[HTCondor-users] Issues Running BLAST through HTCondor

[sameh.abedin@xxxxxxxxx]

Hello,

I am attemptingÂto run BLAST (Basic Local Alignment Search Tool) through HTCondor.

Im notÂsure if this is an HTCondor related issue or a BLAST related issue, but any assistance would be greatly appreciated.

Here is my submit file:Â

universe = vanilla
BlastIndexStr = $(Process) + 1
BlastIndex = $INT(BlastIndexStr,%d)
executable = C:\Program Files\NCBI\blast-2.12.0+\bin\blastn.exe
transfer_executable = False
arguments = -query group_$(BlastIndex).fasta -db blast_databases\16S_ribosomal_RNA -max_target_seqs 1 -outfmt 6
output = results_9\group_$(BlastIndex).report
error = errors_9\blast$(BlastIndex).err
log = logs_9\blast$(BlastIndex).log
transfer_input_files = group_$(BlastIndex).fasta, blast_databases
should_transfer_files = YES
queue 32

Occasionally some of the jobs send this to standard error: "FATAL ERROR: inappropriate recursion initializing NCBI diagnostic framework"ÂWhen this occurs, the output file is empty.ÂWhen that specific error is not there, I think I obtain the expected BLAST output,Âwhich 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_mutex
Error: _expression_ failed: WaitForSingleObject(init_mutex, INFINITE) == WAIT_OBJECT_0
Error: _expression_ failed: ReleaseMutex(init_mutex)
Error: _expression_ failed: init_mutex
Error: _expression_ failed: WaitForSingleObject(init_mutex, INFINITE) == WAIT_OBJECT_0
Error: _expression_ failed: ReleaseMutex(init_mutex)

Again, any help would be much appreciated!

Thanks,

Sameh