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Old 08-08-2013, 11:02 PM   #1
Location: Göttingen, Germany

Join Date: May 2011
Posts: 13
Default Trintiy with Bowtie2 or Bowtie1

Dear all,

I run Trinity to assemble 100bp PE HiSeq2000 data (2x100M reads) on a 256GB RAM cluster with this setting:

perl --seqType fq --JM 240G --left Seq_1.fq  --right Seq_2.fq --single single.fq --output /path/to/output --CPU 6 --min_contig_length 150
I constantly get the following error message:

---- Chrysalis ----

mkdir: cannot create directory `/usr/users/xxx/Gm/Trinity/Assembled/chrysalis': File exists
CMD: ln -sf /home/xxx/xxx/Gm/Trinity/Assembled/inchworm.K25.L25.DS.fa target.fa 
Warning, bowtie-build output already exists and will be re-used: target.fa*
CMD: bowtie -a -m 20 --best --strata --threads 6 --quiet --chunkmbs 512 -q -S --sam-nohead  -f target single.fa > bowtie.out
Error: Could not allocate ChunkPool of 536870912 bytes
terminate called after throwing an instance of 'int'
sh: line 1:  2534 Aborted                 (core dumped) bowtie -a -m 20 --best --strata --threads 6 --quiet --chunkmbs 512 -q -S --sam-nohead -f target single.fa > bowtie.out
COMMAND: bowtie -a -m 20 --best --strata --threads 6 --quiet --chunkmbs 512 -q -S --sam-nohead  -f target single.fa > bowtie.out
Died with exit code 34304
core file size          (blocks, -c) unlimited
data seg size           (kbytes, -d) unlimited
scheduling priority             (-e) 0
file size               (blocks, -f) unlimited
pending signals                 (-i) 2067510
max locked memory       (kbytes, -l) unlimited
max memory size         (kbytes, -m) unlimited
open files                      (-n) 65536
pipe size            (512 bytes, -p) 8
POSIX message queues     (bytes, -q) 819200
real-time priority              (-r) 0
stack size              (kbytes, -s) unlimited
cpu time               (seconds, -t) unlimited
max user processes              (-u) 2067510
virtual memory          (kbytes, -v) unlimited
file locks                      (-x) unlimited

Error, the Chrysalis process failed:
Error, cmd: /home/xxx/xxx/Programme/trinityrnaseq_r2013-02-25/Chrysalis/Chrysalis -i single.fa -iworm /home/xxx/xxx/Gm/Trinity/Assembled/inchworm.K25.L25.DS.fa -o /usr/users/xxx/Gm/Trinity/Assembled/chrysalis -cpu 6  -min_glue 2 -min_iso_ratio 0.05 -glue_factor 0.05 -weldmer_size 48  -min 150 -dist 500 -max_reads 200000  -sort_buffer_size 240G -max_mem_reads 1000000  -paired  -reads_for_pairs single.fa  -butterfly /home/xxx/xxx/Programme/trinityrnaseq_r2013-02-25/Butterfly/Butterfly.jar  2>&1  died with ret 65280 at line 1476.

 at line 1101
	main::run_chrysalis('/home/xxx/xxx/Gm/Trinity/Assembled/inchworm.K25.L25.DS.fa', 'single.fa', 150, 500, undef, 'single.fa') called at line 930
Any idea what is goin wrong there? I have both Bowtie and Bowtie2 installed. Is Trinty able to use Bowtie2?

Any suggestions are high appreciated.
Thanks in advance.
nposnien is offline   Reply With Quote
Old 08-09-2013, 12:03 AM   #2
Location: Europe

Join Date: Feb 2012
Posts: 13

This may not be the cause of the error but I think that in your command line you should not give --left --right and --single parameters. Instead the single reads should be added to the left reads. You may get a quicker answer about the error from the trinity mailing list.
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Old 08-09-2013, 06:02 AM   #3
Rick Westerman
Location: Purdue University, Indiana, USA

Join Date: Jun 2008
Posts: 1,104

Answered, or being tried to be answered, via the Trinity mailing list. We think that Nico's bowtie may be 32-bit instead of 64-bit (which of course has a big effect on memory -- which is what a "could not allocate" message refers to.) We've asked Nico to check his bowtie version.

If I may make a plug, like other program's mailing list (e.g., Mira) the Trinity mailing list is active and the developers chime in frequently. If anyone is using Trinity but is not on the mailing list then I suggest joining it.
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Old 08-14-2013, 07:19 AM   #4
Location: Göttingen, Germany

Join Date: May 2011
Posts: 13

Thanks for all the help! It was actually the bowtie version (I have now clue why compilation of bowtie source on a 464bit machine results in a 32bit version, but ....).
nposnien is offline   Reply With Quote

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