e6_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
openjdk                   20.0.0               h8e330f5_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
openssl                   3.1.2                hd590300_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
pango                     1.50.14              heaa33ce_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
parafly                   r2013_01_21                   0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
pcre2                     10.40                hc3806b6_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
perl                      5.32.1          4_hd590300_perl5    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
perl-business-isbn        3.007           pl5321hdfd78af_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
perl-business-isbn-data   20210112.006    pl5321hdfd78af_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
perl-carp                 1.38            pl5321hdfd78af_4    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
perl-constant             1.33            pl5321hdfd78af_2    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
perl-data-dumper          2.183           pl5321hec16e2b_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
perl-db_file              1.858           pl5321h166bdaf_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
perl-encode               3.19            pl5321hec16e2b_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
perl-exporter             5.72            pl5321hdfd78af_2    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
perl-extutils-makemaker   7.70            pl5321hd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
perl-inc-latest           0.500           pl5321ha770c72_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
perl-mime-base64          3.16            pl5321hec16e2b_2    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
perl-module-build         0.4234          pl5321ha770c72_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
perl-parent               0.236           pl5321hdfd78af_2    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
perl-perlio-gzip          0.20            pl5321he4a0461_5    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
perl-threaded             5.32.1               hdfd78af_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
perl-uri                  5.12            pl5321hdfd78af_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
pip                       23.2.1             pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
pixman                    0.40.0               h36c2ea0_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
pthread-stubs             0.4               h36c2ea0_1001    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
python                    3.8.17          he550d4f_0_cpython    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
python_abi                3.8                      3_cp38    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
r-base                    4.3.1                h29c4799_3    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
r-bitops                  1.0_7             r43h57805ef_2    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
r-blockmodeling           1.1.4             r43h61816a4_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
r-brio                    1.1.3             r43h57805ef_2    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
r-callr                   3.7.3             r43hc72bb7e_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
r-catools                 1.18.2            r43ha503ecb_2    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
r-cli                     3.6.1             r43ha503ecb_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
r-crayon                  1.5.2             r43hc72bb7e_2    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
r-desc                    1.4.2             r43hc72bb7e_2    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
r-diffobj                 0.3.5             r43h57805ef_2    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
r-digest                  0.6.33            r43ha503ecb_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
r-ellipsis                0.3.2             r43h57805ef_2    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
r-evaluate                0.21              r43hc72bb7e_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
r-fansi                   1.0.4             r43h57805ef_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
r-fs                      1.6.3             r43ha503ecb_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
r-glue                    1.6.2             r43h57805ef_2    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
r-gplots                  3.1.3             r43hc72bb7e_2    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
r-gtools                  3.9.4             r43h57805ef_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
r-jsonlite                1.8.7             r43h57805ef_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
r-kernsmooth              2.23_22           r43h13b3f57_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
r-lattice                 0.21_8            r43h57805ef_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
r-lifecycle               1.0.3             r43hc72bb7e_2    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
r-magrittr                2.0.3             r43h57805ef_2    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
r-matrix                  1.6_0             r43h316c678_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
r-pillar                  1.9.0             r43hc72bb7e_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
r-pkgconfig               2.0.3             r43hc72bb7e_3    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
r-pkgload                 1.3.2.1           r43hc72bb7e_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
r-praise                  1.0.0           r43hc72bb7e_1007    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
r-processx                3.8.2             r43h57805ef_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
r-ps                      1.7.5             r43h57805ef_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
r-r6                      2.5.1             r43hc72bb7e_2    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
r-rematch2                2.1.2             r43hc72bb7e_3    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
r-rlang                   1.1.1             r43ha503ecb_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
r-rprojroot               2.0.3             r43hc72bb7e_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
r-testthat                3.1.10            r43ha503ecb_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
r-tibble                  3.2.1             r43h57805ef_2    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
r-utf8                    1.2.3             r43h57805ef_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
r-vctrs                   0.6.3             r43ha503ecb_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
r-waldo                   0.5.1             r43hc72bb7e_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
r-withr                   2.5.0             r43hc72bb7e_2    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
readline                  8.2                  h8228510_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
rocm-smi                  5.6.0                h59595ed_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
rsem                      1.3.3           pl5321h0033a41_7    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
samtools                  1.17                 hd87286a_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
sed                       4.8                  he412f7d_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
setuptools                68.0.0             pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
slclust                   02022010                      1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
sysroot_linux-64          2.12                he073ed8_16    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
tbb                       2021.10.0            h00ab1b0_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
tk                        8.6.12               h27826a3_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
tktable                   2.10                 hb7b940f_3    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
trimmomatic               0.39                 hdfd78af_2    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
trinity                   2.1.1                         6    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
ucsc-bigwigsummary        448                  h2a80c09_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
wheel                     0.41.0             pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
xorg-fixesproto           5.0               h7f98852_1002    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
xorg-inputproto           2.3.2             h7f98852_1002    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
xorg-kbproto              1.0.7             h7f98852_1002    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
xorg-libice               1.1.1                hd590300_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
xorg-libsm                1.2.4                h7391055_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
xorg-libx11               1.8.6                h8ee46fc_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
xorg-libxau               1.0.11               hd590300_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
xorg-libxdmcp             1.1.3                h7f98852_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
xorg-libxext              1.3.4                h0b41bf4_2    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
xorg-libxfixes            5.0.3             h7f98852_1004    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
xorg-libxi                1.7.10               h7f98852_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
xorg-libxrender           0.9.11               hd590300_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
xorg-libxt                1.3.0                hd590300_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
xorg-libxtst              1.2.3             h7f98852_1002    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
xorg-recordproto          1.14.2            h7f98852_1002    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
xorg-renderproto          0.11.1            h7f98852_1002    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
xorg-xextproto            7.3.0             h0b41bf4_1003    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
xorg-xproto               7.0.31            h7f98852_1007    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
xz                        5.2.6                h166bdaf_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
zlib                      1.2.13               hd590300_5    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
zstd                      1.5.2                hfc55251_7    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge

my scripts

Step 1.

$ cat 01.generate_fusion_transcripts.sh
FusionTranscriptSimulator=~/pipeline/dev/FusionSimulatorToolkit/FusionTranscriptSimulator

time /data2/dev_projects/dujun/miniconda3/bin/conda run -n fusion_simulation \
    $FusionTranscriptSimulator \
    gencode.v19.annotation.gff3 \
    GRCh37.p13.genome.primary.fa 100 > chims.fasta && \
echo done at `date` >> 01.generate_fusion_transcripts.sh.sign

Step 2.

$ cat 02.comb_fusion_transcripts_with_reference_cDNAs.sh
cat chims.fasta ref_annot.cdna.fa > combined.transcripts.fasta && \
echo done at `date` >> 02.comb_fusion_transcripts_with_reference_cDNAs.sh.sign

Step 3.

$ cat 03.quantify_transcripts.sh
time /data2/dev_projects/dujun/miniconda3/bin/conda run -n fusion_simulation \
    align_and_estimate_abundance.pl \
    --transcripts combined.transcripts.fasta \
    --est_method RSEM \
    --aln_method bowtie \
    --prep_reference \
    --seqType fq \
    --thread_count 12 \
    --left ERR030880_1.fastq.gz \
    --right ERR030880_2.fastq.gz \
    --output_dir RSEM_outdir && \
echo done at `date` >> 03.quantify_transcripts.sh.sign

Step 4.

$ cat 04.simulate_fusion_trans_expr_vals.sh
project_dir=/home/zb-dujun/pipeline/dev/FusionSimulatorToolkit

time /data2/dev_projects/dujun/miniconda3/bin/conda run -n fusion_simulation \
    $project_dir/simulate_fusion_trans_expr_vals.pl \
        RSEM_outdir/RSEM.isoforms.results \
        combined.transcripts.fasta \
        > target.forSimulation.RSEM.isoforms.results && \
echo done at `date` >> 04.simulate_fusion_trans_expr_vals.sh.sign

Step 5.

$ cat 05.rsem_simulate_read.sh
time /data2/dev_projects/dujun/miniconda3/bin/conda run -n fusion_simulation \
    rsem-simulate-reads combined.transcripts.fasta.RSEM \
        RSEM_outdir/RSEM.stat/RSEM.model \
        target.forSimulation.RSEM.isoforms.results \
        0.01  10000  sim_reads && \
echo done at `date` >> 05.rsem_simulate_read.sh.sign

results

image

RSEM_outdir:

image

BUG

According to the instructions in README.txt, my simulation results should yield the sim_reads_1.fq and sim_reads_2.fq files, not the sim_reads.fa file. Could you please advise me on where I need to make modifications in my script? Thank you very much.

If you need further assistance or explanations, please feel free to let me know anytime.

brianjohnhaas commented 1 year ago

The step 5 there should be generating the reads.

What happens when you run that step? Does it give any errors?

On Tue, Aug 8, 2023 at 11:38 PM jundu @.***> wrote:

Sorry, I was too hasty earlier and failed to provide enough information. Here is all of my scripts and related supporting files information. supporting files

gencode.v19.annotation.gff3

$ head gencode.v19.annotation.gff3 chr1 HAVANA gene 203274619 203278730 . + . ID=BTG2|ENSG00000159388.5;Name=BTG2 chr1 HAVANA mRNA 203274664 203278730 . + . ID=BTG2|ENST00000290551.4;Parent=BTG2|ENSG00000159388.5;Name=BTG2 chr1 HAVANA five_prime_UTR 203274664 203274734 . + . ID=BTG2|ENST00000290551.4.utr5p1;Parent=BTG2|ENST00000290551.4 chr1 HAVANA exon 203274664 203274876 . + . ID=BTG2|ENST00000290551.4.exon1;Parent=BTG2|ENST00000290551.4 chr1 HAVANA CDS 203274735 203274876 . + . ID=cds.BTG2|ENST00000290551.4;Parent=BTG2|ENST00000290551.4 chr1 HAVANA exon 203276232 203278730 . + . ID=BTG2|ENST00000290551.4.exon2;Parent=BTG2|ENST00000290551.4 chr1 HAVANA CDS 203276232 203276566 . + . ID=cds.BTG2|ENST00000290551.4;Parent=BTG2|ENST00000290551.4 chr1 HAVANA three_prime_UTR 203276567 203278730 . + . ID=BTG2|ENST00000290551.4.utr3p1;Parent=BTG2|ENST00000290551.4 chr1 HAVANA mRNA 203274619 203278697 . + . ID=BTG2|ENST00000475157.1;Parent=BTG2|ENSG00000159388.5;Name=BTG2 chr1 HAVANA five_prime_UTR 203274619 203274734 . + . ID=BTG2|ENST00000475157.1.utr5p1;Parent=BTG2|ENST00000475157.1

GRCh37.p13.genome.primary.fa

$ grep '>' GRCh37.p13.genome.primary.fa | head

chr1 1 chr2 2 chr3 3 chr4 4 chr5 5 chr6 6 chr7 7 chr8 8 chr9 9 chr10 10

ref_annot.cdna.fa

ENST00000438210.1 ENSG00000228477.1 RP3-342P20.2 GCCGAAGCTGCGGAGCTTGCTGAGGCAAGGCCGAGGATAAGGAGTGGATGCCTGTCACCA AGCTGGGCCGCTTGGTGAAGGACATGAAGATCAAGTCCCTGCAGGAGATCTATCTCTTCT CTCTGCCCATTAAGGGATCTGAGATCATTGACTTTTTCCTGGGGGCCTCTCTCAAGGATG AGGTTTTGAAGATTATGCCAGTGCAGAAGCAGACCCGTGCCGGCCAGCGCACCAGGTTCA AGGCGTTTGTTGCTATCGGAGACTACAATGGCCATGTCGGTCTGGGTGTTAAGTGCTCCA AGGAGGTGGCCACCGCCATCCGTGGGGCCATCATCCTGGCCAAGCTCTCCATTGTCCCCG TGCGCAGAGGCTACTGGGGGAACAAGATCAGCAAGCCCCACACCGTCCCTTGCAAGGTGA CAGGCCGCTGCGGCTCTGTGCTGGTGCGTCTCATCCCTGCACCCAGGAGCACTGGCATCG TCTCCACACCTGTGCCCAAGAAGCTGCTCATGATGGCTGGTATCGATGACTGCTACACCT

Conda environment

$ conda list

packages in environment at /data2/dev_projects/dujun/miniconda3/envs/fusion_simulation:

#

Name Version Build Channel

_libgcc_mutex 0.1 conda_forge https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge _openmp_mutex 4.5 2_gnu https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge _r-mutex https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge_r-mutex 1.0.1 anacondar_1 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge alsa-lib https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forgealsa-lib 1.2.9 hd590300_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge binutils_impl_linux-64 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forgebinutils_impl_linux-64 2.40 hf600244_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge bioconductor-biobase https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forgebioconductor-biobase 2.60.0 r43ha9d7317_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda bioconductor-biocgenerics https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/biocondabioconductor-biocgenerics 0.46.0 r43hdfd78af_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda bioconductor-ebseq https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/biocondabioconductor-ebseq 1.40.0 r43hdfd78af_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda bowtie 1.3.1 py38h70e88c0_6 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda bwidget 1.9.14 ha770c72_1 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge bzip2 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forgebzip2 1.0.8 h7f98852_4 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge c-ares https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forgec-ares 1.19.1 hd590300_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge ca-certificates https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forgeca-certificates 2023.7.22 hbcca054_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge cairo 1.16.0 hbbf8b49_1016 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge collectl 4.0.4 1 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda curl 8.2.1 hca28451_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge expat 2.5.0 hcb278e6_1 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge fastool 0.1.4 he4a0461_8 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda font-ttf-dejavu-sans-mono https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/biocondafont-ttf-dejavu-sans-mono 2.37 hab24e00_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge font-ttf-inconsolata https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forgefont-ttf-inconsolata 3.000 h77eed37_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge font-ttf-source-code-pro https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forgefont-ttf-source-code-pro 2.038 h77eed37_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge font-ttf-ubuntu https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forgefont-ttf-ubuntu 0.83 hab24e00_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge fontconfig 2.14.2 h14ed4e7_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge fonts-conda-ecosystem https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forgefonts-conda-ecosystem 1 0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge fonts-conda-forge https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forgefonts-conda-forge 1 0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge freetype 2.12.1 hca18f0e_1 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 gcc_impl_linux-64 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forgegcc_impl_linux-64 13.1.0 hc4be1a9_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge gettext 0.21.1 h27087fc_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge gfortran_impl_linux-64 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forgegfortran_impl_linux-64 13.1.0 hd511a9b_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge giflib 5.2.1 h0b41bf4_3 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge graphite2 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forgegraphite2 1.3.13 h58526e2_1001 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge gsl 2.7 he838d99_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge gxx_impl_linux-64 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forgegxx_impl_linux-64 13.1.0 hc4be1a9_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge harfbuzz 7.3.0 hdb3a94d_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge htslib 1.17 h81da01d_2 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda icu 72.1 hcb278e6_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge java-jdk https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forgejava-jdk 7.0.91 1 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda jellyfish 2.2.10 h6bb024c_1 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda jemalloc 4.5.0 0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda kernel-headers_linux-64 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/biocondakernel-headers_linux-64 2.6.32 he073ed8_16 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge keyutils 1.6.1 h166bdaf_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge krb5 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forgekrb5 1.21.1 h659d440_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge lcms2 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forgelcms2 2.15 haa2dc70_1 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge ld_impl_linux-64 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forgeld_impl_linux-64 2.40 h41732ed_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge lerc 4.0.0 h27087fc_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge libblas 3.9.0 17_linux64_openblas https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge libcblas 3.9.0 17_linux64_openblas https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge libcups 2.3.3 h4637d8d_4 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge libcurl 8.2.1 hca28451_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge libdb 6.2.32 h9c3ff4c_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge libdeflate 1.18 h0b41bf4_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge libedit 3.1.20191231 he28a2e2_2 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge libev 4.33 h516909a_1 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge libexpat 2.5.0 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https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge xorg-renderproto https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forgexorg-renderproto 0.11.1 h7f98852_1002 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge xorg-xextproto https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forgexorg-xextproto 7.3.0 h0b41bf4_1003 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge xorg-xproto https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forgexorg-xproto 7.0.31 h7f98852_1007 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge xz 5.2.6 h166bdaf_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge zlib 1.2.13 hd590300_5 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge zstd 1.5.2 hfc55251_7 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge

my scripts Step 1.

$ cat 01.generate_fusion_transcripts.sh FusionTranscriptSimulator=~/pipeline/dev/FusionSimulatorToolkit/FusionTranscriptSimulator

time /data2/dev_projects/dujun/miniconda3/bin/conda run -n fusion_simulation \ $FusionTranscriptSimulator \ gencode.v19.annotation.gff3 \ GRCh37.p13.genome.primary.fa 100 > chims.fasta && \ echo done at date >> 01.generate_fusion_transcripts.sh.sign

Step 2.

$ cat 02.comb_fusion_transcripts_with_reference_cDNAs.sh cat chims.fasta ref_annot.cdna.fa > combined.transcripts.fasta && \ echo done at date >> 02.comb_fusion_transcripts_with_reference_cDNAs.sh.sign

Step 3.

$ cat 03.quantify_transcripts.sh time /data2/dev_projects/dujun/miniconda3/bin/conda run -n fusion_simulation \ align_and_estimate_abundance.pl \ --transcripts combined.transcripts.fasta \ --est_method RSEM \ --aln_method bowtie \ --prep_reference \ --seqType fq \ --thread_count 12 \ --left ERR030880_1.fastq.gz \ --right ERR030880_2.fastq.gz \ --output_dir RSEM_outdir && \ echo done at date >> 03.quantify_transcripts.sh.sign

Step 4.

$ cat 04.simulate_fusion_trans_expr_vals.sh project_dir=/home/zb-dujun/pipeline/dev/FusionSimulatorToolkit

time /data2/dev_projects/dujun/miniconda3/bin/conda run -n fusion_simulation \ $project_dir/simulate_fusion_trans_expr_vals.pl \ RSEM_outdir/RSEM.isoforms.results \ combined.transcripts.fasta \

target.forSimulation.RSEM.isoforms.results && \ echo done at date >> 04.simulate_fusion_trans_expr_vals.sh.sign

Step 5.

$ cat 05.rsem_simulate_read.sh time /data2/dev_projects/dujun/miniconda3/bin/conda run -n fusion_simulation \ rsem-simulate-reads combined.transcripts.fasta.RSEM \ RSEM_outdir/RSEM.stat/RSEM.model \ target.forSimulation.RSEM.isoforms.results \ 0.01 10000 sim_reads && \ echo done at date >> 05.rsem_simulate_read.sh.sign

results

[image: image] https://user-images.githubusercontent.com/44594049/259286461-04d62381-d2e9-4dc0-a597-2141d0e580ef.png

RSEM_outdir:

[image: image] https://user-images.githubusercontent.com/44594049/259286550-2280d32b-c668-4ee4-b383-185b43e23547.png BUG

According to the instructions in README.txt, my simulation results should yield the sim_reads_1.fq and sim_reads_2.fq files, not the sim_reads.fa file. Could you please advise me on where I need to make modifications in my script? Thank you very much.

If you need further assistance or explanations, please feel free to let me know anytime.

— Reply to this email directly, view it on GitHub https://github.com/FusionSimulatorToolkit/FusionSimulatorToolkit.github.io/issues/1#issuecomment-1670604384, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZRKX5Y7LDICASYUMBKM4TXUMA2ZANCNFSM6AAAAAA3IKY7CU . You are receiving this because you commented.Message ID: <FusionSimulatorToolkit/FusionSimulatorToolkit.github. @.***>

bioPG commented 1 year ago

I reran step 5, but still didn't obtain the correct FASTQ files. Below are the relevant screenshots.

image
brianjohnhaas commented 1 year ago

I'm not seeing anything obvious as to what's causing this to not behave properly. It worked fine for me when I ran it years ago.

If you can package the directory up and share it with me, I could take a look at the contents and see if there's anything peculiar there.

best,

~brian

On Wed, Aug 9, 2023 at 12:25 PM jundu @.***> wrote:

I reran step 5, but still didn't obtain the correct FASTQ files. Below are the relevant screenshots. [image: image] https://user-images.githubusercontent.com/44594049/259477654-f91d4196-f871-4bd6-a48b-18c9f8cd03bc.png

— Reply to this email directly, view it on GitHub https://github.com/FusionSimulatorToolkit/FusionSimulatorToolkit.github.io/issues/1#issuecomment-1671752778, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZRKXY3QTDL2VFZWGSKO6DXUO2ZBANCNFSM6AAAAAA3IKY7CU . You are receiving this because you commented.Message ID: <FusionSimulatorToolkit/FusionSimulatorToolkit.github. @.***>

--

Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas