Question: Trinity unusual error
0
gravatar for luca.marisaldi
12 weeks ago by
luca.marisaldi30 wrote:

Hi all!

I got twice the same error by running Trinity on Galaxy, that is:

Thread 1 terminated abnormally: Error, counts of reads in FQ: 40001112.25 (as per cat /pylon5/mc48nsp/xcgalaxy/main_staging//15659867/inputs/dataset_19697450.dat | wc -l) doesn't match fastool's report of FA records: 40001113 at /opt/packages/trinity/2.2.0/Trinity line 3087 thread 1.

As a consequence Trinity stops producing an empty file.

As far as I know that seems to be something related with the number of reads inside the loaded files but I have no idea how to deal with that (it looks more like a Trinity bug on Galaxy). That is, in my opinion, quite unusual because the same workflow has been running multiple times with many samples from the same experiment.

N.B. --> The same error is given independently from two samples processed separately.

Anyone can give me some tips?

Thank you,

Luca

ADD COMMENTlink modified 9 weeks ago by ilange0 • written 12 weeks ago by luca.marisaldi30

Hello, We are testing Trinity again. Would you also please send in a bug report so that we can look at the error within the context of the experiment? Please leave the inputs and error datasets undeleted and include a link to this post. This does look like a server side issue: https://galaxyproject.org/support/tool-error/#determining-the-job-failure-type

More feedback soon.

Thanks, Jen, Galaxy team

ADD REPLYlink written 12 weeks ago by Jennifer Hillman Jackson22k

Hi Jen, well I run the job twice more after posting the question without changing anything (simply using the icon "run this job again")

The last attempt was successful and Trinity proceeded further completing the run properly in both samples.

For this reason I lost the info regarding the error. If it is going to happen again I proceed by submitting the full report as you suggested.

Thank you for helping us!

Bye,

Luca

ADD REPLYlink written 12 weeks ago by luca.marisaldi30
1
gravatar for Jennifer Hillman Jackson
12 weeks ago by
United States
Jennifer Hillman Jackson22k wrote:

Hi Luca,

The connection with Bridges (where Trinity is run) has been problematic on and off for about a week. So, no need to send in the error if it is resolved now for you.

Should this come up again, we want to know, from you and anyone else who runs into a problem.

Thanks for the followup! Jen

ADD COMMENTlink written 12 weeks ago by Jennifer Hillman Jackson22k
0
gravatar for Jennifer Hillman Jackson
11 weeks ago by
United States
Jennifer Hillman Jackson22k wrote:

Update:

Trinity was corrected again mid-day Friday 4/28/17 EST. Please re-run any jobs that failed.

If you have jobs that were started after that time, those will also need to be re-run (and the original grey jobs deleted/purged).

Sorry for the inconvenience, Jen, Galaxy team

ADD COMMENTlink written 11 weeks ago by Jennifer Hillman Jackson22k
0
gravatar for ilange
9 weeks ago by
ilange0
ilange0 wrote:

Hi Jennifer, I have the same error message as Luca Although I was able to run an almost identical trinity assembly in parallel on our cluster and it finished. I rerun the failed assembly once. No luck. Here is the error:

Thread 2 terminated abnormally: Error, counts of reads in FQ: 5045646.25 (as per cat //RNA_assemblies/a/trimmed_SRR515_2.fastq | wc -l) doesn't match fastool's report of FA records: 5045647 at /opt/apps/trinity/2.2.0/Trinity line 3087 thread 2. main::ensure_complete_FQtoFA_conversion('cat /data/cahnrs/lange/RNA_assemblies/a, /RNA_assemblies/) called at /opt/apps/trinity/2.2.0/Trinity line 2116 thread 2 main::prep_seqs('ARRAY(0x1211d38)', 'fq', 'right', 'R') called at /opt/apps/trinity/2.2.0/Trinity line 1317 thread 2 eval {...} called at /opt/apps/trinity/2.2.0/Trinity line 1317 thread 2 -conversion of 29941823 from FQ to FA format succeeded. Trinity run failed. Must investigate error above. Can I change something? Is this a bug? How to fix? Should I recreate this fastq file? I would like to know if this might be a software issue. Thanks, Iris

ADD COMMENTlink written 9 weeks ago by ilange0

Hi - The trinity problems have returned (along with a few cluster issues). The problem is not resolved yet. Please follow this other post for updates: https://biostar.usegalaxy.org/p/23175/

Thanks! Jen, Galaxy team

ADD REPLYlink written 9 weeks ago by Jennifer Hillman Jackson22k
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