I had 48 paired end samples, I concatinae all the 24 forward and reverse paired separately and tried to do denovo assembly for concatinated forward read (64GB) and reverse read (64GB).
Trinity run failed with the fllowing error.
is it due to the concatination or something else, Please suggest how to proceed?
[2018-05-24 05:27:39.893] [jointLog] [warning] Salmon was only able to assign 0 fragments to transcripts in the index, but the minimum number of required assigned fragments (--minAssignedFrags) was 1. This could be indicative of a mismatch between the reference and sample, or a very bad sample. You can change the --minAssignedFrags parameter to force Salmon to quantify with fewer assigned fragments (must have at least 1).
Error, cmd:
salmon --no-version-check quant -i /N/dc2/scratch/trinity/job_working_directory/021/21127/working/trinity_out_dir/read_partitions/Fb_0/CBin_294/c29490.trinity.reads.fa.out/Trinity.fasta.tmp.salmon.idx -l U -r /N/dc2/scratch/trinity/job_working_directory/021/21127/working/trinity_out_dir/read_partitions/Fb_0/CBin_294/c29490.trinity.reads.fa.out/single.fa -o salmon_outdir -p 1 --minAssignedFrags 1
died with ret (256) at /gpfs/hps/soft/rhel7/trinityrnaseq/2.6.6/util/support_scripts/../../PerlLib/Process_cmd.pm line 19.
Process_cmd::process_cmd("salmon --no-version-check quant -i /N/dc2/scratch/trinity/job"...) called at /gpfs/hps/soft/rhel7/trinityrnaseq/2.6.6/util/support_scripts/salmon_runner.pl line 26
Trinity run failed. Must investigate error above.
warning, cmd: /gpfs/hps/soft/rhel7/trinityrnaseq/2.6.6/util/support_scripts/../../Trinity --single "/N/dc2/scratch/trinity/job_working_directory/021/21127/working/trinity_out_dir/read_partitions/Fb_0/CBin_294/c29490.trinity.reads.fa" --output "/N/dc2/scratch/trinity/job_working_directory/021/21127/working/trinity_out_dir/read_partitions/Fb_0/CBin_294/c29490.trinity.reads.fa.out" --CPU 1 --max_memory 1G --run_as_paired --seqType fa --trinity_complete --full_cleanup failed with ret: 512, going to retry.
succeeded(0), failed(1) 50% completed.
succeeded(0), failed(2) 100% completed.
We are sorry, commands in file: [FailedCommands] failed. :-(
Error, cmd: /gpfs/hps/soft/rhel7/trinityrnaseq/2.6.6/trinity-plugins/BIN/ParaFly -c recursive_trinity.cmds -CPU 8 -v -shuffle died with ret 256 at /N/soft/rhel7/trinityrnaseq/2.6.6/Trinity line 2581.
main::process_cmd("/gpfs/hps/soft/rhel7/trinityrnaseq/2.6.6/trinity-plugins/BIN/"...) called at /N/soft/rhel7/trinityrnaseq/2.6.6/Trinity line 3244
main::run_partitioned_cmds("recursive_trinity.cmds") called at /N/soft/rhel7/trinityrnaseq/2.6.6/Trinity line 2239
main::run_recursive_trinity("/N/dc2/scratch/trinity/job_working_directory/021/21127/workin"...) called at /N/soft/rhel7/trinityrnaseq/2.6.6/Trinity line 2001
main::run_chrysalis("/N/dc2/scratch/trinity/job_working_directory/021/21127/workin"..., "/N/dc2/scratch/trinity/job_working_directory/021/21127/workin"..., 200, 500, undef, "/N/dc2/scratch/trinity/job_working_directory/021/21127/workin"..., "/N/dc2/scratch/trinity/job_working_directory/021/21127/workin"...) called at /N/soft/rhel7/trinityrnaseq/2.6.6/Trinity line 1664
main::run_Trinity() called at /N/soft/rhel7/trinityrnaseq/2.6.6/Trinity line 1317
eval {...} called at /N/soft/rhel7/trinityrnaseq/2.6.6/Trinity line 1316
Trinity run failed. Must investigate error above. Command is:
Trinity --left /N/dc2/scratch/trinity/database/files/031/dataset_31753.dat --right /N/dc2/scratch/trinity/database/files/031/dataset_31755.dat --seqType fq --max_memory 248G --CPU 8
Beginning attempt 1 of Trinity job at 23/05/18 03:29 Trinity exited with status 2 Finished and found the success command with grep code 1 Beginning attempt 2 of Trinity job at 24/05/18 05:25 Trinity exited with status 1 Finished and found the success command with grep code 1
