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/ ___\_` __ \__ \ | | \/ __ | | \\_ __\
/ /_/ > | \// __ \| | / /_/ | | || |
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/_____/ \/ \/
grep rough audit - static analysis tool
v2.8 written by @Wireghoul
=================================[justanotherhacker.com]===
mecat2-0.0+git20200428.f54c542+ds/README.MD-77-```
mecat2-0.0+git20200428.f54c542+ds/README.MD:78:After installation, all the executables are found in `${MECAT_PATH}/MECAT/Linux-amd64/bin`. The folder name `Linux-amd64` will vary in operating systems.
mecat2-0.0+git20200428.f54c542+ds/README.MD-79-
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mecat2-0.0+git20200428.f54c542+ds/README.MD-93-* Step 1: Download dataset.
mecat2-0.0+git20200428.f54c542+ds/README.MD:94:We download the raw reads [ecoli_filtered.fastq.gz](http://gembox.cbcb.umd.edu/mhap/raw/ecoli_filtered.fastq.gz) into directory `${MECAT_PATH}/ecoli`
mecat2-0.0+git20200428.f54c542+ds/README.MD-95-``` shell
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mecat2-0.0+git20200428.f54c542+ds/README.MD-99-```
mecat2-0.0+git20200428.f54c542+ds/README.MD:100:After that, we get raw read file `${MECAT_PATH}/ecoli/ecoli_filtered.fastq.gz`:
mecat2-0.0+git20200428.f54c542+ds/README.MD-101-``` shell
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mecat2-0.0+git20200428.f54c542+ds/README.MD-169-
mecat2-0.0+git20200428.f54c542+ds/README.MD:170: * The file `${MECAT_PATH}/eocli/ecoli/1-consensus/cns_reads_list.txt` contains the full path of all corrected reads files.
mecat2-0.0+git20200428.f54c542+ds/README.MD-171- ``` shell
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mecat2-0.0+git20200428.f54c542+ds/README.MD-174- ```
mecat2-0.0+git20200428.f54c542+ds/README.MD:175: * The extracted longest 30x (The number 30 is indidated by the `CNS_OUTPUT_COVERAGE` option in the config file) corrected reads used for trimming is `${MECAT_PATH}/ecoli/ecoli/1-consensus/cns_final.fasta`.
mecat2-0.0+git20200428.f54c542+ds/README.MD:176: * The trimmed reads is `${MECAT_PATH}/ecoli/ecoli/2-trim_bases/trimReads.fasta`
mecat2-0.0+git20200428.f54c542+ds/README.MD:177: * The assembled contigs is `${MECAT_PATH}/ecoli/ecoli/4-fsa/contigs.fasta`
mecat2-0.0+git20200428.f54c542+ds/README.MD-178-
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mecat2-0.0+git20200428.f54c542+ds/README.MD-184-
mecat2-0.0+git20200428.f54c542+ds/README.MD:185:* `H5` format. `H5` file format must first be transfered to `FASTA` format with `${MECAT_PATH}/DEXTRACT/dextract`. For example:
mecat2-0.0+git20200428.f54c542+ds/README.MD-186-```shell
##############################################
mecat2-0.0+git20200428.f54c542+ds/src/pipeline/Plgd/GridLsf.pm-38- plgdInfo("Sumbit command: $cmd");
mecat2-0.0+git20200428.f54c542+ds/src/pipeline/Plgd/GridLsf.pm:39: my $result = `$cmd`;
mecat2-0.0+git20200428.f54c542+ds/src/pipeline/Plgd/GridLsf.pm-40-
##############################################
mecat2-0.0+git20200428.f54c542+ds/src/pipeline/Plgd/GridLsf.pm-55- plgdInfo("Stop script: $cmd");
mecat2-0.0+git20200428.f54c542+ds/src/pipeline/Plgd/GridLsf.pm:56: `$cmd`;
mecat2-0.0+git20200428.f54c542+ds/src/pipeline/Plgd/GridLsf.pm-57-}
##############################################
mecat2-0.0+git20200428.f54c542+ds/src/pipeline/Plgd/GridPbs.pm-63- plgdInfo("Sumbit command: $cmd");
mecat2-0.0+git20200428.f54c542+ds/src/pipeline/Plgd/GridPbs.pm:64: my $result = `$cmd`;
mecat2-0.0+git20200428.f54c542+ds/src/pipeline/Plgd/GridPbs.pm-65-
##############################################
mecat2-0.0+git20200428.f54c542+ds/src/pipeline/Plgd/GridPbs.pm-76- plgdInfo("Stop script: $cmd");
mecat2-0.0+git20200428.f54c542+ds/src/pipeline/Plgd/GridPbs.pm:77: `$cmd`;
mecat2-0.0+git20200428.f54c542+ds/src/pipeline/Plgd/GridPbs.pm-78-}
##############################################
mecat2-0.0+git20200428.f54c542+ds/src/pipeline/Plgd/GridSge.pm-37- plgdInfo("Sumbit command: $cmd");
mecat2-0.0+git20200428.f54c542+ds/src/pipeline/Plgd/GridSge.pm:38: my $result = `$cmd`;
mecat2-0.0+git20200428.f54c542+ds/src/pipeline/Plgd/GridSge.pm-39- my @items = split(" ", $result);
##############################################
mecat2-0.0+git20200428.f54c542+ds/src/pipeline/Plgd/GridSge.pm-51- plgdInfo("Stop script: $cmd");
mecat2-0.0+git20200428.f54c542+ds/src/pipeline/Plgd/GridSge.pm:52: `$cmd`;
mecat2-0.0+git20200428.f54c542+ds/src/pipeline/Plgd/GridSge.pm-53-}
##############################################
mecat2-0.0+git20200428.f54c542+ds/src/pipeline/Plgd/GridSlurm.pm-39- plgdInfo("Sumbit command: $cmd");
mecat2-0.0+git20200428.f54c542+ds/src/pipeline/Plgd/GridSlurm.pm:40: my $result = `$cmd`;
mecat2-0.0+git20200428.f54c542+ds/src/pipeline/Plgd/GridSlurm.pm-41-
##############################################
mecat2-0.0+git20200428.f54c542+ds/src/pipeline/Plgd/GridSlurm.pm-55- plgdInfo("Stop script: $cmd");
mecat2-0.0+git20200428.f54c542+ds/src/pipeline/Plgd/GridSlurm.pm:56: `$cmd`;
mecat2-0.0+git20200428.f54c542+ds/src/pipeline/Plgd/GridSlurm.pm-57-}
##############################################
mecat2-0.0+git20200428.f54c542+ds/src/pipeline/Plgd/Script.pm-146- plgdInfo("Run script: $script 2>&1 |tee $script.log");
mecat2-0.0+git20200428.f54c542+ds/src/pipeline/Plgd/Script.pm:147: my $r = system($script . " 2>&1 | tee $script.log");
mecat2-0.0+git20200428.f54c542+ds/src/pipeline/Plgd/Script.pm-148- if ($r != 0) {
mecat2-0.0+git20200428.f54c542+ds/src/pipeline/Plgd/Script.pm:149: `echo $r > $script.done`; #
mecat2-0.0+git20200428.f54c542+ds/src/pipeline/Plgd/Script.pm-150- }
##############################################
mecat2-0.0+git20200428.f54c542+ds/src/pipeline/mecat.pl-314- my $cmd = %$env{"BinPath"} . "/mecat2viewdb $prjDir/1-consensus/cns_final.fasta";
mecat2-0.0+git20200428.f54c542+ds/src/pipeline/mecat.pl:315: system($cmd);
mecat2-0.0+git20200428.f54c542+ds/src/pipeline/mecat.pl-316-}
##############################################
mecat2-0.0+git20200428.f54c542+ds/src/pipeline/mecat.pl-323- my $cmd = %$env{"BinPath"} . "/mecat2viewdb $prjDir/2-trim_bases/trimReads.fasta";
mecat2-0.0+git20200428.f54c542+ds/src/pipeline/mecat.pl:324: system($cmd);
mecat2-0.0+git20200428.f54c542+ds/src/pipeline/mecat.pl-325-}
##############################################
mecat2-0.0+git20200428.f54c542+ds/src/pipeline/mecat.pl-332- plgdInfo("N50 of contigs: $prjDir/4-fsa/contigs.fasta");
mecat2-0.0+git20200428.f54c542+ds/src/pipeline/mecat.pl:333: system($cmd);
mecat2-0.0+git20200428.f54c542+ds/src/pipeline/mecat.pl-334-}
##############################################
mecat2-0.0+git20200428.f54c542+ds/src/pipeline/mecat.sh-39-
mecat2-0.0+git20200428.f54c542+ds/src/pipeline/mecat.sh:40:basepath=$(cd `dirname $0`; pwd)
mecat2-0.0+git20200428.f54c542+ds/src/pipeline/mecat.sh-41-echo $basepath
##############################################
mecat2-0.0+git20200428.f54c542+ds/src/pipeline/mecat2fsa.sh-34-
mecat2-0.0+git20200428.f54c542+ds/src/pipeline/mecat2fsa.sh:35:basepath=$(cd `dirname $0`; pwd)
mecat2-0.0+git20200428.f54c542+ds/src/pipeline/mecat2fsa.sh-36-echo $basepath
##############################################
mecat2-0.0+git20200428.f54c542+ds/src/pipeline/mecat2fsa.sh-53- while read line ; do
mecat2-0.0+git20200428.f54c542+ds/src/pipeline/mecat2fsa.sh:54: #cat `echo ${line} | tr -d '\n'` >> $alignRRDir/rawreads.${line#*.}
mecat2-0.0+git20200428.f54c542+ds/src/pipeline/mecat2fsa.sh-55- #cat ${line} >> $alignRRDir/rawreads.${line#*.}
##############################################
mecat2-0.0+git20200428.f54c542+ds/src/pipeline/mecat2fsa.sh-91- while read line ; do
mecat2-0.0+git20200428.f54c542+ds/src/pipeline/mecat2fsa.sh:92: #cat `echo ${line} | tr -d '\n'` >> $alignRRDir/rawreads.${line#*.}
mecat2-0.0+git20200428.f54c542+ds/src/pipeline/mecat2fsa.sh-93- cat ${line} >> $rawreads
##############################################
mecat2-0.0+git20200428.f54c542+ds/src/pipeline/org_mecat.pl-368- my $cmd = %$env{"BinPath"} . "/fsa_rd_stat $prjDir/1-consensus/cns_final.fasta";
mecat2-0.0+git20200428.f54c542+ds/src/pipeline/org_mecat.pl:369: system($cmd);
mecat2-0.0+git20200428.f54c542+ds/src/pipeline/org_mecat.pl-370-
##############################################
mecat2-0.0+git20200428.f54c542+ds/src/pipeline/org_mecat.pl-378- plgdInfo("N50 of contigs: $prjDir/4-fsa/contigs.fasta");
mecat2-0.0+git20200428.f54c542+ds/src/pipeline/org_mecat.pl:379: system($cmd);
mecat2-0.0+git20200428.f54c542+ds/src/pipeline/org_mecat.pl-380-}
##############################################
mecat2-0.0+git20200428.f54c542+ds/debian/patches/modify_makefiles.patch-54-- mkdir -p ${BUILD_DIR}
mecat2-0.0+git20200428.f54c542+ds/debian/patches/modify_makefiles.patch:55:- version_major_minor=`echo "$(HDF5_VERSION)" | sed -E 's/\.[0-9]+$$//'`; \
mecat2-0.0+git20200428.f54c542+ds/debian/patches/modify_makefiles.patch-56-- cp third_party/hdf5-1.10.4.tar.gz ${BUILD_TOP_DIR}/
##############################################
mecat2-0.0+git20200428.f54c542+ds/.pc/modify_makefiles.patch/Makefile-50- mkdir -p ${BUILD_DIR}
mecat2-0.0+git20200428.f54c542+ds/.pc/modify_makefiles.patch/Makefile:51: version_major_minor=`echo "$(HDF5_VERSION)" | sed -E 's/\.[0-9]+$$//'`; \
mecat2-0.0+git20200428.f54c542+ds/.pc/modify_makefiles.patch/Makefile-52- cp third_party/hdf5-1.10.4.tar.gz ${BUILD_TOP_DIR}/