died with ret 256 at ../../Trinity line 2116

[Dror Hibsh]

Hi,

I am using the latest version of trinity (trinityrnaseq-2.0.6).

i was trying the sample data on my linux server and i got error message.

I am attaching here the output after the cmd make.

Any idea?

It looks like i the bowtie-build doesnt work well...

Thanks!

Dror

[Dror Hibsh]

Hi, I am sorry for the wrong title for this post..

I had this error as in the title, but it solved somehow..

The error is what i posted in the first post..

But, still i dont know how to solve this..

Thanks!

[Will Holtz]

I don't see any useful error messages in your attachment. Perhaps running Trinity with the --verbose flag will provide more insight.

-Will

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[Dror Hibsh]

That is the problem.. its only the sample data, so i just typed : make..

and this is the output..

When i was trying to figure out the problem i saw the it printed 54 times : "Note - bowtie-build indices do not yet exist. Indexing genome now".

Any ideas????

On Thursday, March 19, 2015 at 7:20:55 PM UTC+2, Will Holtz wrote:

I don't see any useful error messages in your attachment. Perhaps running Trinity with the --verbose flag will provide more insight.

-Will

On Thu, Mar 19, 2015 at 10:15 AM, Dror Hibsh <dro...@gmail.com> wrote:

Hi, I am sorry for the wrong title for this post..

I had this error as in the title, but it solved somehow..

The error is what i posted in the first post..

But, still i dont know how to solve this..

Thanks!

On Thursday, March 19, 2015 at 1:25:06 AM UTC+2, Dror Hibsh wrote:

Hi,

I am using the latest version of trinity (trinityrnaseq-2.0.6).

i was trying the sample data on my linux server and i got error message.

I am attaching here the output after the cmd make.

Any idea?

It looks like i the bowtie-build doesnt work well...

Thanks!

Dror

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[Will Holtz]

You can edit sample_data/test_Trinity_Assembly/runMe.sh and add the --verbose flag to the line with the Trinity command

-Will

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[Dror Hibsh]

Thanks Will!

I edited the runMe.sh as you suggested and attached here the output file..

Does it help?

Thanks

Dror

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[Dror Hibsh]

Any ideas?

[Dror Hibsh]

I can see that the error is about flushing and closing the output:

TIMING PROG_RUNTIME 2 s.

CMD finished (2 seconds)

Sunday, March 22, 2015: 17:49:22 CMD: touch /private3/tmp/Dror/trinityrnaseq-2.0.6/sample_data/test_Trinity_Assembly/trinity_out_dir/inchworm.K25.L25.fa.finished

CMD finished (0 seconds)

Running cmd: /private3/tmp/Dror/trinityrnaseq-2.0.6/util/misc/fasta_filter_by_min_length.pl /private3/tmp/Dror/trinityrnaseq-2.0.6/sample_data/test_Trinity_Assembly/trinity_out_dir/inchworm.K25.L25.fa 100 > /private3/tmp/Dror/trinityrnaseq-2.0.6/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/inchworm.K25.L25.fa.min100

Running cmd: bowtie-build -q /private3/tmp/Dror/trinityrnaseq-2.0.6/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/inchworm.K25.L25.fa.min100 /private3/tmp/Dror/trinityrnaseq-2.0.6/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/inchworm.K25.L25.fa.min100

Running cmd: bash -c " set -o pipefail; bowtie -a -m 20 --best --strata --threads 4  --chunkmbs 512 -q -S -f /private3/tmp/Dror/trinityrnaseq-2.0.6/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/inchworm.K25.L25.fa.min100 both.fa  | samtools view -@ 4 -F4 -Sb - | samtools sort -@ 4 -no - - > /private3/tmp/Dror/trinityrnaseq-2.0.6/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/iworm.bowtie.nameSorted.bam" 

view: invalid option -- '@'

sort: invalid option -- '@'

open: No such file or directory

[bam_sort_core] fail to open file 4

Error while flushing and closing output

terminate called after throwing an instance of 'int'

Error, cmd: bash -c " set -o pipefail; bowtie -a -m 20 --best --strata --threads 4  --chunkmbs 512 -q -S -f /private3/tmp/Dror/trinityrnaseq-2.0.6/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/inchworm.K25.L25.fa.min100 both.fa  | samtools view -@ 4 -F4 -Sb - | samtools sort -@ 4 -no - - > /private3/tmp/Dror/trinityrnaseq-2.0.6/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/iworm.bowtie.nameSorted.bam"  died with ret 256 at /private3/tmp/Dror/trinityrnaseq-2.0.6/PerlLib/Pipeliner.pm line 56

Pipeliner::run('Pipeliner=HASH(0x278b4c0)') called at ../../Trinity line 1463

main::run_chrysalis('/private3/tmp/Dror/trinityrnaseq-2.0.6/sample_data/test_Trini...', 'both.fa', 200, 500, 'RF', 'both.fa', 'both.fa') called at ../../Trinity line 1355

main::run_Trinity() called at ../../Trinity line 1098

eval {...} called at ../../Trinity line 1097

Trinity run failed. Must investigate error above.

make[1]: *** [test] Error 2

make[1]: Leaving directory `/private3/tmp/Dror/trinityrnaseq-2.0.6/sample_data/test_Trinity_Assembly'

make: *** [test] Error 2

I saw that it might be related for RAM.

When typing free -g

the output is:

             total       used       free     shared    buffers     cached

Mem:            94         93          0          0          0         83

-/+ buffers/cache:         10         84

Swap:           15          0         15

Any ideas?

Thanks 
On Monday, March 23, 2015 at 12:57:31 PM UTC+2, Dror Hibsh wrote:

Any ideas?

[Brian Haas]

The 

  view: invalid option -- '@'

error means that you need to upgrade your samtools to a newer version.   

best,

~b

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[Dror Hibsh]

Hi Brian,

I changed the default in Trinity code line 897 to be:

my $samtools_path =  '/private3/tmp/Dror/samtools-1.2/samtools';

and that is the latest version of samtools.

But, i still have the same error:

#######################################################################

Inchworm file: /private3/tmp/Dror/trinityrnaseq-2.0.6/sample_data/test_Trinity_Assembly/trinity_out_dir/inchworm.K25.L25.fa detected.

Skipping Inchworm Step, Using Previous Inchworm Assembly

#######################################################################

--Skipping cmd: /private3/tmp/Dror/trinityrnaseq-2.0.6/util/misc/fasta_filter_by_min_length.pl /private3/tmp/Dror/trinityrnaseq-2.0.6/sample_data/test_Trinity_Assembly/trinity_out_dir/inchworm.K25.L25.fa 100 > /private3/tmp/Dror/trinityrnaseq-2.0.6/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/inchworm.K25.L25.fa.min100, checkpoint exists.

--Skipping cmd: bowtie-build -q /private3/tmp/Dror/trinityrnaseq-2.0.6/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/inchworm.K25.L25.fa.min100 /private3/tmp/Dror/trinityrnaseq-2.0.6/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 /private3/tmp/Dror/trinityrnaseq-2.0.6/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/inchworm.K25.L25.fa.min100 both.fa  | samtools view -@ 4 -F4 -Sb - | samtools sort -@ 4 -no - - > /private3/tmp/Dror/trinityrnaseq-2.0.6/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/iworm.bowtie.nameSorted.bam"

view: invalid option -- '@'

[main_samview] fail to open "4" for reading.

sort: invalid option -- '@'

open: No such file or directory

[bam_sort_core] fail to open file 4

Error while flushing and closing output

terminate called after throwing an instance of 'int'

Error, cmd: bash -c " set -o pipefail; bowtie -a -m 20 --best --strata --threads 4  --chunkmbs 512 -q -S -f /private3/tmp/Dror/trinityrnaseq-2.0.6/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/inchworm.K25.L25.fa.min100 both.fa  | samtools view -@ 4 -F4 -Sb - | samtools sort -@ 4 -no - - > /private3/tmp/Dror/trinityrnaseq-2.0.6/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/iworm.bowtie.nameSorted.bam"  died with ret 256 at /private3/tmp/Dror/trinityrnaseq-2.0.6/PerlLib/Pipeliner.pm line 56

        Pipeliner::run('Pipeliner=HASH(0x1c06ce0)') called at ../../Trinity line 1464

        main::run_chrysalis('/private3/tmp/Dror/trinityrnaseq-2.0.6/sample_data/test_Trini...', 'both.fa', 200, 500, 'RF', 'both.fa', 'both.fa') called at ../../Trinity line 1356

        main::run_Trinity() called at ../../Trinity line 1099

        eval {...} called at ../../Trinity line 1098

Trinity run failed. Must investigate error above.

make: *** [test_trinity] Error 2

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[Brian Haas]

It looks like it's not using that version of samtools.

Try updating your PATH setting to have the path to your new samtools directory before the rest of your PATH settings:

export PATH=/private3/tmp/Dror/samtools-1.2/:${PATH}

and then run it.

best,

~b

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[Dror Hibsh]

You were right!

Thanks!

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