segfault when running queries over multiple threads

Description

Running reindeer in query mode using multiple threads throws a Segmentation fault (core dumped) error. I tested this using the "test" miniature dataset that comes with reindeer itself, and using my own data. In both cases, using the -t parameter and specifying any number other than 1 throws the previously mentionned error.

Steps to reproduce

Create index files using ./Reindeer --index -f fof.txt --bcalm -t 4
Use ./Reindeer --query -l output_reindeer/ -q query_file.fa -t 4. (This throws a segfault error)
Use ./Reindeer --query -l output_reindeer/ -q query_file.fa. (This query is successful)

Raw terminal output

[jacquinn@golem REINDEER]$ module load gcc/4.9.3
[jacquinn@golem REINDEER]$ module load cmake/3.14.5
[jacquinn@golem REINDEER]$ ./Reindeer --query -l out_test -q  test/output_bcalm/SRR10092187_10k.unitigs.fa
############# REINDEER version v1.0.2 #############
Command line was: ./Reindeer --query -l out_test -q test/output_bcalm/SRR10092187_10k.unitigs.fa

Querying...

#Loading index...
Index loaded
Index loading total: 0.15784 seconds.

#Computing query...
Result will be written in output_reindeer/query_results/out_query_Reindeer_P40_SRR10092187_10k_0.out
--
Query done: 0.03368 seconds.
Querying sequences took 0.0336991 seconds in total.
Max Memory used: 43056
[jacquinn@golem REINDEER]$ ./Reindeer --query -l out_test -q  test/output_bcalm/SRR10092187_10k.unitigs.fa -t 4
############# REINDEER version v1.0.2 #############
Command line was: ./Reindeer --query -l out_test -q test/output_bcalm/SRR10092187_10k.unitigs.fa -t 4

Querying...

#Loading index...
Index loaded
Index loading total: 0.151806 seconds.

#Computing query...
Result will be written in output_reindeer/query_results/out_query_Reindeer_P40_SRR10092187_10k_0.out
Segmentation fault (core dumped)

kamimrcht / REINDEER

segfault when running queries over multiple threads #14