After concatenating the all the forward reads together and doing the same with the reverse reads, all in fastqsanger format, I tried assembling with trinity, but it gave me this error and an empty fasta file.
Wednesday, December 13, 2017: 21:28:31 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 Wednesday, December 13, 2017: 21:28:31 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 Wednesday, December 13, 2017: 21:28:32 CMD: mkdir -p /local/2059621/trinity_out_dir Wednesday, December 13, 2017: 21:28:32 CMD: mkdir -p /local/2059621/trinity_out_dir/chrysalis
-------------- Trinity Phase 1: Clustering of RNA-Seq Reads ---------------------
Converting input files. (in parallel)Wednesday, December 13, 2017: 21:28:32 CMD: cat /pylon5/mc48nsp/xcgalaxy/main_staging//17802259/inputs/dataset_22757341.dat | /opt/packages/trinity/2.2.0/trinity-plugins/fastool/fastool --append /1 --to-fasta >> left.fa 2> /pylon5/mc48nsp/xcgalaxy/main_staging//17802259/inputs/dataset_22757341.dat.readcount Wednesday, December 13, 2017: 21:28:32 CMD: cat /pylon5/mc48nsp/xcgalaxy/main_staging//17802259/inputs/dataset_22757340.dat | /opt/packages/trinity/2.2.0/trinity-plugins/fastool/fastool --append /2 --to-fasta >> right.fa 2> /pylon5/mc48nsp/xcgalaxy/main_staging//17802259/inputs/dataset_22757340.dat.readcount Thread 2 terminated abnormally: Error, cmd: cat /pylon5/mc48nsp/xcgalaxy/main_staging//17802259/inputs/dataset_22757340.dat | /opt/packages/trinity/2.2.0/trinity-plugins/fastool/fastool --append /2 --to-fasta >> right.fa 2> /pylon5/mc48nsp/xcgalaxy/main_staging//17802259/inputs/dataset_22757340.dat.readcount died with ret 256 at /opt/packages/trinity/2.2.0/Trinity line 2206. Thread 1 terminated abnormally: Error, counts of reads in FQ: 212144040.25 (as per cat /pylon5/mc48nsp/xcgalaxy/main_staging//17802259/inputs/dataset_22757341.dat | wc -l) doesn't match fastool's report of FA records: 212144041 at /opt/packages/trinity/2.2.0/Trinity line 3087 thread 1. main::ensure_complete_FQtoFA_conversion('cat /pylon5/mc48nsp/xcgalaxy/main_staging//17802259/inputs/da...', '/pylon5/mc48nsp/xcgalaxy/main_staging//17802259/inputs/datase...') called at /opt/packages/trinity/2.2.0/Trinity line 2116 thread 1 main::prep_seqs('ARRAY(0x1199418)', '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.
