Could Not Open 1 file "hg38.d14.cdx"

[yubau1112]

git clone https://bitbucket.org/wingolab/mpd-dat.git

and

my config.yaml is:

---

BedFile: markers.txt.bed isPcrBinary: /home/yubau/bin/x86_64/isPcr TwoBitFile: hg38.2bit MpdBinary: mpd-c/bin/mpd MpdIdx: mpd-dat/hg38/hg38.d14.sdx dbSnpIdx: mpd-dat/ds_flat/ds_flat.sdx

CoverageThreshold: 0.8 PrimerSizeMin: 17 PrimerSizeMax: 27 PadSize: 60 PoolMax: 10 PoolMin: 5

AmpSizeMax: 260 AmpSizeMin: 230 TmMax: 62 TmMin: 57 GcMax: 0.7 GcMin: 0.3

Iter: 2 IncrTm: 1 IncrTmStep: 1 IncrAmpSize: 10

my command is : perl design.pl -a -b markers.txt.bed -c config.yaml -d test -o test.txt

than I got: Could Not Open 1 file "hg38.d14.cdx"

What can I do?

thanks

[wingolab]

Can you verify that mpd-dat/hg38 contains a genomic index? For instance, I'd expect it might contain the content from: https://bitbucket.org/wingolab/mpd-dat/

[yubau1112]

I git clone https://bitbucket.org/wingolab/mpd-dat.git so mpd-dat dir file have same with https://bitbucket.org/wingolab/mpd-dat/

-rw-rw-r-- 1 yubau yubau 128M Mar 17 17:11 hg38.d14.15x -rw-rw-r-- 1 yubau yubau 740M Mar 17 17:11 hg38.d14.cdx -rw-rw-r-- 1 yubau yubau 1.4G Mar 17 17:11 hg38.d14.idx -rw-rw-r-- 1 yubau yubau 13K Mar 17 17:11 hg38.d14.in -rw-rw-r-- 1 yubau yubau 31M Mar 17 17:11 hg38.d14.rdx -rw-rw-r-- 1 yubau yubau 5.5K Mar 17 17:11 hg38.d14.sdx

Can you re index genome and used mpd to check hg38.d14 can work than reupload to https://bitbucket.org/wingolab/mpd-dat/?

or

Can you tell me what is you used parameter for index_genome?

I download a new hg38.fa file from UCSC and run index_genome

Send Output to Screen or Disk? [S,D] S Number of Contig Fasta Files to Process 1 Please Enter Name For Contig Fasta File 1 hg38.fa Basename to save compressed Genome and Indexes hg38 Maximum Number Of Sites in a contig 100000 Index Depth 100000

but I want to use your parameter for index_genome

thanks!

oh I change path now!

BedFile: markers.txt.bed isPcrBinary: /home/yubau/bin/x86_64/isPcr TwoBitFile: hg38.2bit MpdBinary: mpd-c/bin/mpd MpdIdx: mpd-dat/hg38.d14.sdx dbSnpIdx: mpd-dat/ds_flat.sdx

but still get "Could Not Open 1 file "hg38.d14.cdx""

[yubau1112]

I move all "git clone https://bitbucket.org/wingolab/mpd-dat.git" file to same with "design.pl" file directory

AND it's can work!

ask a question

my $m = MPD->new_with_config( { configfile => $config_file, BedFile => 'target_regions.bed', OutExt => 'myGreatPrimerPools', OutDir => '/temp/', InitTmMin => 58, InitTmMax => 61, PoolMin => 5, Debug => 0, IterMax => 2, RunIsPcr => undef, # set to something perl evaluates to true if you want isPcr to check the in-silico PCR Act => 1, # set to something perl evaluates to true if you want the program to execute the mpd-c binary ProjectName => $out_ext, FwdAdapter => '', # your fwd adapter RevAdapter => '', # your rev adapter Offset => 0, # when printing pools where do we start? Randomize => 1, # should we shuffle the pools so they are in random order? } );

if I want to RunIsPcr, I just need to change "RunIsPcr => undef" to "RunIsPcr => 1"?

thank you so much!

[zyh2016]

I have the same question...