Did not see Trinity.fasta

[Yifang Tan]

Hello group,
I ran Trinity which seems successful, but I did not get the Trinity.fasta file of the final assembly result according to the manual:
"When Trinity completes, it will create a Trinity.fasta output file in the trinity_out_dir/ output directory (or output directory you specify)."

Here is my command line:

location_of/Trinity --seqType fq --left /my_path_to/reads_1.fq --right /my_path_to/reads_2.fq --CPU 18 --max_memory 120G

I am using Trinity-2.0.5 under Debian 3.10.3 x86_64 GNU/Linux.
What did I possibly miss?
Thanks a lot!

Yifang

[Tiago Hori]

Did you capture the standard output and or standard error?

T.

Sent from my iPhone

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[Yifang Tan]

Thanks Triago!
I'm aware the network is out as we have some issues with the network at this moment, but this should not affect Trinity assembly, of which .

I tried the latest version (2.0.6), and got the same thing.
Here is the STDOUT:
-----------------------------------------------BEGIN-----------------------------------------------
Trinity version: v2.0.6
-ERROR: couldn't run the network check to confirm latest Trinity software version.
Tuesday, March 3, 2015: 11:20:40    CMD: java -Xmx64m -jar /home/yifang/download-software/trinityrnaseq-2.0.6/util/support_scripts/ExitTester.jar 0
Tuesday, March 3, 2015: 11:20:40    CMD: java -Xmx64m -jar /home/yifang/download-software/trinityrnaseq-2.0.6/util/support_scripts/ExitTester.jar 1
Tuesday, March 3, 2015: 11:20:40    CMD: mkdir -p /storage/ppl/yifang/20150219_Mon/results/trinity_assembly_S2/chrysalis

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

Converting input files. (in parallel)Tuesday, March 3, 2015: 11:20:41    CMD: /home/yifang/download-software/trinityrnaseq-2.0.6/trinity-plugins/fastool/fastool --illumina-trinity --to-fasta /storage/ppl/yifang/20150219_Mon/reads/S2_trimmomated_PE_R1.fq >> left.fa 2> /storage/ppl/yifang/20150219_Mon/reads/S2_trimmomated_PE_R1.fq.readcount
Tuesday, March 3, 2015: 11:20:41    CMD: /home/yifang/download-software/trinityrnaseq-2.0.6/trinity-plugins/fastool/fastool --illumina-trinity --to-fasta /storage/ppl/yifang/20150219_Mon/reads/S2_trimmomated_PE_R2.fq >> right.fa 2> /storage/ppl/yifang/20150219_Mon/reads/S2_trimmomated_PE_R2.fq.readcount
Tuesday, March 3, 2015: 12:19:34    CMD: cat left.fa right.fa > both.fa
-----------------------------------------------
------- Jellyfish  --------------------
-- (building a k-mer catalog from reads) --
--------------------------------------------

Tuesday, March 3, 2015: 12:56:49    CMD: /home/yifang/download-software/trinityrnaseq-2.0.6/trinity-plugins/jellyfish/bin/jellyfish count -t 18 -m 25 -s 30410233306  --canonical  both.fa 2> /dev/null
Tuesday, March 3, 2015: 13:20:00    CMD: /home/yifang/download-software/trinityrnaseq-2.0.6/trinity-plugins/jellyfish/bin/jellyfish dump -L 1 mer_counts.jf > jellyfish.kmers.fa 2>/dev/null
Tuesday, March 3, 2015: 13:28:56    CMD: /home/yifang/download-software/trinityrnaseq-2.0.6/trinity-plugins/jellyfish/bin/jellyfish histo -t 18 -o jellyfish.kmers.fa.histo mer_counts.jf 2>/dev/null
Tuesday, March 3, 2015: 13:29:15    CMD: touch jellyfish.1.finished
----------------------------------------------
--------------- Inchworm ---------------------
-- (Linear contig construction from k-mers) --
----------------------------------------------
Tuesday, March 3, 2015: 13:29:15    CMD: /home/yifang/download-software/trinityrnaseq-2.0.6/Inchworm/bin//inchworm --kmers jellyfish.kmers.fa --run_inchworm -K 25 -L 25 --monitor 1   --DS  --keep_tmp_files  --num_threads 6  --PARALLEL_IWORM  > /storage/ppl/yifang/20150219_Mon/results/trinity_assembly_S2/inchworm.K25.L25.DS.fa.tmp 2>/dev/null

Tuesday, March 3, 2015: 14:10:25    CMD: touch /storage/ppl/yifang/20150219_Mon/results/trinity_assembly_S2/inchworm.K25.L25.DS.fa.finished

Running cmd: /home/yifang/download-software/trinityrnaseq-2.0.6/util/misc/fasta_filter_by_min_length.pl /storage/ppl/yifang/20150219_Mon/results/trinity_assembly_S2/inchworm.K25.L25.DS.fa 100 > /storage/ppl/yifang/20150219_Mon/results/trinity_assembly_S2/chrysalis/inchworm.K25.L25.DS.fa.min100
Running cmd: bowtie-build -q /storage/ppl/yifang/20150219_Mon/results/trinity_assembly_S2/chrysalis/inchworm.K25.L25.DS.fa.min100 /storage/ppl/yifang/20150219_Mon/results/trinity_assembly_S2/chrysalis/inchworm.K25.L25.DS.fa.min100 2>/dev/null

Running cmd: bash -c " set -o pipefail; bowtie -a -m 20 --best --strata --threads 18  --chunkmbs 512 -q -S -f /storage/ppl/yifang/20150219_Mon/results/trinity_assembly_S2/chrysalis/inchworm.K25.L25.DS.fa.min100 both.fa  | samtools view -@ 18 -F4 -Sb - | samtools sort -@ 18 -no - - > /storage/ppl/yifang/20150219_Mon/results/trinity_assembly_S2/chrysalis/iworm.bowtie.nameSorted.bam"  2>/dev/null
Trinity run failed. Must investigate error above.
-----------------------------------------------END-----------------------------------------------
The default error goes to /dev/null. How do I get more details of stderror?
Thanks!

[Tiago Hori]

Your run failed, that is why you don't have Trinity.fasta 

It is very likely that it crashed because you don't have samtools v1. There is a new flag for multi threading that only works with samtools v1.

T.

Sent from my iPhone

[Tiago Hori]

Hi Yifang,

Any v1.x should work. Can you run it again with --verbose flag?

T.

PS: Please reply all so the list also gets your next question, there are far more experienced users in the list than me.

Ultimate stresses sportsmanship and fair play. Competitive play is encouraged, but NEVER AT THE EXPENSE OF RESPECT BETWEEN PLAYERS, adherence to the rules and the BASIC JOY OF PLAY.

On Mar 04, 2015, at 11:53 AM, Yifang Tan <yif...@gmail.com> wrote:

Thanks Tiago!

Samtools(Version 1.1) is installed in my box.

$ which samtools

/home/yifang/download-software/samtools

$ samtools

Program: samtools (Tools for alignments in the SAM format)
Version: 1.1 (using htslib 1.1)
Usage:   samtools <command> [options]
Commands:
  -- indexing

......

The difference is v1.1. Do you mean samtools ONLY v1. is acceptable?

And anything else I may have missed?

Thank you again!

Yifang

[Yifang Tan]

Thanks!

I gave it another try with --verbose option. Found this line in the STDERR

----------------------------------------------------------------------------------------------------------
. . . . . .
Found samtools at: /home/yifang/download-software/samtools-0.1.18/samtools
. . . . . .
----------------------------------------------------------------------------------------------------------

The problem is there are two copies of samtools in my box, and Trinity always uses version 0.1.18, which is related to my PATH setting.
When I changed the PATH in my .bashrc setting, it worked!

Thank you for your help!

Yifang