trinity assembly error, run failed
1
1
Entering edit mode
6.5 years ago

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.
trinity rna seq rna • 2.3k views
ADD COMMENT
0
Entering edit mode
6.4 years ago

Did you ever figure this out?

ADD COMMENT

Login before adding your answer.

Traffic: 1509 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6