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Old 10-22-2015, 02:11 AM   #1
TomBoy
Junior Member
 
Location: china

Join Date: Oct 2015
Posts: 2
Default trinity run error

Hi,everyone

I am using trinity for assembly.I installed trinity according to this website https://github.com/trinityrnaseq/trinityrnaseq/wiki ,but when I use this commands to test it,it running failure.The commands is:

cd sample_data/test_Trinity_Assembly/

./runMe.sh

After I use that commands to test trinity,it feedback the following error.



----------------------------------------------------------------------------------
-------------- Trinity Phase 1: Clustering of RNA-Seq Reads ---------------------
----------------------------------------------------------------------------------



#######################################################################
Inchworm file: /home/hanxuan/trinityrnaseq-2.1.1/sample_data/test_Trinity_Assembly/trinity_out_dir/inchworm.K25.L25.fa detected.
Skipping Inchworm Step, Using Previous Inchworm Assembly
#######################################################################

-- Skipping CMD: /home/hanxuan/trinityrnaseq-2.1.1/util/misc/fasta_filter_by_min_length.pl /home/hanxuan/trinityrnaseq-2.1.1/sample_data/test_Trinity_Assembly/trinity_out_dir/inchworm.K25.L25.fa 100 > /home/hanxuan/trinityrnaseq-2.1.1/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/inchworm.K25.L25.fa.min100, checkpoint exists.
-- Skipping CMD: bowtie-build -q /home/hanxuan/trinityrnaseq-2.1.1/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/inchworm.K25.L25.fa.min100 /home/hanxuan/trinityrnaseq-2.1.1/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/inchworm.K25.L25.fa.min100, checkpoint exists.
* Running CMD: bash -c " set -o pipefail; bowtie -a -m 20 --best --strata --threads 4 --chunkmbs 512 -q -S -f /home/hanxuan/trinityrnaseq-2.1.1/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/inchworm.K25.L25.fa.min100 both.fa | samtools view -@ 4 -F4 -Sb - | samtools sort -m 536870912 -@ 4 -no - - > /home/hanxuan/trinityrnaseq-2.1.1/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/iworm.bowtie.nameSorted.bam"
[bam_header_read] EOF marker is absent. The input is probably truncated.
[samopen] SAM header is present: 342 sequences.
# reads processed: 122300
# reads with at least one reported alignment: 106930 (87.43%)
# reads that failed to align: 15370 (12.57%)
Reported 127560 alignments to 1 output stream(s)
[bam_header_read] invalid BAM binary header (this is not a BAM file).
bash: 行 1: 8337 已完成 bowtie -a -m 20 --best --strata --threads 4 --chunkmbs 512 -q -S -f /home/hanxuan/trinityrnaseq-2.1.1/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/inchworm.K25.L25.fa.min100 both.fa
8338 段错误 (核心已转储) | samtools view -@ 4 -F4 -Sb -
8339 段错误 (核心已转储) | samtools sort -m 536870912 -@ 4 -no - - > /home/hanxuan/trinityrnaseq-2.1.1/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/iworm.bowtie.nameSorted.bam
Trinity run failed. Must investigate error above.





Would you please give me some advice to solve this problem? I cant't solve it.Pleasre help me!

thanks
TomBoy;
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Old 10-22-2015, 10:01 AM   #2
westerman
Rick Westerman
 
Location: Purdue University, Indiana, USA

Join Date: Jun 2008
Posts: 1,104
Default

I would take the failing command:

Code:
set -o pipefail; bowtie -a -m 20 --best --strata --threads 4 --chunkmbs 512 -q -S -f /home/hanxuan/trinityrnaseq-2.1.1/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/inchworm.K25.L25.fa.min100 both.fa | samtools view -@ 4 -F4 -Sb - | samtools sort -m 536870912 -@ 4 -no - - > /home/hanxuan/trinityrnaseq-2.1.1/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/iworm.bowtie.nameSorted.bam"
And run each of the sub-programs (i.e., those within a pipe) one at a time to see if the individual programs throws up an error.

It is very hard to debug a large command with lots of pipes. Better to break down the large command.
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Old 10-24-2015, 01:56 AM   #3
TomBoy
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Location: china

Join Date: Oct 2015
Posts: 2
Default

Dear westernman

To tell the truth,I'm a college student major in software engineering.I had not used it before.
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