Open bioPG opened 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
Sorry, I was too hasty earlier and failed to provide enough information. Here is all of my scripts and related supporting files information.
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 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
$ 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
$ 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
$ 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
$ 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
$ 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
RSEM_outdir:
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.
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 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 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forgelibgcc-devel_linux-64 13.1.0 he3cc6c4_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge libgcc-ng https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forgelibgcc-ng 13.1.0 he5830b7_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge libgfortran-ng https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forgelibgfortran-ng 13.1.0 h69a702a_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge libgfortran5 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forgelibgfortran5 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 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forgelibjpeg-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 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forgelibnghttp2 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 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forgelibssh2 1.11.0 h0841786_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge libstdcxx-devel_linux-64 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forgelibstdcxx-devel_linux-64 13.1.0 he3cc6c4_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge libstdcxx-ng https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forgelibstdcxx-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 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forgelibwebp-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 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forgelibxml2 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 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forgemysql-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 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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.signStep 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.signStep 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.signStep 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.signStep 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
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>> 05.rsem_simulate_read.sh.signresults
[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.
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I reran step 5, but still didn't obtain the correct FASTQ files. Below are the relevant screenshots.
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
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Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas
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.signoutput: sim_reads.fa