pasapipeline-users

Contact owners and managers

1–30 of 161

0 selected

Apr 16

PASA is no longer being maintained or supported

Please note that, after over 20 years since its initial development and release, PASA is no longer

unread,

PASA is no longer being maintained or supported

Please note that, after over 20 years since its initial development and release, PASA is no longer

Apr 16

Mar 5

Error, need all method parameters

Hi, ı have two problems about both need all method parametersand No such file or directory. Can you

unread,

Error, need all method parameters

Hi, ı have two problems about both need all method parametersand No such file or directory. Can you

Mar 5

12/16/23

Thread 8 terminated abnormally: Error, spliced orient in db (-) differs from calculated spliced orient (+)

Hello, everyone I used the PASA (v2.5.3) pipeline to update the annotations from EVM with the

unread,

Thread 8 terminated abnormally: Error, spliced orient in db (-) differs from calculated spliced orient (+)

Hello, everyone I used the PASA (v2.5.3) pipeline to update the annotations from EVM with the

12/16/23

Juan Cerda-Herrera, Brian Haas4

9/25/23

DBD::SQLite::db do failed: UNIQUE constraint failed:

Hi Juan, The name it's complaining about 'TRINITY_DN21455_c0_g1_i1' should probably not

unread,

DBD::SQLite::db do failed: UNIQUE constraint failed:

Hi Juan, The name it's complaining about 'TRINITY_DN21455_c0_g1_i1' should probably not

9/25/23

Juan Cerda-Herrera, Brian Haas4

9/20/23

Error on sample data

Hi Juan, It sounds like maybe the identifiers in the annotated gff3 file and those in the genome

unread,

Error on sample data

Hi Juan, It sounds like maybe the identifiers in the annotated gff3 file and those in the genome

9/20/23

6/1/23

Announcement: PASA release v2.5.3

https://github.com/PASApipeline/PASApipeline/releases/tag/pasa-v2.5.3 PASA release v2.5.3 June 1,

unread,

Announcement: PASA release v2.5.3

https://github.com/PASApipeline/PASApipeline/releases/tag/pasa-v2.5.3 PASA release v2.5.3 June 1,

6/1/23

Maria Stager, Brian Haas4

5/30/23

GFF3 compatibility error

Great to hear! :-) On Tue, May 30, 2023 at 1:11 PM Maria Stager <mst...@umass.edu> wrote: Ah,

unread,

GFF3 compatibility error

Great to hear! :-) On Tue, May 30, 2023 at 1:11 PM Maria Stager <mst...@umass.edu> wrote: Ah,

5/30/23

Krešimir Križanović, Brian Haas8

2/13/23

Some basic statistics about transcriptome

Yes, that looks *very* promising! On Mon, Feb 13, 2023 at 7:08 AM Krešimir Križanović <kkrizanovic

unread,

Some basic statistics about transcriptome

Yes, that looks *very* promising! On Mon, Feb 13, 2023 at 7:08 AM Krešimir Križanović <kkrizanovic

2/13/23

Kris Alavattam, Brian Haas2

1/6/23

Questions: Running Launch_PASA_pipeline.pl in "gene_overlap mode" with a gff3 that contains whole-chromosome annotations: Effect on how --gene_overlap operates?

Hi Kris, I'm pretty sure PASA will parse and use only the features that are annotated as genes.

unread,

Questions: Running Launch_PASA_pipeline.pl in "gene_overlap mode" with a gff3 that contains whole-chromosome annotations: Effect on how --gene_overlap operates?

Hi Kris, I'm pretty sure PASA will parse and use only the features that are annotated as genes.

1/6/23

Kris Alavattam, Brian Haas2

12/27/22

Error in which PASA scripts/assembly_db_loader.dbi can't connect to SQLite database

Hi Kris, so if you run: ls /home/kalavatt/tsukiyamalab/kalavatt/2022_transcriptome-construction/

unread,

Error in which PASA scripts/assembly_db_loader.dbi can't connect to SQLite database

Hi Kris, so if you run: ls /home/kalavatt/tsukiyamalab/kalavatt/2022_transcriptome-construction/

12/27/22

Kris Alavattam, Brian Haas2

12/24/22

Question: What's reasonable to delete following a successful PASA run?

Hi Kris, You might want to hold onto the pasa.sqlite.pasa_assemblies.*, pasa.sqlite.assemblies.fasta,

unread,

Question: What's reasonable to delete following a successful PASA run?

Hi Kris, You might want to hold onto the pasa.sqlite.pasa_assemblies.*, pasa.sqlite.assemblies.fasta,

12/24/22

Kris Alavattam, Brian Haas2

12/20/22

Question: Launch_PASA_pipeline.pl options --stringent_alignment_overlap and --gene_overlap

Hi Kris, Yes, these options are mutually exclusive, and the stringent alignment overlap takes

unread,

Question: Launch_PASA_pipeline.pl options --stringent_alignment_overlap and --gene_overlap

Hi Kris, Yes, these options are mutually exclusive, and the stringent alignment overlap takes

12/20/22

Kris Alavattam, Brian Haas4

12/11/22

Question about small and/or microbial genomes and --trans_gtf (in Launch_PASA_pipeline.pl)

Hi Kris, Responses below: On Sun, Dec 11, 2022 at 3:40 PM Kris Alavattam <kalav...@gmail.com>

unread,

Question about small and/or microbial genomes and --trans_gtf (in Launch_PASA_pipeline.pl)

Hi Kris, Responses below: On Sun, Dec 11, 2022 at 3:40 PM Kris Alavattam <kalav...@gmail.com>

12/11/22

Krešimir Križanović, Brian Haas4

11/30/22

Help for a beginner

Usually this happens for a few reasons. 1. Only the subset of transcripts that meet rigorous

unread,

Help for a beginner

Usually this happens for a few reasons. 1. Only the subset of transcripts that meet rigorous

11/30/22

Tiago Hori, Brian Haas2

9/8/22

Alternative Splicing

Probably. ;-). I'm considering looking into future funding for PASA so we can have sustained

unread,

Alternative Splicing

Probably. ;-). I'm considering looking into future funding for PASA so we can have sustained

9/8/22

5/18/22

PASA align and assembly stopped prematurely

Dear Brian, I was running alignment assembly pipeline using sqlite with the following command

unread,

PASA align and assembly stopped prematurely

Dear Brian, I was running alignment assembly pipeline using sqlite with the following command

5/18/22

4/15/22

which de novo software tool should i choose?

Hi everyone, So my question is a little bit silly, In the first step of a Complete Eukaryotic

unread,

which de novo software tool should i choose?

Hi everyone, So my question is a little bit silly, In the first step of a Complete Eukaryotic

4/15/22

on the road, Brian Haas3

3/11/22

cDNA_annotation_comparer

Hi, With mysql, it's supposed to allow for multithreading. The way the multithreading is

unread,

cDNA_annotation_comparer

Hi, With mysql, it's supposed to allow for multithreading. The way the multithreading is

3/11/22

2/11/22

PASA Release v2.5.2

Greetings all, We have a patch release: https://github.com/PASApipeline/PASApipeline/releases/tag/

unread,

PASA Release v2.5.2

Greetings all, We have a patch release: https://github.com/PASApipeline/PASApipeline/releases/tag/

2/11/22

11/10/21

no modifications after running annotCompare.config

$PASAHOME/scripts/create_sqlite_cdnaassembly_db.dbi -c alignAssembly.config -S /home/data/pasa/opt/

unread,

no modifications after running annotCompare.config

$PASAHOME/scripts/create_sqlite_cdnaassembly_db.dbi -c alignAssembly.config -S /home/data/pasa/opt/

11/10/21

brianjohnhaas, Brian Haas2

9/3/21

Announcement: PASA Release v2.5.0

Please note - I just release v2.5.1 which includes a bugfix to allow for pblat to actually use the

unread,

Announcement: PASA Release v2.5.0

Please note - I just release v2.5.1 which includes a bugfix to allow for pblat to actually use the

9/3/21

Zin Win Latt, Brian Haas3

8/6/21

Resume PASA alignment Assembly

hi - it looks like it's not finding the database that should be listed in the config file. For

unread,

Resume PASA alignment Assembly

hi - it looks like it's not finding the database that should be listed in the config file. For

8/6/21

8/5/21

working on new pasa release

Greetings all, It's been a while.... I'm back to working on updating pasa for an upcoming

unread,

working on new pasa release

Greetings all, It's been a while.... I'm back to working on updating pasa for an upcoming

8/5/21

Tiago Hori, Brian Haas6

7/26/21

Gotcha. Yes, that's all for generating EVM predictions that eventually get fed back into PASA for

unread,

Gotcha. Yes, that's all for generating EVM predictions that eventually get fed back into PASA for

7/26/21

Nadal Tegstrom, Brian Haas6

1/30/21

ERROR, Specified key was too long; max key length is 767 bytes

Great news!! Thx -via googleFi On Sat, Jan 30, 2021, 2:25 PM Nadal Tegstrom <nadaltegstrom@gmail.

unread,

ERROR, Specified key was too long; max key length is 767 bytes

Great news!! Thx -via googleFi On Sat, Jan 30, 2021, 2:25 PM Nadal Tegstrom <nadaltegstrom@gmail.

1/30/21

Zin Win Latt, Brian Haas2

11/10/20

PASA installation error

hi, it looks like you're missing a zlib library installation. Google the error and you'll

unread,

PASA installation error

hi, it looks like you're missing a zlib library installation. Google the error and you'll

11/10/20

Andor Kiss, Brian Haas2

8/7/20

TWO Installation Questions | MySQL & "missing" dependencies on 18.02

Hi Andor, I'm not sure how this is integrated with Augustus, but I can comment on the pasa-

unread,

TWO Installation Questions | MySQL & "missing" dependencies on 18.02

Hi Andor, I'm not sure how this is integrated with Augustus, but I can comment on the pasa-

8/7/20

3/24/20

Adding UTR on existing annotation file.

Dear Brian, I am using PASA for adding UTR locus to the existing genome annotation file by using this

unread,

Adding UTR on existing annotation file.

Dear Brian, I am using PASA for adding UTR locus to the existing genome annotation file by using this

3/24/20

Carol Buitrago, Brian Haas5

3/11/20

Split genes interpretation

Also, the pasa web portal connects to the pasa database, so you shouldn't need to upload anything

unread,

Split genes interpretation

Also, the pasa web portal connects to the pasa database, so you shouldn't need to upload anything

3/11/20

xiaojing shi, Brian Haas2

2/13/20

DBD::SQLite::db do failed: attempt to write a readonly database

Hi, The error DBD::SQLite::db do failed: attempt to write a readonly database at /share/pkg/condas/

unread,

DBD::SQLite::db do failed: attempt to write a readonly database

Hi, The error DBD::SQLite::db do failed: attempt to write a readonly database at /share/pkg/condas/

2/13/20

Search

Clear search

Close search

Google apps

Main menu