hmmpgmd test error

[erick-dorlass]

Hi,

I'm trying to use the hmmpgmd_client_example.pl script for testing the hmmpgmd connection. I executed thehmmpgmd --master --hmmdb virus.hmm and hmmpgmd --worker 127.0.0.1 --cpu 4

I have changed the line 104 in hmmpgmd_client_example.pl script for using hmm database

I'm using this command to execute the script ./hmmpgmd_client_example.pl -file ../teste.faa and I receive this error:

Timeout on the socket:Negative length at ./hmmpgmd_client_example.pl line 490.

In the master and worker servers, this are the messages that are printed on screen:

MASTER: Queuing scan LNCMODLF_00002 from 127.0.0.1 (6) hmmpgmd --hmmdb 1 Processing command 10002 from 127.0.0.1 WORKER 127.0.0.1 COMPLETED: 0.20 sec received 2583 bytes 0x0 Results for 127.0.0.1 (6) sent 2571 bytes Hits:1 reported:1 included:1 Closing 127.0.0.1 (6)

WORKER: Fri Jun 3 19:01:11 2022 Search seq LNCMODLF_00002 [L=545] vs HMM DB 0 [0 - 8317] Sequences Residues Elapsed 0 1 545 123 122 12 1 00:00.19 99 1 545 123 122 12 1 00:00.19 Bytes: 2571 hits: 1 sent on socket 3

Could you help me to understand what this "Timeout on the socket" error means and how to solve it?

Thank you

[npcarter]

Hello, I'm Nick Carter, a programmer on the HMMER effort, and I'll be taking a look at this bug. I'm pretty swamped this week, so probably won't get to it until next week, but I had a couple of questions. First, is the error reproducible? Timeouts are sometimes caused by transient network issues, although the "negative length" part of the error makes me think it's a bug. Second, does the hmmpgmd_client_example.pl script print out any information about the hit?

My first guess is that the hmmpgmd_client_example.pl script may have gotten out of sync with the hmmpgmd server, particularly since I hadn't realized we have such a script and I'm the one who's been doing most of the work on the server for the last few years.

-Nick

On Fri, Jun 3, 2022 at 6:08 PM erick-dorlass @.***> wrote:

Hi,

I'm trying to use the hmmpgmd_client_example.pl script for testing the hmmpgmd connection. I executed the hmmpgmd --master --hmmdb virus.hmm and hmmpgmd --worker 127.0.0.1 --cpu 4

I have changed the line 104 in hmmpgmd_client_example.pl script for using hmm database

I'm using this command to execute the script ./hmmpgmd_client_example.pl -file ../teste.faa and I receive this error:

Timeout on the socket:Negative length at ./hmmpgmd_client_example.pl line 490.

In the master and worker servers, this are the messages that are printed on screen:

MASTER: Queuing scan LNCMODLF_00002 from 127.0.0.1 (6) hmmpgmd --hmmdb 1 Processing command 10002 from 127.0.0.1 WORKER 127.0.0.1 COMPLETED: 0.20 sec received 2583 bytes 0x0 Results for 127.0.0.1 (6) sent 2571 bytes Hits:1 reported:1 included:1 Closing 127.0.0.1 (6)

WORKER: Fri Jun 3 19:01:11 2022 Search seq LNCMODLF_00002 [L=545] vs HMM DB 0 [0 - 8317] Sequences Residues Elapsed 0 1 545 123 122 12 1 00:00.19 99 1 545 123 122 12 1 00:00.19 Bytes: 2571 hits: 1 sent on socket 3

Could you help me to understand what this "Timeout on the socket" error means and how to solve it?

Thank you

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[npcarter]

Hello,

I've been able to reproduce this bug. It doesn't seem to be connected to your attempt to search a HMM database, as I get the same problem when using a sequence database. Unfortunately, I don't know PERL, so I'm going to have to see if Sean can take a look at this.

As a workaround, you could use the hmmc2 client program for your tests. Instructions for it are in the documentation/userguide/daemon.tex file.

[erick-dorlass]

Thank you.

I was able to use version 3.1b2 for executing this script for testing hmmpgmd.

[npcarter]

Thanks for that pointer. Given that, I've been able to verify that the problem is that the format of the data that the hmmpgmd server returns in response to a search has changed since version 3.1b2 but the test script hasn't been updated to conform to the changes. I'm going to send mail to the original author and see if he's interested in updating the script to match the new version, but I'm not sure if he will be. I think that the best option at this point remains the hmmc2 client program, which has been kept up to date with changes to hmmpgmd.

-Nick

On Fri, Jun 10, 2022 at 3:36 PM erick-dorlass @.***> wrote:

Thank you.

I was able to use version 3.1b2 for executing this script for testing hmmpgmd.

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[cryptogenomicon]

Nick, do we have any update on this issue?

[npcarter]

No update from the original test author. I'm going to call this "not a bug," in the sense that the hmmpgmd unit test works correctly as-is, and only has issues if you try to generalize it to other daemon searches. If you want to run other searches, the right approach is to use the hmmc2 client in conjunction with hmmpgmd, as that client is kept up to date with all changes to the hmmpgmd program.