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?
