Question: Trinity Error, thread exited with error/Thread 5 terminated abnormally
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gravatar for clockdive
16 days ago by
clockdive0
clockdive0 wrote:

Hi all,

I am attempting to run a trinity De novo assembly on some reads with the following command:

nice -2 Trinity --seqType fq --left 4t1_S15_R1_001_val_1.fq.gz,4t2_S2_R1_001_val_1.fq.gz,4t4_S11_R1_001_val_1.fq.gz,4t5_S14_R1_001_val_1.fq.gz,4t6_S5_R1_001_val_1.fq.gz,5t1_S1_R1_001_val_1.fq.gz,5t2_S9_R1_001_val_1.fq.gz,5t4_S12_R1_001_val_1.fq.gz,5t5_S3_R1_001_val_1.fq.gz,5t6_S7_R1_001_val_1.fq.gz,6t1_S6_R1_001_val_1.fq.gz,6t2_S10_R1_001_val_1.fq.gz,6t4_S13_R1_001_val_1.fq.gz,6t5_S4_R1_001_val_1.fq.gz,6t6_S8_R1_001_val_1.fq.gz --right 4t1_S15_R2_001_val_2.fq.gz,4t2_S2_R2_001_val_2.fq.gz,4t4_S11_R2_001_val_2.fq.gz,4t5_S14_R2_001_val_2.fq.gz,4t6_S5_R2_001_val_2.fq.gz,5t1_S1_R2_001_val_2.fq.gz,5t2_S9_R2_001_val_2.fq.gz,5t4_S12_R2_001_val_2.fq.gz,5t5_S3_R2_001_val_2.fq.gz,5t6_S7_R2_001_val_2.fq.gz,6t1_S6_R2_001_val_2.fq.gz,6t2_S10_R2_001_val_2.fq.gz,6t4_S13_R2_001_val_2.fq.gz,6t5_S4_R2_001_val_2.fq.gz,6t6_S8_R2_001_val_2.fq.gz --full_cleanup --CPU 8 --max_memory 100G --bflyCalculateCPU --output ~/run1/trinity

I have tried adjusting the memory allocation (and added the bflyCalculateCPU tag) with no luck. Everytime my Trinity run exits with some type of thread exited with error/Thread terminated abnormally issue. Here is the exact output I have experienced.

 STATS_GENERATION_TIME: 9674 seconds.
CMD finished (11891 seconds)
CMD finished (12423 seconds)
CMD: touch left.fa.K25.stats.ok
CMD finished (1 seconds)
CMD: touch right.fa.K25.stats.ok
CMD finished (0 seconds)
-sorting each stats file by read name.
CMD: /usr/bin/sort --parallel=4 -k5,5 -T . -S 50G left.fa.K25.stats > left.fa.K25.stats.sort
CMD: /usr/bin/sort --parallel=4 -k5,5 -T . -S 50G right.fa.K25.stats > right.fa.K25.stats.sort
bash: line 1: 28074 Killed                  /usr/bin/sort --parallel=4 -k5,5 -T . -S 50G left.fa.K25.stats > left.fa.K25.stats.sort
Thread 5 terminated abnormally: Error, cmd: /usr/bin/sort --parallel=4 -k5,5 -T . -S 50G left.fa.K25.stats > left.fa.K25.stats.sort died with ret 35072 at /usr/local/src/trinityrnaseq/util/insilico_read_normalization.pl line 758.
Error, thread exited with error Error, cmd: /usr/bin/sort --parallel=4 -k5,5 -T . -S 50G left.fa.K25.stats > left.fa.K25.stats.sort died with ret 35072 at /usr/local/src/trinityrnaseq/util/insilico_read_normalization.pl line 758.

If anyone has some suggestions of what I could try to fix this issue, I would greatly appreciate it. Thank you.

rna-seq assembly • 54 views
ADD COMMENTlink modified 14 days ago by Biostar ♦♦ 20 • written 16 days ago by clockdive0
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