We are sorry, commands in file: [failed_butterfly_commands.74150.txt] failed. :-(

[Wyclif Odago]

Hi Brian,

I run trinity on multiple samples of 50 paired end reads then after four samples were assembled the command kept returning an error. I am not sure if trinity butterfly component is processing the data correctly.

Error:

Trinity run failed. Must investigate error above.
warning, cmd: /software/trinityrnaseq-v2.13.2/util/support_scripts/../../Trinity --single "/home/odago/hoya/03.trinity/trinity_output/trinity_Hoya_australis_ZCF_combined/read_partitions/Fb_0/CBin_764/c76472.trinity.reads.fa" --output "/home/odago/hoya/03.trinity/trinity_output/trinity_Hoya_australis_ZCF_combined/read_partitions/Fb_0/CBin_764/c76472.trinity.reads.fa.out" --CPU 1 --max_memory 1G --run_as_paired --seqType fa --trinity_complete --full_cleanup --no_salmon   failed with ret: 65280, going to retry.
succeeded(146333), failed(1)   47.2044% completed.    

We are sorry, commands in file: [failed_butterfly_commands.74150.txt] failed.  :-(



Error encountered::  <!----
CMD: /software/trinityrnaseq-v2.13.2/trinity-plugins/BIN/ParaFly -c /home/odago/hoya/03.trinity/trinity_output/trinity_Hoya_australis_ZCF_combined/read_partitions/Fb_0/CBin_764/c76472.trinity.reads.fa.out/chrysalis/butterfly_commands -shuffle -CPU 1 -failed_cmds failed_butterfly_commands.74150.txt  2>tmp.74150.1723047681.stderr

Errmsg:
Exception in thread "main" java.lang.NullPointerException: Cannot invoke "String.length()" because "res" is null
at SeqVertex.getShortSeq(SeqVertex.java:431)
at SeqVertex.getShortSeqWID(SeqVertex.java:478)
at SeqVertex.toString(SeqVertex.java:260)
at java.base/java.lang.String.valueOf(String.java:4216)
at java.base/java.lang.StringBuilder.append(StringBuilder.java:173)
at TransAssembly_allProbPaths.removeLightFlowEdges(TransAssembly_allProbPaths.java:14640)
at TransAssembly_allProbPaths.removeLightEdges(TransAssembly_allProbPaths.java:14596)
at TransAssembly_allProbPaths.main(TransAssembly_allProbPaths.java:809)

What could be the problem? 

Thank you.