bt2 version: 2.5.1
permissions for everything is 777
I have 43gb+ of free RAM and the genome is just a 1.3gb zebra fish fasta. It indexed in about 2 minutes. But when I align, it quickly errors out:
$ bowtie/bt/bowtie2 -x zfish -f mydata/zfish.fa -S zfish_aligned.sam
terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc
Aborted
(ERR): bowtie2-align exited with value 134
--verbose shows it failing here:
Ebwt (memory):
zOff: 1104853334
zEbwtByteOff: 368284437
zEbwtBpOff: 2
nPat: 993
plen: non-NULL, [0] = 59578282
rstarts: NULL
ebwt: non-NULL, [0] =
fchr: non-NULL, [0] = 0
ftab: non-NULL, [0] = 0
eftab: non-NULL, [0] = 57565572
offs: NULL
terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc
Aborted
(ERR): bowtie2-align exited with value 134
bt2 version: 2.5.1 permissions for everything is 777
I have 43gb+ of free RAM and the genome is just a 1.3gb zebra fish fasta. It indexed in about 2 minutes. But when I align, it quickly errors out:
$ bowtie/bt/bowtie2 -x zfish -f mydata/zfish.fa -S zfish_aligned.sam terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc Aborted (ERR): bowtie2-align exited with value 134
--verbose shows it failing here: Ebwt (memory): zOff: 1104853334 zEbwtByteOff: 368284437 zEbwtBpOff: 2 nPat: 993 plen: non-NULL, [0] = 59578282 rstarts: NULL ebwt: non-NULL, [0] = fchr: non-NULL, [0] = 0 ftab: non-NULL, [0] = 0 eftab: non-NULL, [0] = 57565572 offs: NULL terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc Aborted (ERR): bowtie2-align exited with value 134
$top shows: MiB Mem : 48175.5 total, 43316.0 free, 1405.8 used, 3453.6 buff/cache MiB Swap: 12288.0 total, 12288.0 free, 0.0 used. 46245.5 avail Mem
$df -h Filesystem Size Used Avail Use% Mounted on none 24G 4.0K 24G 1% /mnt/wsl none 954G 435G 519G 46% /usr/lib/wsl/drivers none 24G 0 24G 0% /usr/lib/wsl/lib /dev/sdc 1007G 11G 946G 2% / none 24G 84K 24G 1% /mnt/wslg rootfs 24G 1.9M 24G 1% /init none 24G 900K 24G 1% /run none 24G 0 24G 0% /run/lock none 24G 0 24G 0% /run/shm none 24G 0 24G 0% /run/user tmpfs 4.0M 0 4.0M 0% /sys/fs/cgroup none 24G 76K 24G 1% /mnt/wslg/versions.txt none 24G 76K 24G 1% /mnt/wslg/doc drvfs 954G 435G 519G 46% /mnt/c snapfuse 128K 128K 0 100% /snap/bare/5 snapfuse 73M 73M 0 100% /snap/core22/607 snapfuse 92M 92M 0 100% /snap/gtk-common-themes/1535 snapfuse 41M 41M 0 100% /snap/snapd/20290 snapfuse 74M 74M 0 100% /snap/core22/864 snapfuse 54M 54M 0 100% /snap/snapd/18933 snapfuse 131M 131M 0 100% /snap/ubuntu-desktop-installer/1260 snapfuse 131M 131M 0 100% /snap/ubuntu-desktop-installer/1267
$ulimit -a real-time non-blocking time (microseconds, -R) unlimited core file size (blocks, -c) 0 data seg size (kbytes, -d) unlimited scheduling priority (-e) 0 file size (blocks, -f) unlimited pending signals (-i) 192676 max locked memory (kbytes, -l) 65536 max memory size (kbytes, -m) unlimited open files (-n) 1048576 pipe size (512 bytes, -p) 8 POSIX message queues (bytes, -q) 819200 real-time priority (-r) 0 stack size (kbytes, -s) 8192 cpu time (seconds, -t) unlimited max user processes (-u) 192676 virtual memory (kbytes, -v) unlimited file locks (-x) unlimited