trinity assembly error, run failed

Question

[nikelle.petrillo]

Hi all,

I am running a de novo trinity assembly. Trinity through an error and the run failed. Can anyone help me make sense of this error?

Thank you,
Nikelle

----------------------------------------------
--------------- Inchworm ---------------------
-- (Linear contig construction from k-mers) --
----------------------------------------------

* Running CMD: /common/opt/bioinformatics/trinityrnaseq-2.1.1/Inchworm/bin//inchworm --kmers jellyfish.kmers.fa --run_inchworm -K 25 -L 25 --monitor 1   --DS  --num_threads 6  --PARALLEL_IWORM  > /archive/npetrill/sampletrinityassembly/allsampletrinityassembly/inchworm.K25.L25.DS.fa.tmp
* Running CMD: mv /archive/npetrill/sampletrinityassembly/allsampletrinityassembly/inchworm.K25.L25.DS.fa.tmp /archive/npetrill/sampletrinityassembly/allsampletrinityassembly/inchworm.K25.L25.DS.fa
Tuesday, May 17, 2016: 22:47:00 CMD: touch /archive/npetrill/sampletrinityassembly/allsampletrinityassembly/inchworm.K25.L25.DS.fa.finished
* Running CMD: /common/opt/bioinformatics/trinityrnaseq-2.1.1/util/misc/fasta_filter_by_min_length.pl /archive/npetrill/sampletrinityassembly/allsampletrinityassembly/inchworm.K25.L25.DS.fa 100 > /archive/npetrill/sampletrinityassembly/allsampletrinityassembly/chrysalis/inchworm.K25.L25.DS.fa.min100
* Running CMD: bowtie-build -q /archive/npetrill/sampletrinityassembly/allsampletrinityassembly/chrysalis/inchworm.K25.L25.DS.fa.min100 /archive/npetrill/sampletrinityassembly/allsampletrinityassembly/chrysalis/inchworm.K25.L25.DS.fa.min100
* Running CMD: bash -c " set -o pipefail; bowtie -a -m 20 --best --strata --threads 6  --chunkmbs 512 -q -S -f /archive/npetrill/sampletrinityassembly/allsampletrinityassembly/chrysalis/inchworm.K25.L25.DS.fa.min100 both.fa  | samtools view -@ 6 -F4 -Sb - | samtools sort -m 44739242666 -@ 6 -no - - > /archive/npetrill/sampletrinityassembly/allsampletrinityassembly/chrysalis/iworm.bowtie.nameSorted.bam" 
[bam_header_read] EOF marker is absent. The input is probably truncated.
[samopen] SAM header is present: 1547795 sequences.
Error while flushing and closing output
terminate called after throwing an instance of 'int'
bash: line 1: 62207 Aborted                 (core dumped) bowtie -a -m 20 --best --strata --threads 6 --chunkmbs 512 -q -S -f /archive/npetrill/sampletrinityassembly/allsampletrinityassembly/chrysalis/inchworm.K25.L25.DS.fa.min100 both.fa
     62208 Broken pipe             | samtools view -@ 6 -F4 -Sb -
     62209 Killed                  | samtools sort -m 44739242666 -@ 6 -no - - > /archive/npetrill/sampletrinityassembly/allsampletrinityassembly/chrysalis/iworm.bowtie.nameSorted.bam
Trinity run failed. Must investigate error above.

[tirza.doniger]

Did you ever figure this out?