[HTCondor-users] Issues Running BLAST through HTCondor

[sameh.abedin@xxxxxxxxx]

I have 3 hosts that can execute jobs. 1 host has 16 slots, and the other 2 have 8 slots. So, 32 slots total.

Thanks,

Sameh

On Tue, Mar 8, 2022 at 1:00 PM <htcondor-users-request@xxxxxxxxxxx> wrote:

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Today's Topics:

 Â1. Issues Running BLAST through HTCondor (sameh.abedin@xxxxxxxxx)
 Â2. Re: Issues Running BLAST through HTCondor
   (dmitri.maziuk@xxxxxxxxx)
 Â3. Re: Issues Running BLAST through HTCondor
   (dmitri.maziuk@xxxxxxxxx)


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Message: 1
Date: Mon, 07 Mar 2022 16:04:02 -0500
From: sameh.abedin@xxxxxxxxx
To: htcondor-users@xxxxxxxxxxx
Subject: [HTCondor-users] Issues Running BLAST through HTCondor
Message-ID:
    <CAL+EDRBUfsMfGPoG+MA_2UR_DUFduc-b_MbDmAeTLTBHEa0-1w@xxxxxxxxxxxxxx>
Content-Type: text/plain; charset="utf-8"

Hello,

I am attempting to run BLAST (Basic Local Alignment Search Tool) through
HTCondor.
Im not sure if this is an HTCondor related issue or a BLAST related issue,
but any assistance would be greatly appreciated.

Here is my submit file:












*universe = vanillaBlastIndexStr = $(Process) + 1BlastIndex =
$INT(BlastIndexStr,%d)executable = C:\Program
Files\NCBI\blast-2.12.0+\bin\blastn.exetransfer_executable = Falsearguments
= -query group_$(BlastIndex).fasta -db blast_databases\16S_ribosomal_RNA
-max_target_seqs 1 -outfmt 6output =
results_9\group_$(BlastIndex).reporterror =
errors_9\blast$(BlastIndex).errlog =
logs_9\blast$(BlastIndex).logtransfer_input_files =
group_$(BlastIndex).fasta, blast_databasesshould_transfer_files = YESqueue
32*

Occasionally some of the jobs send this to standard error: "*FATAL ERROR:
inappropriate recursion initializing NCBI diagnostic framework*" When this
occurs, the output file is empty. When that specific error is not there, I
think I obtain the expected BLAST output, which is a large file that looks
like this (first 8 lines):

SRR10211832.1.1 NR_121731.1 98.311 296 5 0 6 301 5 300 2.53e-147 520
SRR10211832.1.2 NR_113069.1 80.144 277 46 9 6 277 1 273 1.35e-50 198
SRR10211832.1.3 NR_044972.1 83.389 301 44 3 6 301 1 300 2.18e-73 274
SRR10211832.1.5 NR_144745.1 82.796 279 32 13 6 276 1 271 1.03e-61 235
SRR10211832.1.6 NR_074809.1 91.864 295 24 0 5 299 2 296 4.42e-115 412
SRR10211832.1.7 NR_113152.1 90.236 297 24 5 6 301 1 293 3.47e-106 383
SRR10211832.1.8 NR_113069.1 80.743 296 52 5 6 298 1 294 6.19e-59 226
SRR10211832.1.9 NR_024673.1 87.043 301 29 9 6 300 1 297 1.27e-90 331.

Additionally, there is occasionally an issue with mutex errors (error log
shown below) even though the BLAST executable should be running in a single
thread:






*Error: _expression_ failed: init_mutexError: _expression_ failed:
WaitForSingleObject(init_mutex, INFINITE) == WAIT_OBJECT_0Error: _expression_
failed: ReleaseMutex(init_mutex)Error: _expression_ failed: init_mutexError:
_expression_ failed: WaitForSingleObject(init_mutex, INFINITE) ==
WAIT_OBJECT_0Error: _expression_ failed: ReleaseMutex(init_mutex)*

Again, any help would be much appreciated!

Thanks,
Sameh
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Message: 2
Date: Mon, 07 Mar 2022 15:28:23 -0600
From: dmitri.maziuk@xxxxxxxxx
To: htcondor-users@xxxxxxxxxxx
Subject: Re: [HTCondor-users] Issues Running BLAST through HTCondor
Message-ID: <8a3d342e-0f62-1b6d-b74a-c21c1ce6420b@xxxxxxxxx>
Content-Type: text/plain; charset=UTF-8; format=flowed

On 2022-03-07 3:04 PM, sameh.abedin@xxxxxxxxx wrote:
> Hello,
>
> I am attempting?to run BLAST (Basic Local Alignment Search Tool) through
> HTCondor.
> Im not?sure if this is an HTCondor related issue or a BLAST related
> issue, but any assistance would be greatly appreciated.

How many nodes per host do you have?

Dima



------------------------------

Message: 3
Date: Mon, 07 Mar 2022 15:29:44 -0600
From: dmitri.maziuk@xxxxxxxxx
To: htcondor-users@xxxxxxxxxxx
Subject: Re: [HTCondor-users] Issues Running BLAST through HTCondor
Message-ID: <74eb37e5-ca97-030b-9adf-1848653b3701@xxxxxxxxx>
Content-Type: text/plain; charset=UTF-8; format=flowed

... and by "nodes" I meant condor slots

sorry, brane fart
Dima


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