Execution halted at mergepool stage

[KristinaGagalova]

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

• [x] rna bloom version - 1.3.1
• [x] java version 11.0.8
• [x] options java -Xmx200g
• [x] comand

  rnabloom -k 25-75:5 -fpr 0.005 -extend -savebf -t 48 -ref ${refs} -pool ${readslist} -mergepool -rcr -ntcard -stranded -outdir ${outdir}

[kmnip]

It appears that minimap2 died as the index was built.

Can you please list the files for one of the samples in your pooled assembly?

[KristinaGagalova]

Hi Ka Ming, I did a bit of cleaning on the large files

rm */*.cbf */*.rpkbf */*.nbits

And this is what's left in one of the samples directories after the cleaning

total 266812
drwxrwxr-x 2 kgagalova kgagalova        12 Oct 29 16:29 ./
drwxrwxr-x 9 kgagalova kgagalova        26 Oct 29 16:29 ../
-rw-rw-r-- 1 kgagalova kgagalova         0 Oct 15 18:18 FRAGMENTS.DONE
-rw-rw-r-- 1 kgagalova kgagalova        35 Oct 15 18:18 Harvest_flower.fragstats
-rw-rw-r-- 1 kgagalova kgagalova        98 Oct 15 18:18 Harvest_flower.graph
-rw-rw-r-- 1 kgagalova kgagalova       736 Oct 15 21:18 Harvest_flower.tmp_ava_cat_nr.fa.log
-rw-rw-r-- 1 kgagalova kgagalova 195414931 Oct 15 21:18 Harvest_flower.transcripts.fa
-rw-rw-r-- 1 kgagalova kgagalova 169052948 Oct 15 21:18 Harvest_flower.transcripts.nr.fa
-rw-rw-r-- 1 kgagalova kgagalova  16853138 Oct 15 21:18 Harvest_flower.transcripts.nr.short.fa
-rw-rw-r-- 1 kgagalova kgagalova  18554017 Oct 15 21:18 Harvest_flower.transcripts.short.fa
-rw-rw-r-- 1 kgagalova kgagalova         0 Oct 15 21:18 TRANSCRIPTS.DONE
-rw-rw-r-- 1 kgagalova kgagalova         0 Oct 15 21:18 TRANSCRIPTS_NR.DONE

Is there any particular file that you are looking for?

[kmnip]

This is fixed in the new release.