pinellolab / primedesign Goto Github PK

Software tool for the flexible design of pegRNAs and ngRNAs for prime editing!

License: Other

Dockerfile 0.39% Shell 0.04% Python 95.90% CSS 3.67%

primedesign's Introduction

PrimeDesign

PrimeDesign is a software tool for the flexible and comprehensive design of prime editing. PrimeDesign is an edit-centric design tool for the installation of substitution, insertion, and deletion edits, and is generalizable for both single and combinatorial edits. Taking a single input that encodes both the reference and edit sequence, PrimeDesign enumerates all possible pegRNA protospacers, pegRNA extensions, and ngRNAs within set parameter ranges to install the desired edit(s).

Installation with Docker

With Docker, no installation is required - the only dependence is Docker itself. Users will not need to deal with installation and configuration issues.

Docker can be downloaded freely here: https://store.docker.com/search?offering=community&type=edition

Following the installation of Docker, simply execute the following command in the terminal for a local version of PrimeDesign:

docker pull pinellolab/primedesign

PrimeDesign web application

Run the PrimeDesign web application locally with the command:

docker run -p 9994:9994 pinellolab/primedesign:latest primedesign_webapp

After execution of the command, the user will have a local instance of the website accessible at the URL: http://localhost:9994

PrimeDesign command line tool

Run the PrimeDesign command line interface (CLI) with the command in the terminal:

docker run -v ${PWD}/:/DATA -w /DATA pinellolab/primedesign primedesign_cli [options]

Users can specify the following options:

-f, --file
      Input file (.txt or .csv) with sequences for PrimeDesign. Format: target_name,target_sequence (column names required)

-pbs, --pbs_length_list
      List of primer binding site (PBS) lengths for the pegRNA extension (Default: 10 to 15 nt). Example: 12 13 14 15
-rtt, --rtt_length_list
      List of reverse transcription (RT) template lengths for the pegRNA extension (Default: 10 to 30 nt). Example: 10 15 20
-nick_dist_min, --nicking_distance_minimum
      Minimum nicking distance for designing ngRNAs upstream and downstream of a pegRNA (Default: 0 bp).
-nick_dist_max, --nicking_distance_maximum
      Maximum nicking distance for designing ngRNAs upstream and downstream of a pegRNA (Default: 100 bp).
-filter_c1, --filter_c1_extension
      Option to filter against pegRNA extensions that start with a C base.
-silent_mut, --silent_mutation
      Introduce silent mutation into PAM assuming sequence is in-frame. Currently only available with SpCas9.
-genome_wide, --genome_wide_design
      Whether or not this is a genome-wide pooled design. This option designs a set of pegRNAs per input without ranging PBS and RTT parameters.
-sat_mut, --saturation_mutagenesis
      Saturation mutagenesis design with prime editing. The 'aa' option makes amino acid changes and the 'base' option makes DNA base changes. (Options: aa, base)
-n_pegrnas, --number_of_pegrnas
      The maximum number of pegRNAs to design for each input sequence. The pegRNAs are ranked by 1) PAM disrupted > PAM intact then 2) distance to edit. (Default: 3)
n_ngrnas, --number_of_ngrnas
      The maximum number of ngRNAs to design for each input sequence. The ngRNAs are ranked by 1) PE3b-seed > PE3b-nonseed > PE3 then 2) deviation from nicking_distance_pooled. (Default: 3)
-nick_dist_pooled, --nicking_distance_pooled
      The nicking distance between pegRNAs and ngRNAs for pooled designs. PE3b annotation is priority (PE3b seed -> PE3b non-seed), followed by nicking distance closest to this parameter. (Default: 75 bp)
-homology_downstream, --homology_downstream
      For pooled designs (genome_wide or saturation_mutagenesis needs to be indicated), this parameter determines the RT extension length downstream of an edit for pegRNA designs. (Default: 10)
-pbs_pooled, --pbs_length_pooled
      The PBS length to design pegRNAs for pooled design applications. (Default: 14 nt)
rtt_pooled, --rtt_max_length_pooled
      The maximum RTT length to design pegRNAs for pooled design applications. (Default: 50 nt)
-out, --out_dir
      Name of output directory. (Default: ./DATETIMESTAMP_PrimeDesign)

PrimeDesign input sequence format

PrimeDesign takes in a single input sequence to design pegRNAs and ngRNAs for prime editing. The input sequence encodes both the reference and edited sequence with the following formatting:

Substitution: (reference/edit)
Insertion: (+insertion) or (/insertion)
Deletion: (-deletion) or (deletion/)

Examples

Reference sequence: GCCTGTGACTAACTGCGCCAAAACGTCTTCCAATCCCCTTATCCAATTTA

Substitution edit sequence: GCCTGTGACTAACTGCGCCAAAACGACTTCCAATCCCCTTATCCAATTTA
PrimeDesign input sequence: GCCTGTGACTAACTGCGCCAAAACG(T/A)CTTCCAATCCCCTTATCCAATTTA

Insertion edit sequence: GCCTGTGACTAACTGCGCCAAAACGTCTTCTTCCAATCCCCTTATCCAATTTA
PrimeDesign input sequence: GCCTGTGACTAACTGCGCCAAAACGT(+CTT)CTTCCAATCCCCTTATCCAATTTA

Deletion edit sequence: GCCTGTGACTAACTGCGCCAAAAC----TCCAATCCCCTTATCCAATTTA
PrimeDesign input sequence: GCCTGTGACTAACTGCGCCAAAAC(-GTCT)TCCAATCCCCTTATCCAATTTA

Combinatorial edit sequence: GCCTGTGACTAACTGCTCCAATCGAAACGTC----AATCCCCTTATCCAATTTA
PrimeDesign input sequence: GCCTGTGACTAACTGC(G/T)CCA(+ATCG)AAACGTC(-TTCC)AATCCCCTTATCCAATTTA

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primedesign's Issues

CFD Scores aren't in "Download Designs" spreadsheet

I have been using the hosted PrimeDesign at https://drugthatgene.pinellolab.partners.org/. I have checked the option to calcuate CFD score, and these scores do display correctly in my browser for the sgRNAs. However, when I download designs using the "Download Designs" button, there is a column for CFD score in the spreadsheet for which no values are given. I suspect this is a bug.

Flag duplicate ngRNA oligos when designing multiple guides

When designing multiple pegRNAs + ngRNAs for a given gene using the PE3 or PE3b strategy , the set of ngRNAs identified for each pegRNA may end up being the same sequence. To avoid manual quality control of sequences, duplication of purchases of oligos, and duplication of cloning, it would be useful to flag the ngRNA sequences output as duplicates or identical sequences at alert the user. Either adding another column to the output csv or a warning on the web tool / Docker output.

Nicking Dist Min and max no longer function

python /seqprg/scripts/gene_editing/primedesign.py -f design.txt -pbs 10 11 12 13 14 15 -rtt 10 11 12 -nick_dist_max 10

2022-07-28 21:00:47,188 - INFO - Searching for pegRNAs and nicking gRNAs for target sequences ...
Traceback (most recent call last):
File "/seqprg/scripts/gene_editing/primedesign.py", line 1359, in
if (abs(nick_distance) >= nicking_distance_minimum) and (abs(nick_distance) <= nicking_distance_maximum):
TypeError: '<=' not supported between instances of 'int' and 'list'

If I do not use the nicking distance min and max, then the tools functions fine. But when I go to pass in a number, I keep getting this error. This just started recently

Inserts longer than 33 bp are not supported?

Hi! I am trying to generate a pegRNA to use for twin prime editing, i.e. inserting the full AttB site at a genomic site of interest, as discussed in this paper. Yet, AttB site is at least 38 bp long, while any insertion longer than 33 bp yields N/A as a suggested pegRNA. Is there an easy fix that doesn't involve re-training the model with longer inserts?

Web interface returning '502 Bad Gateway'

Hi,

I have noticed the web interface @ https://primedesign.pinellolab.partners.org/ is directing to a '502 Bad Gateway' page.

Thanks,
Dan

SCN5A site in Supplementary Data 2 not correct?

Hello,

Please see the illustration. The expected mutation from PrimeDesign Input is G4CTTCT. When mapping the PBS and RTT sequences, the mutation I got is actually the deletion of CTGGGGCTT.

Thanks,
Yichao

Failure to generate guides when CFD scores are to be calculated on locally (and publicly?) hosted client.

Hello,

I am once again trying to calculate CFD scores for a set of guides, but if I have "Calculate CFD score" switched to "Yes", then there is no output. This seems to be true for the publicly hosted client, and it is certainly true for the locally hosted client. Here is my terminal output as I first change my desired settings in "Prime editing parameters" and then paste in the correctly formated sequence and edit:

[2021-02-27 00:39:27 +0000] [8] [INFO] Starting gunicorn 20.0.4
[2021-02-27 00:39:27 +0000] [8] [INFO] Listening at: http://0.0.0.0:9994 (8)
[2021-02-27 00:39:27 +0000] [8] [INFO] Using worker: sync
[2021-02-27 00:39:27 +0000] [10] [INFO] Booting worker with pid: 10
[2021-02-27 00:39:27 +0000] [11] [INFO] Booting worker with pid: 11
[2021-02-27 00:39:27 +0000] [12] [INFO] Booting worker with pid: 12
[2021-02-27 00:39:27 +0000] [13] [INFO] Booting worker with pid: 13
172.17.0.1 - - [27/Feb/2021:00:39:32 +0000] "GET / HTTP/1.1" 200 618 "-" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:33 +0000] "GET /_dash-dependencies HTTP/1.1" 200 1205 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:33 +0000] "GET /_dash-layout HTTP/1.1" 200 568 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:33 +0000] "POST /_dash-update-component HTTP/1.1" 200 3528 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:33 +0000] "POST /_dash-update-component HTTP/1.1" 200 42 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:33 +0000] "POST /_dash-update-component HTTP/1.1" 200 3528 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:33 +0000] "POST /_dash-update-component HTTP/1.1" 200 40 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:34 +0000] "POST /_dash-update-component HTTP/1.1" 200 146 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:34 +0000] "POST /_dash-update-component HTTP/1.1" 200 63 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:34 +0000] "POST /_dash-update-component HTTP/1.1" 200 147 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:34 +0000] "POST /_dash-update-component HTTP/1.1" 200 83 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:34 +0000] "POST /_dash-update-component HTTP/1.1" 200 263 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:34 +0000] "POST /_dash-update-component HTTP/1.1" 200 349 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:34 +0000] "POST /_dash-update-component HTTP/1.1" 200 63 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:34 +0000] "POST /_dash-update-component HTTP/1.1" 200 37 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:34 +0000] "POST /_dash-update-component HTTP/1.1" 200 69 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:34 +0000] "POST /_dash-update-component HTTP/1.1" 200 75 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:34 +0000] "POST /_dash-update-component HTTP/1.1" 200 37 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:34 +0000] "POST /_dash-update-component HTTP/1.1" 200 83 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:34 +0000] "POST /_dash-update-component HTTP/1.1" 200 349 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:34 +0000] "POST /_dash-update-component HTTP/1.1" 200 263 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:34 +0000] "POST /_dash-update-component HTTP/1.1" 200 37 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:35 +0000] "POST /_dash-update-component HTTP/1.1" 200 37 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:35 +0000] "POST /_dash-update-component HTTP/1.1" 200 37 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:35 +0000] "POST /_dash-update-component HTTP/1.1" 200 37 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:42 +0000] "POST /_dash-update-component HTTP/1.1" 200 63 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:42 +0000] "POST /_dash-update-component HTTP/1.1" 200 37 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:42 +0000] "POST /_dash-update-component HTTP/1.1" 200 349 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:42 +0000] "POST /_dash-update-component HTTP/1.1" 200 37 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:42 +0000] "POST /_dash-update-component HTTP/1.1" 200 37 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:42 +0000] "POST /_dash-update-component HTTP/1.1" 200 37 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:42 +0000] "POST /_dash-update-component HTTP/1.1" 200 37 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:45 +0000] "POST /_dash-update-component HTTP/1.1" 200 63 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:45 +0000] "POST /_dash-update-component HTTP/1.1" 200 37 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:45 +0000] "POST /_dash-update-component HTTP/1.1" 200 349 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:46 +0000] "POST /_dash-update-component HTTP/1.1" 200 37 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:46 +0000] "POST /_dash-update-component HTTP/1.1" 200 37 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:46 +0000] "POST /_dash-update-component HTTP/1.1" 200 37 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:46 +0000] "POST /_dash-update-component HTTP/1.1" 200 37 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:46 +0000] "POST /_dash-update-component HTTP/1.1" 200 63 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:47 +0000] "POST /_dash-update-component HTTP/1.1" 200 37 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:47 +0000] "POST /_dash-update-component HTTP/1.1" 200 349 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:47 +0000] "POST /_dash-update-component HTTP/1.1" 200 37 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:47 +0000] "POST /_dash-update-component HTTP/1.1" 200 37 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:47 +0000] "POST /_dash-update-component HTTP/1.1" 200 37 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:47 +0000] "POST /_dash-update-component HTTP/1.1" 200 37 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:49 +0000] "POST /_dash-update-component HTTP/1.1" 200 37 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:49 +0000] "POST /_dash-update-component HTTP/1.1" 200 349 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:50 +0000] "POST /_dash-update-component HTTP/1.1" 200 37 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:50 +0000] "POST /_dash-update-component HTTP/1.1" 200 37 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:50 +0000] "POST /_dash-update-component HTTP/1.1" 200 37 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:50 +0000] "POST /_dash-update-component HTTP/1.1" 200 37 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
ERROR! /PrimeDesign/hg38_chromosomes is not a directory.
Exception on /_dash-update-component [POST]
Traceback (most recent call last):
  File "/opt/conda/lib/python3.8/site-packages/flask/app.py", line 2447, in wsgi_app
    response = self.full_dispatch_request()
  File "/opt/conda/lib/python3.8/site-packages/flask/app.py", line 1952, in full_dispatch_request
    rv = self.handle_user_exception(e)
  File "/opt/conda/lib/python3.8/site-packages/flask/app.py", line 1821, in handle_user_exception
    reraise(exc_type, exc_value, tb)
  File "/opt/conda/lib/python3.8/site-packages/flask/_compat.py", line 39, in reraise
    raise value
  File "/opt/conda/lib/python3.8/site-packages/flask/app.py", line 1950, in full_dispatch_request
    rv = self.dispatch_request()
  File "/opt/conda/lib/python3.8/site-packages/flask/app.py", line 1936, in dispatch_request
    return self.view_functions[rule.endpoint](**req.view_args)
  File "/opt/conda/lib/python3.8/site-packages/dash/dash.py", line 1461, in dispatch
    response.set_data(self.callback_map[output]["callback"](*args))
  File "/opt/conda/lib/python3.8/site-packages/dash/dash.py", line 1341, in add_context
    output_value = func(*args, **kwargs)  # %% callback invoked %%
  File "/PrimeDesign/web_app/app.py", line 3607, in run_primedesign
    with open('/PrimeDesign/web_app/crispritz_output_%s.scores.txt' % session_id, 'r') as f:
FileNotFoundError: [Errno 2] No such file or directory: '/PrimeDesign/web_app/crispritz_output_20210227_12.39.33.61.scores.txt'
172.17.0.1 - - [27/Feb/2021:00:39:52 +0000] "POST /_dash-update-component HTTP/1.1" 500 290 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:58 +0000] "POST /_dash-update-component HTTP/1.1" 200 139 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:59 +0000] "POST /_dash-update-component HTTP/1.1" 200 83 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:59 +0000] "POST /_dash-update-component HTTP/1.1" 200 359 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
ERROR! /PrimeDesign/hg38_chromosomes is not a directory.
Exception on /_dash-update-component [POST]
Traceback (most recent call last):
  File "/opt/conda/lib/python3.8/site-packages/flask/app.py", line 2447, in wsgi_app
    response = self.full_dispatch_request()
  File "/opt/conda/lib/python3.8/site-packages/flask/app.py", line 1952, in full_dispatch_request
    rv = self.handle_user_exception(e)
  File "/opt/conda/lib/python3.8/site-packages/flask/app.py", line 1821, in handle_user_exception
    reraise(exc_type, exc_value, tb)
  File "/opt/conda/lib/python3.8/site-packages/flask/_compat.py", line 39, in reraise
    raise value
  File "/opt/conda/lib/python3.8/site-packages/flask/app.py", line 1950, in full_dispatch_request
    rv = self.dispatch_request()
  File "/opt/conda/lib/python3.8/site-packages/flask/app.py", line 1936, in dispatch_request
    return self.view_functions[rule.endpoint](**req.view_args)
  File "/opt/conda/lib/python3.8/site-packages/dash/dash.py", line 1461, in dispatch
    response.set_data(self.callback_map[output]["callback"](*args))
  File "/opt/conda/lib/python3.8/site-packages/dash/dash.py", line 1341, in add_context
    output_value = func(*args, **kwargs)  # %% callback invoked %%
  File "/PrimeDesign/web_app/app.py", line 3607, in run_primedesign
    with open('/PrimeDesign/web_app/crispritz_output_%s.scores.txt' % session_id, 'r') as f:
FileNotFoundError: [Errno 2] No such file or directory: '/PrimeDesign/web_app/crispritz_output_20210227_12.39.33.61.scores.txt'
172.17.0.1 - - [27/Feb/2021:00:39:59 +0000] "POST /_dash-update-component HTTP/1.1" 500 290 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"

Thank you!

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