Salmon Run error

[Julian Rozenberg]

Dear Brian.

I am trying to assemble transcriptome with -150G RAM and 10 CPU 

After about 2 days of running smoothly, I am getting an error apparently running Salmon that is recorded in the output.

I will deeply appreciate of you can suggest how to deal with it.

Thank you in advance.

Sincerely.

Julian Rozenberg, PhD.

Error encountered::  <!----

CMD: /nas/longleaf/apps/trinity/2.8.6/trinityrnaseq-2.8.6/util/support_scripts/salmon_runner.pl /proj/macklab/projects/JR/Snail/1/Trinity_out4/read_partitions/Fb_1/CBin_1120/c112066.trinity.reads.fa.out/Trinity.tmp.fasta /proj/macklab/projects/JR/Snail/1/Trinity_out4/read_partitions/Fb_1/CBin_1120/c112066.trinity.reads.fa.out/single.fa 2>tmp.277167.1611853323.stderr

Errmsg:

CMD: salmon --no-version-check index -t /proj/macklab/projects/JR/Snail/1/Trinity_out4/read_partitions/Fb_1/CBin_1120/c112066.trinity.reads.fa.out/Trinity.tmp.fasta -i /proj/macklab/projects/JR/Snail/1/Trinity_out4/read_partitions/Fb_1/CBin_1120/c112066.trinity.reads.fa.out/Trinity.tmp.fasta.salmon.idx --type quasi -k 25 -p 1

Exception : [Error: RapMap-based indexing is not supported in this version of salmon.]

salmon index was invoked improperly.

For usage information, try salmon index --help

Exiting.

Error, cmd:

salmon --no-version-check index -t /proj/macklab/projects/JR/Snail/1/Trinity_out4/read_partitions/Fb_1/CBin_1120/c112066.trinity.reads.fa.out/Trinity.tmp.fasta -i /proj/macklab/projects/JR/Snail/1/Trinity_out4/read_partitions/Fb_1/CBin_1120/c112066.trinity.reads.fa.out/Trinity.tmp.fasta.salmon.idx --type quasi -k 25 -p 1

 died with ret (256) at /nas/longleaf/apps/trinity/2.8.6/trinityrnaseq-2.8.6/util/support_scripts/../../PerlLib/Process_cmd.pm line 19.

Process_cmd::process_cmd('salmon --no-version-check index -t /proj/macklab/projects/JR/...') called at /nas/longleaf/apps/trinity/2.8.6/trinityrnaseq-2.8.6/util/support_scripts/salmon_runner.pl line 23

--->

-salmon error reported: Error, cmd: /nas/longleaf/apps/trinity/2.8.6/trinityrnaseq-2.8.6/util/support_scripts/salmon_runner.pl /proj/macklab/projects/JR/Snail/1/Trinity_out4/read_partitions/Fb_1/CBin_1120/c112066.trinity.reads.fa.out/Trinity.tmp.fasta /proj/macklab/projects/JR/Snail/1/Trinity_out4/read_partitions/Fb_1/CBin_1120/c112066.trinity.reads.fa.out/single.fa 2>tmp.277167.1611853323.stderr died with ret 256  at /nas/longleaf/apps/trinity/2.8.6/trinityrnaseq-2.8.6/PerlLib/Pipeliner.pm line 186.

Pipeliner::run('Pipeliner=HASH(0x10de3a0)') called at /nas/longleaf/apps/trinity/2.8.6/trinityrnaseq-2.8.6/util/support_scripts/../../Trinity line 1819

eval {...} called at /nas/longleaf/apps/trinity/2.8.6/trinityrnaseq-2.8.6/util/support_scripts/../../Trinity line 1818

main::run_Trinity() called at /nas/longleaf/apps/trinity/2.8.6/trinityrnaseq-2.8.6/util/support_scripts/../../Trinity line 1382

eval {...} called at /nas/longleaf/apps/trinity/2.8.6/trinityrnaseq-2.8.6/util/support_scripts/../../Trinity line 1381

WARNING - salmon failure mode not recognized by Trinity:

Error, cmd: /nas/longleaf/apps/trinity/2.8.6/trinityrnaseq-2.8.6/util/support_scripts/salmon_runner.pl /proj/macklab/projects/JR/Snail/1/Trinity_out4/read_partitions/Fb_1/CBin_1120/c112066.trinity.reads.fa.out/Trinity.tmp.fasta /proj/macklab/projects/JR/Snail/1/Trinity_out4/read_partitions/Fb_1/CBin_1120/c112066.trinity.reads.fa.out/single.fa 2>tmp.277167.1611853323.stderr died with ret 256  at /nas/longleaf/apps/trinity/2.8.6/trinityrnaseq-2.8.6/PerlLib/Pipeliner.pm line 186.

Pipeliner::run('Pipeliner=HASH(0x10de3a0)') called at /nas/longleaf/apps/trinity/2.8.6/trinityrnaseq-2.8.6/util/support_scripts/../../Trinity line 1819

eval {...} called at /nas/longleaf/apps/trinity/2.8.6/trinityrnaseq-2.8.6/util/support_scripts/../../Trinity line 1818

main::run_Trinity() called at /nas/longleaf/apps/trinity/2.8.6/trinityrnaseq-2.8.6/util/support_scripts/../../Trinity line 1382

eval {...} called at /nas/longleaf/apps/trinity/2.8.6/trinityrnaseq-2.8.6/util/support_scripts/../../Trinity line 1381

 - retaining Trinity transcripts provided as input to salmon, w/o filtering (pre-salmon mode).

[Julian Rozenberg]

P.S. I am using Trinity-v2.8.6

Thank you

[Brian Haas]

Hi Julian,

Trinity v2.8.6 uses salmon 0.9.1.

Here's the installation command in the v2.8.6 dockerfile: https://github.com/trinityrnaseq/trinityrnaseq/blob/v2.8.6/Docker/Dockerfile

## Salmon
WORKDIR $SRC
RUN wget https://github.com/COMBINE-lab/salmon/releases/download/v0.9.1/Salmon-0.9.1_linux_x86_64.tar.gz && \
tar xvf Salmon-0.9.1_linux_x86_64.tar.gz && \
ln -s $SRC/Salmon-latest_linux_x86_64/bin/salmon $BIN/.

If salmon gives you any trouble, though, you can just turn it off via.   Trinity --no_salmon

It only makes a minor difference, but it was fast enough that I figured I'd include it to help remove some of the minimally supported contigs.

best,

~brian

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--
--
Brian J. Haas
The Broad Institute
http://broadinstitute.org/~bhaas

 

[Julian Rozenberg]

Hi Brian!

Thank you very much for the quick reply.

I am running the second stage based on the previous assembled data. I am also using --FORCE option just in case...

Is there any documentation that summarises usage of trinity with 3-rd party software? 

Such as, my understanding is that it is possible to do DGE analysis (deSeq2 or EdgeR?) and, if  possible, annotation of the functional domains in the assembled transcripts?

Also, my understanding is that it is possible to use Salmon with a .fasta file to estimate gene expression.

How about clustering? 

Again, thank you very much for your help.

Sincerely.

Julian Rozenberg, PhD

Senior Scientist

Laboratory of Cell Signalling Regulation

MIPT

пт, 29 янв. 2021 г., 0:10 Brian Haas <bh...@broadinstitute.org>:

[Brian Haas]

Hi Julian,

All our usage info for the various analyses and 3rd party tools can be accessed from our wiki:

https://github.com/trinityrnaseq/trinityrnaseq/wiki

and reflects updates and extensions  of our Nat.Protocols paper from 2013.

Wrt software installations, all the linux installation instructions are available in our Dockerfile:

https://github.com/trinityrnaseq/trinityrnaseq/blob/master/Docker/Dockerfile

or you can just use the Docker or Singularity images that we provide:
https://github.com/trinityrnaseq/trinityrnaseq/wiki/Trinity-in-Docker

or

https://github.com/trinityrnaseq/trinityrnaseq/wiki/Trinity-in-Docker#trinity_singularity

all the best,

~brian

[Julian Rozenberg]

Terrific!

I just got Trinity.fasta file and I will go from here.

Thank you.

Julian

--

Julian Rozenberg, Ph.D.