With best regards,
Baradwaj
Hello Brian.The trinity run failed during phase 2.There are 3 logs files attached with this email.The first log was generated when the Trinity run was ended by mistake.Trinity_Run1.logThe second log shows some errors generated during Phase 2, but the run continued and finally failed.Trinity_Run2.logThe last few lines of the log are as follows.---------------------------------------------------------------------------------------------------succeeded(15087), failed(1) 99.9969% completed.
succeeded(15088), failed(1) 99.9974% completed.
succeeded(15089), failed(1) 99.9978% completed.
succeeded(15090), failed(1) 99.9982% completed.
succeeded(15091), failed(1) 99.9987% completed.
succeeded(15092), failed(1) 99.9991% completed.
succeeded(15093), failed(1) 99.9996% completed.
succeeded(15094), failed(1) 100% completed.
We are sorry, commands in file: [FailedCommands] failed. :-(
Error, cmd: /usr/local/bin/trinity-plugins/BIN/ParaFly -c recursive_trinity.cmds -CPU 6 -v -shuffle died with ret 256 at /usr/local/bin/Trinity line 2919.
main::process_cmd("/usr/local/bin/trinity-plugins/BIN/ParaFly -c recursive_trini"...) called at /usr/local/bin/Trinity line 3653
main::run_partitioned_cmds("recursive_trinity.cmds") called at /usr/local/bin/Trinity line 2528
main::run_recursive_trinity("/media/baradwaj/My_Volume/TRINITY/Gymnema/Trinity_Runs/chrysa"...) called at /usr/local/bin/Trinity line 2271
main::run_chrysalis("/media/baradwaj/My_Volume/TRINITY/Gymnema/Trinity_Runs/inchwo"..., "/media/baradwaj/My_Volume/TRINITY/Gymnema/Trinity_Runs/both.fa", 200, 500, undef, "/media/baradwaj/My_Volume/TRINITY/Gymnema/Trinity_Runs/both.fa", "/media/baradwaj/My_Volume/TRINITY/Gymnema/Trinity_Runs/both.fa") called at /usr/local/bin/Trinity line 1895
main::run_Trinity() called at /usr/local/bin/Trinity line 1500
eval {...} called at /usr/local/bin/Trinity line 1499
Trinity run failed. Must investigate error above.---------------------------------------------------------------------------------------------------The 3rd log was generated when the run was restarted.Trinity_Run3.logThe last few lines of the log are as follows.---------------------------------------------------------------------------------------------------------Error encountered:: <!----
CMD: /usr/local/bin/Inchworm/bin//inchworm --reads /media/baradwaj/My_Volume/TRINITY/Gymnema/Trinity_Runs/read_partitions/Fb_1/CBin_1449/c146444.trinity.reads.fa.out/single.fa --run_inchworm -K 18 --monitor 1 --DS --num_threads 1 -L 50 --make_super_reads > /media/baradwaj/My_Volume/TRINITY/Gymnema/Trinity_Runs/read_partitions/Fb_1/CBin_1449/c146444.trinity.reads.fa.out/inchworm.DS.fa.SR.18.tmp 2>tmp.657097.1723171038.stderr
Errmsg:
Kmer length set to: 18
Min assembly length set to: 50
Running Inchworm in Super-Reads mode
Monitor turned on, set to: 1
double stranded mode set
setting number of threads to: 1
-storing Kmers...
<stacktrace off>
Error, cannot open file /media/baradwaj/My_Volume/TRINITY/Gymnema/Trinity_Runs/read_partitions/Fb_1/CBin_1449/c146444.trinity.reads.fa.out/single.fa
--->
Error, cmd: /usr/local/bin/Inchworm/bin//inchworm --reads /media/baradwaj/My_Volume/TRINITY/Gymnema/Trinity_Runs/read_partitions/Fb_1/CBin_1449/c146444.trinity.reads.fa.out/single.fa --run_inchworm -K 18 --monitor 1 --DS --num_threads 1 -L 50 --make_super_reads > /media/baradwaj/My_Volume/TRINITY/Gymnema/Trinity_Runs/read_partitions/Fb_1/CBin_1449/c146444.trinity.reads.fa.out/inchworm.DS.fa.SR.18.tmp 2>tmp.657097.1723171038.stderr died with ret 256 at /usr/local/bin/PerlLib/Pipeliner.pm line 187.
Pipeliner::run(Pipeliner=HASH(0x556f155e54c0)) called at /usr/local/bin/util/support_scripts/../../Trinity line 2729
eval {...} called at /usr/local/bin/util/support_scripts/../../Trinity line 2719
main::run_inchworm("/media/baradwaj/My_Volume/TRINITY/Gymnema/Trinity_Runs/read_p"..., "/media/baradwaj/My_Volume/TRINITY/Gymnema/Trinity_Runs/read_p"..., undef, "", 18, 1) called at /usr/local/bin/util/support_scripts/../../Trinity line 1784
main::run_Trinity() called at /usr/local/bin/util/support_scripts/../../Trinity line 1500
eval {...} called at /usr/local/bin/util/support_scripts/../../Trinity line 1499
If it indicates bad_alloc(), then Inchworm ran out of memory. You'll need to either reduce the size of your data set or run Trinity on a server with more memory available.
** The inchworm process failed.warning, cmd: /usr/local/bin/util/support_scripts/../../Trinity --single "/media/baradwaj/My_Volume/TRINITY/Gymnema/Trinity_Runs/read_partitions/Fb_1/CBin_1449/c146444.trinity.reads.fa" --output "/media/baradwaj/My_Volume/TRINITY/Gymnema/Trinity_Runs/read_partitions/Fb_1/CBin_1449/c146444.trinity.reads.fa.out" --CPU 1 --max_memory 1G --run_as_paired --seqType fa --trinity_complete --full_cleanup --no_salmon failed with ret: 256, going to retry.
succeeded(0), failed(1) 100% completed.
We are sorry, commands in file: [FailedCommands] failed. :-(
Error, cmd: /usr/local/bin/trinity-plugins/BIN/ParaFly -c recursive_trinity.cmds -CPU 6 -v -shuffle died with ret 256 at /usr/local/bin/Trinity line 2919.
main::process_cmd("/usr/local/bin/trinity-plugins/BIN/ParaFly -c recursive_trini"...) called at /usr/local/bin/Trinity line 3653
main::run_partitioned_cmds("recursive_trinity.cmds") called at /usr/local/bin/Trinity line 2528
main::run_recursive_trinity("/media/baradwaj/My_Volume/TRINITY/Gymnema/Trinity_Runs/chrysa"...) called at /usr/local/bin/Trinity line 2271
main::run_chrysalis("/media/baradwaj/My_Volume/TRINITY/Gymnema/Trinity_Runs/inchwo"..., "/media/baradwaj/My_Volume/TRINITY/Gymnema/Trinity_Runs/both.fa", 200, 500, undef, "/media/baradwaj/My_Volume/TRINITY/Gymnema/Trinity_Runs/both.fa", "/media/baradwaj/My_Volume/TRINITY/Gymnema/Trinity_Runs/both.fa") called at /usr/local/bin/Trinity line 1895
main::run_Trinity() called at /usr/local/bin/Trinity line 1500
eval {...} called at /usr/local/bin/Trinity line 1499
Trinity run failed. Must investigate error above.----------------------------------------------------------------------------------------------------------kindly help!With best regards,
Baradwaj
With best regards,
Baradwaj