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ndierckx / Sim-it

Versatile simulator for structural variance and Nanopore/PacBio sequencing reads
Apache License 2.0
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Errorr on sequencing depth #14

Open 11malong opened 1 year ago

11malong commented 1 year ago

Hi, I have a question: my config.txt is like:

Project:

Project name = Test Reference sequence = /mnt/f/mshunter/chm13_1000000/chm13_after.5.fa Replace ambiguous nts(N) = Max threads = 8

Structural variation:

VCF input = Foreign sequences =

Deletions = 0 Length (bp) = 30-150000

Insertions = 0 Length (bp) = 30-100000

Tandem duplications = 0 Length (bp) = 50-10000 Copies = 1-20

Inversions = 0 Length (bp) = 150-1300000

Complex substitutions = 0 Length (bp) = 30-100000

Inverted duplications = 0 Length (bp) = 150-350000

Heterozygosity = 60%

Long Read simulation:

Sequencing depth = 30 Median length = 15000 Length range = 10000-20000 Accuracy = 95% Error profile = error_profile_PB_Sequel_CCS_hifi.txt

and my command is like: perl ./Sim-it1.3.4.pl -c ./config_Sim-it_my.txt -o ./output

but I got error like: --------------------------READ SEQUENCING DEPTH FILE---------------------------- , No such file or directoryr can't open sequencing depth file 30

How can I solve this? Thank you so much.

Oieswarya commented 1 year ago

I am having the same issue. Is there any fix for this?

ndierckx commented 1 year ago

Hi, Sorry I recently moved to Japan and lost track of this issue.

This should be easy to fix, seems like the config file got corrupted and it doesn't recognize the numeric value 30 anymore.

Did you run it on Windows, Linux or Mac

And can you redownload the Sim-it perl file and try again?

ndierckx commented 1 year ago

I found the issue, by altering the config file in certain windows software, windows carriage return are added to the file, which is not recognized by my script.

But I added some lines to remove them, so they should not be an issue anymore, you can try again by redownloading the script