Trying Trinity on paired end reads after Trim Galore does not work. I get an error, but am not sure how to solve the issue given the information it supplies.
CernVM-FS: loading Fuse module… done
CernVM-FS: mounted cvmfs on /scratch/03166/xcgalaxy/main/staging/61356740/.cvmfsexec/dist/cvmfs/data.galaxyproject.org
CernVM-FS: loading Fuse module… done
CernVM-FS: mounted cvmfs on /scratch/03166/xcgalaxy/main/
Hi @David_Morse
What Galaxy server do you use?
Maybe check the standard output and standard error log files via Info (i) icon. Expand the black boxes by clicking on double(?) error icon on the right side of the boxes. Do you see more info?
You can check Trinity on a small dataset, for example, any suitable RNA-Seq dataset from GTN tutorials. You can try Trinity on other public Galaxy server. It is OK to have accounts on different public Galaxy servers (one account per user per server).
You can report the failed job to the server admins, or post a link to shared history here, so someone can have a look.
Kind regards,
Igor
Hi
Trinity does work on the tutorial datasets, so there is something wrong with mine I guess. I sed trim galore to get rid of the adaptors, since if I use trimmomatic Trinity does not see the files.
The expanded boxes show additional information, but I don’t know how to read and interpret it.
For command line:
if [ -z “$GALAXY_MEMORY_MB” ] ; then GALAXY_MEMORY_GB=1 ; else GALAXY_MEMORY_GB=$((GALAXY_MEMORY_MB / 1024)) ; fi ; TRINITY_SCRATCH_DIR=${TRINITY_SCRATCH_DIR:-${TMPDIR:-$_GALAXY_JOB_TMP_DIR}} workdir=$(pwd) scratchfolder=$(mktemp -d -p “$TRINITY_SCRATCH_DIR”); emptyfolder=$(mktemp -d -p “$TRINITY_SCRATCH_DIR”); cd “$scratchfolder” ; ln -s ‘/scratch/03166/xcgalaxy/main/staging//61761377/inputs/dataset_4691047f-e4ba-4a6f-85bb-1ecac08d771a.dat’ left_input0.fastqsanger.gz && ln -s ‘/scratch/03166/xcgalaxy/main/staging//61761377/inputs/dataset_9ea92ccb-0612-4ce9-bde3-33c348119ed2.dat’ right_input0.fastqsanger.gz && Trinity --no_version_check --output ./trinity_out_dir --no_parallel_norm_stats --left ‘left_input0.fastqsanger.gz’ --right ‘right_input0.fastqsanger.gz’ --seqType fq --SS_lib_type FR --min_contig_length 200 --min_kmer_cov 1 --CPU ${GALAXY_SLOTS:-4} --max_memory ${GALAXY_MEMORY_GB:-1}G --bflyHeapSpaceMax ${GALAXY_MEMORY_GB:-1}G --bfly_opts ‘-V 10 --stderr’ && rsync -a --delete “$emptyfolder/” “$scratchfolder/” --exclude=trinity_out_dir.Trinity.fasta --exclude=trinity_out_dir.Trinity.fasta.gene_trans_map; mv “$scratchfolder/trinity_out_dir.Trinity.fasta” ‘/scratch/03166/xcgalaxy/main/staging//61761377/outputs/dataset_ad0f36d9-4de4-4f84-a9b1-e6055279c2db.dat’; mv “$scratchfolder/trinity_out_dir.Trinity.fasta.gene_trans_map” ‘/scratch/03166/xcgalaxy/main/staging//61761377/outputs/dataset_5ff88595-db7d-4f83-ad34-952a569139d1.dat’; cd “$workdir”; rmdir “$emptyfolder” “$scratchfolder”
The tool standard error:
This is super curious. Can you explain more? Maybe screenshot what is going on. The datasets in the history expanded to show the metadata and peek view might be enough. Fastq reads are just reads, I can’t think of a reason why one QA tool would produce reads this tool can see, and another doesn’t. We can help to figure out why. It could be the “shape” of the data, not the files themselves, but we can confirm and help.
And, did you mean to post back more from the stderr log?
Hi
From memory, when I tried to find files to assemble inside trinity, it did not show the trimmomatic files and said it needed fastqsanger or fastqsanger.gz (which seemed funny as the file type listed in the information was fastqsanger.gz).
I unfortunately deleted and purged the trimmomatic files, and I can’t rerun them yet because I am out of space.
That was all from the standard error box.
David
Ok, it was probably the shape of the data if the datatypes were correct (matched the forms “accepted formats” toggle).
The data shape is determined by how it is nested inside a collection, or not, and how that collection is organized. Next time it comes up, you can post the example and we can explain what to do. Or, search the tutorial site with “collection” directly for examples.
Then if the stderr message was empty, expand the red error dataset itself. Do you see a message? You can post that back if you can copy it out, or screenshot and post that.
You can also check the stdout message. That is on the same view, one log up.
And, we still don’t know what server you are working at. Find that in your web browser, the first part of the URL. I can guess but let’s be exact with this or we won’t be able to help with what to do next, after we know what exactly is going wrong.
Thanks!
I am using usegalaxy.org
I enclose screen shots of the red box Assembled transcripts.
The standard error contains only
“mv: cannot stat ‘/tmp/tmp.ENCy8oCVnz/trinity_out_dir.Trinity.fasta’: No such file or directory”
The standard output has
“CernVM-FS: loading Fuse module… done
CernVM-FS: mounted cvmfs on /scratch/03166/xcgalaxy/main/staging/61761377/.cvmfsexec/dist/cvmfs/data.galaxyproject.org
CernVM-FS: loading Fuse module… done
CernVM-FS: mounted cvmfs on /scratch/03166/xcgalaxy/main/staging/61761377/.cvmfsexec/dist/cvmfs/singularity.galaxyproject.org
\ | || \ | || || | |
D ) | | | _ | | | | || | |
| ||| / | | | | | | | || ||| ~ |
\ | | | | | | | | | |___, |
. \ | | | | | | | | | | |
| ||_|||||||| |__| |____/
Trinity-v2.15.1
Left read files: $VAR1 = [
‘left_input0.fastqsanger.gz’
];
Right read files: $VAR1 = [
‘right_input0.fastqsanger.gz’
];
Monday, October 28, 2024: 08:32:30 CMD: java -Xmx64m -XX:ParallelGCThreads=2 -jar /usr/local/opt/trinity-2.15.1/util/support_scripts/ExitTester.jar 0
Picked up _JAVA_OPTIONS: -Xmx244G -Xms1G
Monday, October 28, 2024: 08:32:30 CMD: java -Xmx4g -XX:ParallelGCThreads=2 -jar /usr/local/opt/trinity-2.15.1/util/support_scripts/ExitTester.jar 1
Picked up _JAVA_OPTIONS: -Xmx244G -Xms1G
Monday, October 28, 2024: 08:32:30 CMD: mkdir -p /tmp/tmp.ENCy8oCVnz/./trinity_out_dir
Monday, October 28, 2024: 08:32:30 CMD: mkdir -p /tmp/tmp.ENCy8oCVnz/./trinity_out_dir/chrysalis
Hi @David_Morse
Thanks for posting back the details. We are in the process of deprecating Trinity at UseGalaxy.org (technical reasons). Sorry for the confusion here … it is still in the tool panel but we are working on that part and it will be cleared up some time this week probably.
The solution is to try at a different UseGalaxy server → UseGalaxy.eu or UseGalaxy.org.au both still host it. 
These links can explain how to get an account at the others, why this is a good idea anyway, and how to move data around.
