Issue with BWA on prebuilt dbs

[dcdanko]

Hello,

I'm having some issues with BWA running on one the prebuilt databases and the error message is not particularly helpful.

Any idea what's going wrong?

$ /home/dcd3001/bin/gottcha -t 6 --input foo.fq --database /athena/masonlab/scratch/users/dcd3001/Refs/CAP_databases/microbial_genomes/gottcha_dbs/gottcha_bacteria_species/GOTTCHA_BACTERIA_c4937_k24_u30.species --mode full --outdir temp_gottcha_Ip_11_S11
...
[00:00:08] Done merging splitrim stats.

                                    RAW         SPLIT-TRIMMED
                                    ===         =============
      # of Reads:               408,632             1,338,538  (327.57 %)
      # of Bases:            60,812,494            44,447,868  (73.09 %)
Mean Read Length:                   148                    33  (22.17 %)

[00:00:08] Mapping split-trimmed reads to GOTTCHA database and profiling...
[00:00:42] ERROR: Failed running BWA or profileGottcha.pl. Please check temp_gottcha_Ip_11_S11/foo.gottcha.log for detail.

logs

$ cat temp_gottcha_Ip_11_S11/foo.gottcha.log
----> ENTRY HEADER:@FFSP226:6:BNS41704-1927:1:1101:3320:1000 1:N:0:TAAGGCGA+TACTCCTT
Threads: 1 (effective)  1 (requested)
IDX = 0: reading from 0 to 150400419
Staggering at 125000 reads; processed 125000 reads
IDX(0) counted 408632 reads
GLOBAL READ COUNT = 408632
Trim Time: 7548 ms

PROGRAM ELAPSED TIME: 8322 ms
[M::bwa_idx_load_from_disk] read 0 ALT contigs

[poeli]

It seems BWA failed due to running out of memory. You might want to increase memory allocation and tried again. Thanks.

[dcdanko]

Fairly certain that's not the issue. The machine in use has a terabyte of RAM.

[poeli]

I see, but the log indicates BWA got interrupted. I would suggest you run gottcha with "--debug" flag. It will display the exact BWA command that is being run in the pipeline. Then, we can run BWA independently and try to figure out why BWA failed.