Execution halted at mergepool stage #13
Description
Hi,
I am running a pooled assembly with -mergepool and I get the following at the last stage.
>> Merging transcripts from all samples...
/home/kgagalova/miniconda3/envs/py3.6/bin/rnabloom: line 2: 2782284 Killed java -jar "/home/kgagalova/miniconda3/envs/py3.6/lib/rnabloom-v1.3.1.jar" "$@"
Those are all my files in the working directory
total 25843292
drwxrwxr-x 9 kgagalova kgagalova 28 Oct 15 22:12 ./
drwxrwxr-x 5 kgagalova kgagalova 9 Oct 22 13:25 ../
-rw-rw-r-- 1 kgagalova kgagalova 0 Oct 15 16:50 DBG.DONE
-rw-rw-r-- 1 kgagalova kgagalova 0 Oct 15 20:50 FRAGMENTS.DONE
-rw-rw-r-- 1 kgagalova kgagalova 1134665888 Oct 15 22:12 rnabloom.all.fa
-rw-rw-r-- 1 kgagalova kgagalova 426 Oct 15 22:13 rnabloom.all_nr.fa.log
-rw-rw-r-- 1 kgagalova kgagalova 98 Oct 15 16:48 rnabloom.graph
-rw-rw-r-- 1 kgagalova kgagalova 21385170463 Oct 15 16:49 rnabloom.graph.cbf
-rw-rw-r-- 1 kgagalova kgagalova 44 Oct 15 16:49 rnabloom.graph.cbf.desc
-rw-rw-r-- 1 kgagalova kgagalova 15643353278 Oct 15 16:49 rnabloom.graph.dbgbf
-rw-rw-r-- 1 kgagalova kgagalova 44 Oct 15 16:48 rnabloom.graph.dbgbf.desc
-rw-rw-r-- 1 kgagalova kgagalova 15643353278 Oct 15 16:50 rnabloom.graph.rpkbf
-rw-rw-r-- 1 kgagalova kgagalova 45 Oct 15 16:49 rnabloom.graph.rpkbf.desc
-rw-rw-r-- 1 kgagalova kgagalova 543760 Oct 15 15:46 rnabloom_k25.hist
-rw-rw-r-- 1 kgagalova kgagalova 541968 Oct 15 15:47 rnabloom_k30.hist
-rw-rw-r-- 1 kgagalova kgagalova 540583 Oct 15 15:49 rnabloom_k35.hist
-rw-rw-r-- 1 kgagalova kgagalova 538669 Oct 15 15:50 rnabloom_k40.hist
-rw-rw-r-- 1 kgagalova kgagalova 537163 Oct 15 15:51 rnabloom_k45.hist
-rw-rw-r-- 1 kgagalova kgagalova 535593 Oct 15 15:52 rnabloom_k50.hist
-rw-rw-r-- 1 kgagalova kgagalova 2573 Oct 15 15:45 rnabloom.ntcard.readslist.txt
-rw-rw-r-- 1 kgagalova kgagalova 253 Oct 15 15:52 STARTED
I believe it crashes after minimap. This is the log file - rnabloom.all_nr.fa.log:
[M::mm_idx_gen::15.105*1.58] collected minimizers
[M::mm_idx_gen::15.898*3.57] sorted minimizers
[M::main::15.898*3.57] loaded/built the index for 1528110 target sequence(s)
[M::mm_mapopt_update::16.192*3.52] mid_occ = 659
[M::mm_idx_stat] kmer size: 15; skip: 5; is_hpc: 0; #seq: 1528110
[M::mm_idx_stat::16.333*3.50] distinct minimizers: 24112798 (28.61% are singletons); average occurrences: 15.092; average spacing: 2.999
Any suggestions? I did a test with downsizing my pooled assembly by about the half, I still get the same error
- rna bloom version - 1.3.1
- java version 11.0.8
- options java -Xmx200g
- comand
rnabloom -k 25-75:5 -fpr 0.005 -extend -savebf -t 48 -ref ${refs} -pool ${readslist} -mergepool -rcr -ntcard -stranded -outdir ${outdir}