Question: empty file returned after Trinity run
gravatar for khh
13 months ago by
khh0 wrote:

After atempting to run Trinity (3rd time!) I received the following log:

-------------- Trinity Phase 1: Clustering of RNA-Seq Reads --------------------- Converting input files. (in parallel)Sunday, December 11, 2016: 15:52:06 CMD: cat /pylon1/mc48nsp/xcgalaxy/main_staging//14543806/inputs/dataset_18062260.dat | /opt/packages/trinity/2.2.0/trinity-plugins/fastool/fastool --append /1 --to-fasta >> left.fa 2> /pylon1/mc48nsp/xcgalaxy/main_staging//14543806/inputs/dataset_18062260.dat.readcount Sunday, December 11, 2016: 15:52:06 CMD: cat /pylon1/mc48nsp/xcgalaxy/main_staging//14543806/inputs/dataset_17720650.dat | /opt/packages/trinity/2.2.0/trinity-plugins/fastool/fastool --append /2 --to-fasta >> right.fa 2> /pylon1/mc48nsp/xcgalaxy/main_staging//14543806/inputs/dataset_17720650.dat.readcount Thread 1 terminated abnormally: Error, counts of reads in FQ: 13425498 (as per cat /pylon1/mc48nsp/xcgalaxy/main_staging//14543806/inputs/dataset_18062260.dat | wc -l) doesn't match fastool's report of FA records: 13425499 at /opt/packages/trinity/2.2.0/Trinity line 3087 thread 1. main::ensure_complete_FQtoFA_conversion("cat /pylon1/mc48nsp/xcgalaxy/main_staging//14543806/inputs/da"..., "/pylon1/mc48nsp/xcgalaxy/main_staging//14543806/inputs/datase"...) called at /opt/packages/trinity/2.2.0/Trinity line 2116 thread 1 main::prep_seqs(ARRAY(0x15a1108), "fq", "left", undef) called at /opt/packages/trinity/2.2.0/Trinity line 1314 thread 1 eval {...} called at /opt/packages/trinity/2.2.0/Trinity line 1314 thread 1 -conversion of 16132740 from FQ to FA format succeeded. *Trinity run failed. Must investigate error above.*

Although 'green' on the history panel, the returned files was 'empty'. What can I do to get Trinity to run?

trinity • 331 views
ADD COMMENTlink modified 13 months ago by Jennifer Hillman Jackson23k • written 13 months ago by khh0
gravatar for Jennifer Hillman Jackson
13 months ago by
United States
Jennifer Hillman Jackson23k wrote:


There were recent job failures at Please try a rerun now. Details:

That said, this could be an input problem. If the job fails, check the inputs to ensure they are intact (uploaded fully) and in the correct format.

Should problems continue after that, a bug report can be sent in and we can help review/test to make sure there is not a tool issue. Please include a link to this post and leave all datasets undeleted, including those from the failed job, the rerun, and the data load/content checks done.

Help links:

Best, Jen, Galaxy team

ADD COMMENTlink written 13 months ago by Jennifer Hillman Jackson23k
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