Error mapping

[jbruxaux]

Hi!

I tried to use bwa-mem2 to map reads against a reference. The indexing of the reference went well (at least I didn't get any error message), but I cannot map for a reason I do not understand. I am using reads cleaned by fastp, but my colleague performed the same thing with raw reads and got the same error.

Here is the error log:

Looking to launch executable "/hpc2n/eb/software/bwa-mem2/2.2.1-GCCcore-11.2.0/bin/bwa-mem2.avx2", simd = .avx2
Launching executable "/hpc2n/eb/software/bwa-mem2/2.2.1-GCCcore-11.2.0/bin/bwa-mem2.avx2"
-----------------------------
Executing in AVX2 mode!!
-----------------------------
* SA compression enabled with xfactor: 8
* Ref file: /pfs/stor10/projects/projnb10/wanglab-2020/Reference/Pinus_tabuliformis/P.tabuliformis_V1.0_corrected.fa
* Entering FMI_search
* Index file found. Loading index from /pfs/stor10/projects/projnb10/wanglab-2020/Reference/Pinus_tabuliformis/P.tabuliformis_V1.0_corrected.fa.bwt.2bit.64
* Reference seq len for bi-index = 50845757857
* sentinel-index: 27922254887
* Count:
0,      1
1,      15725484908
2,      25422878929
3,      35120272950
4,      50845757857

* Reading other elements of the index from files /pfs/stor10/projects/projnb10/wanglab-2020/Reference/Pinus_tabuliformis/P.tabuliformis_V1.0_corrected.fa
* Index prefix: /pfs/stor10/projects/projnb10/wanglab-2020/Reference/Pinus_tabuliformis/P.tabuliformis_V1.0_corrected.fa
* Read 0 ALT contigs
* Done reading Index!!
* Reading reference genome..
* Binary seq file = /pfs/stor10/projects/projnb10/wanglab-2020/Reference/Pinus_tabuliformis/P.tabuliformis_V1.0_corrected.fa.0123
* Reference genome size: 50845757856 bp
* Done reading reference genome !!

------------------------------------------
1. Memory pre-allocation for Chaining: 2508.0984 MB
2. Memory pre-allocation for BSW: 4313.1064 MB
3. Memory pre-allocation for BWT: 1391.6552 MB
------------------------------------------
* Threads used (compute): 18
* No. of pipeline threads: 2

[0000] read_chunk: 180000000, work_chunk_size: 180000248, nseq: 1206750
        [0000][ M::kt_pipeline] read 1206750 sequences (180000248 bp)...
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 0
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 180000000, work_chunk_size: 180000074, nseq: 1206750
        [0000][ M::kt_pipeline] read 1206750 sequences (180000074 bp)...
[0000] 2. Calling kt_for - worker_aln
bwa-mem2: src/bwamem.cpp:1780: uint8_t* bns_get_seq_v2(int64_t, const uint8_t*, int64_t, int64_t, int64_t*, uint8_t*, uint8_t*): Assertion `end-beg < BATCH_SIZE * SEEDS_PER_READ * sizeof(SeqPair)' failed.
/var/spool/slurmd/job21444015/slurm_script: line 59: 419678 Aborted                 (core dumped) bwa-mem2 mem ${ref} ${fileR1} ${fileR2} -R "@RG\tID:${path##*/}\tSM:${path##*/}\tLB:WGS\tPL:Illumina" -t 18 > ${path}${sample}/${sample}.sam

Any idea of what could be wrong? We are using version 2.2.1.

Thanks in advance!

Jade

[Mushill]

I got the same error.
In some samples, it worked well, while others were wrong.