FASTA program discussion list

[William Pearson <>]

A new version of the FASTA package is available as 

http://faculty.virginia.edu/wrpearson/fasta/fasta36/fasta-36.3.6d.tar.gz

This file has the same name, but the version in the code refers to November 2013, instead of October.

Two changes have been made:

(1) the problem with mis-reading libraries that lack a terminal newline (‘\n’, reported below) has been fixed.

(2) another bug with map_db.c, which caused it to crash, has also been fixed.

Please let me know if you find other problems.

Bill Pearson

From: William Pearson []
Sent: Friday, November 01, 2013 12:34 PM
To: Helena Storvall
Cc: John Wise; Georgios Magklaras;
Subject: Re: [admin] segmentation fault

This is definitely a bug in the current version of FASTA, and will be fixed in the next few days.

Bill Pearson

Begin forwarded message:

From: Helena Storvall <>

Subject: RE: [admin] segmentation fault

Date: November 1, 2013 at 7:31:52 AM EDT

To: John Wise <>

Cc: Georgios Magklaras <>, "" <>

Hi John,

Yes, you are right. That is strange. The sequence is only 277 residues.

I experimented a bit, and it turns out that when I add newline to the end of the file things work just fine. 

Is this a known issue? And is it intentional?

best,

Helena

the command that worked:

fasta /tmp/50438.seq1.newline /tmp/50438.seq2.newline > /tmp/50438.grasta_result.newline

output:

# fasta /tmp/50438.seq1.newline /tmp/50438.seq2.newline

FASTA searches a protein or DNA sequence data bank

 version 36.3.6 Sep, 2013(preload9)

Please cite:

 W.R. Pearson & D.J. Lipman PNAS (1988) 85:2444-2448

Query: /tmp/50438.seq1.newline

  1>>>seq1 - 342 aa

Library: /tmp/50438.seq2.newline

      278 residues in     1 sequences

Statistics: (shuffled [158]) MLE statistics: Lambda= 0.1118;  K=0.0008651

 statistics sampled from 1 (1) to 158 sequences

Algorithm: FASTA (3.8 Nov 2011) [optimized]

Parameters: BL50 matrix (15:-5), open/ext: -10/-2

 ktup: 2, E-join: 1 (1), E-opt: 0.2 (1), width:  16

 Scan time:  0.070

The best scores are:                                      opt bits E(1)

seq2                                               ( 278) 1854 311.6 1.5e-89

>>seq2                                                    (278 aa)

 initn: 1854 init1: 1854 opt: 1854  Z-score: 1640.2  bits: 311.6 E(1): 1.5e-89

Smith-Waterman score: 1854; 100.0% identity (100.0% similar) in 278 aa overlap (65-342:1-278)

           40        50        60        70        80        90    

seq1   CDQISDAVLDAHLSQDPDAKVACETVCKTGMVLLCGEITSRAVVDYQKIVRDTIKYIGYD

                                     ::::::::::::::::::::::::::::::

seq2                                 MVLLCGEITSRAVVDYQKIVRDTIKYIGYD

                                             10        20        30

          100       110       120       130       140       150    

seq1   DSEKGFDYKTCNVLVALEQQSPDIAQGVHLDRQEEDIGAGDQGLMFGYATDETEECMPLT

       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::

seq2   DSEKGFDYKTCNVLVALEQQSPDIAQGVHLDRQEEDIGAGDQGLMFGYATDETEECMPLT

               40        50        60        70        80        90

          160       170       180       190       200       210    

seq1   IVLAHKLNAKLAELRRNGVLPWLRPDSKTQVTVKYIQKNGAVIPVRVHTIVISVQHDETI

       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::

seq2   IVLAHKLNAKLAELRRNGVLPWLRPDSKTQVTVKYIQKNGAVIPVRVHTIVISVQHDETI

              100       110       120       130       140       150

          220       230       240       250       260       270    

seq1   SLSDMQDALKEQVIKAVVPEKYLDEKTVYHLQPSGRFVIGGPQGDAGVTGRKIIVDTYGG

       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::

seq2   SLSDMQDALKEQVIKAVVPEKYLDEKTVYHLQPSGRFVIGGPQGDAGVTGRKIIVDTYGG

              160       170       180       190       200       210

          280       290       300       310       320       330    

seq1   WGAHGGGAFSGKDYTKVDRSAAYAARWVAKSLVHAKLCHRVLVQVHLIWVFMKQIKLHIS

       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::

seq2   WGAHGGGAFSGKDYTKVDRSAAYAARWVAKSLVHAKLCHRVLVQVHLIWVFMKQIKLHIS

              220       230       240       250       260       270

          340  

seq1   KHIVRDW*

       ::::::::

seq2   KHIVRDW*

               

342 residues in 1 query   sequences

278 residues in 1 library sequences

 Tcomplib [36.3.6 Sep, 2013(preload9)] (64 proc in memory [0G])

 start: Fri Nov  1 12:24:33 2013 done: Fri Nov  1 12:24:33 2013

 Total Scan time:  0.070 Total Display time:  0.020

Function used was FASTA [36.3.6 Sep, 2013(preload9)]

---

From: [] on behalf of John Wise []
Sent: Thursday, October 31, 2013 5:38 PM
To: Helena Storvall
Cc: Georgios Magklaras;
Subject: Re: [admin] segmentation fault

I am curious about the following

Query: /tmp/50438.seq1
  1>>>seq1 - 342 aa
Library: /tmp/50438.seq2
    44997 residues in     1 sequences

is 50438.seq2 really 44997 residues?  Or is something odd happening there?

john

John Wise
University of Nebraska-Lincoln
345 Food Industry Complex
Lincoln, NE 68583-0919
402-770-2705

On Thu, Oct 31, 2013 at 10:53 AM, Helena Storvall <> wrote:

Hi Georgios,
Thanks for your reply.
No, there is no pasa_killer.input file unfortunately.
Is there any other info I could give that would help?

Best regards,
Helena


________________________________________
From: Georgios Magklaras []
Sent: Thursday, October 31, 2013 4:44 PM
To:
Cc: Helena Storvall
Subject: Re: [admin] segmentation fault

On 31/10/13 15:25, wrote:
> Hi,
> I am running into a problem with segmentation fault while using fasta through
> another program (PASA, http://pasa.sourceforge.net).
>
> Here is the command and the error message:
> fasta /tmp/50438.seq1 /tmp/50438.seq2 > /tmp/50438.grasta_result
> Segmentation fault
>
> The server I'm running on:
> Linux rna 3.0.0 #1 SMP Thu Aug 4 15:10:31 CEST 2011 x86_64 Intel(R) Xeon(R) CPU
> X7550 @ 2.00GHz GenuineIntel GNU/Linux
>
> Fasta version: version 36.3.6 Sep, 2013(preload9)
>
> Below is what the three files look like.
>
> 1. /tmp/50438.seq1:
>> seq1
> MNGPVDYIQEHTLKDVGAFMFTSESVGEGHPDKICDQISDAVLDAHLSQDPDAKVACETV
> CKTGMVLLCGEITSRAVVDYQKIVRDTIKYIGYDDSEKGFDYKTCNVLVALEQQSPDIAQ
> GVHLDRQEEDIGAGDQGLMFGYATDETEECMPLTIVLAHKLNAKLAELRRNGVLPWLRPD
> SKTQVTVKYIQKNGAVIPVRVHTIVISVQHDETISLSDMQDALKEQVIKAVVPEKYLDEK
> TVYHLQPSGRFVIGGPQGDAGVTGRKIIVDTYGGWGAHGGGAFSGKDYTKVDRSAAYAAR
> WVAKSLVHAKLCHRVLVQVHLIWVFMKQIKLHISKHIVRDW*
>
> 2. /tmp/50438.seq2:
>> seq2
> MVLLCGEITSRAVVDYQKIVRDTIKYIGYDDSEKGFDYKTCNVLVALEQQSPDIAQGVHL
> DRQEEDIGAGDQGLMFGYATDETEECMPLTIVLAHKLNAKLAELRRNGVLPWLRPDSKTQ
> VTVKYIQKNGAVIPVRVHTIVISVQHDETISLSDMQDALKEQVIKAVVPEKYLDEKTVYH
> LQPSGRFVIGGPQGDAGVTGRKIIVDTYGGWGAHGGGAFSGKDYTKVDRSAAYAARWVAK
> SLVHAKLCHRVLVQVHLIWVFMKQIKLHISKHIVRDW*
>
>
> 3. /tmp/50438.grasta_result:
> # fasta /tmp/50438.seq1 /tmp/50438.seq2
> FASTA searches a protein or DNA sequence data bank
>   version 36.3.6 Sep, 2013(preload9)
> Please cite:
>   W.R. Pearson & D.J. Lipman PNAS (1988) 85:2444-2448
>
> Query: /tmp/50438.seq1
>    1>>>seq1 - 342 aa
> Library: /tmp/50438.seq2
>      44997 residues in          1 sequences
>
> Statistics: Altschul/Gish params: n0: 342 Lambda: 0.158 K: 0.019 H: 0.100
>   statistics sampled from 0 (1) to 0 sequences
> Algorithm: FASTA (3.8 Nov 2011) [optimized]
> Parameters: BL50 matrix (15:-5), open/ext: -10/-2
>   ktup: 2, E-join: 1 (0.5), E-opt: 0.2 (0.5), width:  16
>   Scan time:  0.040
>
> The best scores are:                                    opt bits E(2)
> seq2                                             (44997) 1854 429.0 2.2e-122
> seq2                                             (44997)    0 6.9       2
>
>
> Could someone explain why I get a segmentation fault? And how to get around it
> so I can continue the PASA run?
>
> Best regards,
> Helena
>
> Helena Storvall
> PhD student
> Sandberg lab
> Karolinska Institutet
> Stockholm, Sweden
> email:
>

Hei,

There could be a number of different reasons why the PASA pipeline
segfaults and one needs more info.

1)On the working directory is there a pasa_killer.input file after the
crash?

2)If yes, then could you do a: pasa pasa_killer.input and post here the
output?


GM


Best regards,

--
--
George Magklaras PhD
RHCE no: 110-320-413

Head of IT/Senior Systems Engineer
Biotechnology Center of Oslo and
the Norwegian Center for Molecular Medicine/
Vitenskapelig Databehandling (VD) -
Research Computing Services - USIT

EMBnet TMPC Chair

http://folk.uio.no/georgios
http://www.uio.no/english/services/it/research/hpc/abel/

Tel: +47 22840535