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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 ....).
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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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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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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:
Code:perl Trinity.pl --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
Code:------------------- ---- 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 Exiting. 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 Trinity.pl line 1476. at Trinity.pl 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 Trinity.pl line 930
Any suggestions are high appreciated.
Thanks in advance.Tags: None
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