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;
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;
Comment