I'm trying to use Trinity to do a de novo assembly from short reads. However the output file "Assembled Transcripts" is empty, and includes an accopanying error message "A data display parameter is in the error state: fai_file".
The output log file seems to be implying incomplete conversion of FASTQ to FASTA, though I don't know why that should be so, since I ran the conversion already using FASTQ-to-FASTA tool.
Any ideas what I'm doing wrong?
Actual log file content follows:
CMD: java -Xmx64m -XX:ParallelGCThreads=6 -jar /opt/packages/trinity/2.2.0/util/support_scripts/ExitTester.jar 0 Picked up _JAVA_OPTIONS: -Dsun.zip.disableMemoryMapping=true Thursday, December 14, 2017: 20:24:44 CMD: java -Xmx64m -XX:ParallelGCThreads=6 -jar /opt/packages/trinity/2.2.0/util/support_scripts/ExitTester.jar 1 Picked up _JAVA_OPTIONS: -Dsun.zip.disableMemoryMapping=true Thursday, December 14, 2017: 20:24:44 CMD: mkdir -p /local/2066002/trinity_out_dir Thursday, December 14, 2017: 20:24:44 CMD: mkdir -p /local/2066002/trinity_out_dir/chrysalis
-------------- Trinity Phase 1: Clustering of RNA-Seq Reads ---------------------
Converting input files. (in parallel)Thursday, December 14, 2017: 20:24:44 CMD: cat /pylon5/mc48nsp/xcgalaxy/main_staging//17813697/inputs/dataset_22774423.dat | /opt/packages/trinity/2.2.0/trinity-plugins/fastool/fastool --append /1 --to-fasta >> left.fa 2> /pylon5/mc48nsp/xcgalaxy/main_staging//17813697/inputs/dataset_22774423.dat.readcount Thursday, December 14, 2017: 20:24:44 CMD: cat /pylon5/mc48nsp/xcgalaxy/main_staging//17813697/inputs/dataset_22774423.dat | /opt/packages/trinity/2.2.0/trinity-plugins/fastool/fastool --append /2 --to-fasta >> right.fa 2> /pylon5/mc48nsp/xcgalaxy/main_staging//17813697/inputs/dataset_22774423.dat.readcount Thread 2 terminated abnormally: Error, counts of reads in FQ: 207480 (as per cat /pylon5/mc48nsp/xcgalaxy/main_staging//17813697/inputs/dataset_22774423.dat | wc -l) doesn't match fastool's report of FA records: 414960 at /opt/packages/trinity/2.2.0/Trinity line 3087 thread 2. main::ensure_complete_FQtoFA_conversion('cat /pylon5/mc48nsp/xcgalaxy/main_staging//17813697/inputs/da...', '/pylon5/mc48nsp/xcgalaxy/main_staging//17813697/inputs/datase...') called at /opt/packages/trinity/2.2.0/Trinity line 2116 thread 2 main::prep_seqs('ARRAY(0x2620418)', 'fq', 'right', undef) called at /opt/packages/trinity/2.2.0/Trinity line 1317 thread 2 eval {...} called at /opt/packages/trinity/2.2.0/Trinity line 1317 thread 2 Thread 1 terminated abnormally: Error, counts of reads in FQ: 207480 (as per cat /pylon5/mc48nsp/xcgalaxy/main_staging//17813697/inputs/dataset_22774423.dat | wc -l) doesn't match fastool's report of FA records: 414960 at /opt/packages/trinity/2.2.0/Trinity line 3087 thread 1. main::ensure_complete_FQtoFA_conversion('cat /pylon5/mc48nsp/xcgalaxy/main_staging//17813697/inputs/da...', '/pylon5/mc48nsp/xcgalaxy/main_staging//17813697/inputs/datase...') called at /opt/packages/trinity/2.2.0/Trinity line 2116 thread 1 main::prep_seqs('ARRAY(0x2453a40)', '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 Trinity run failed. Must investigate error above.
